From 3f7a1d1c07ef3147d35cd04805e9abf7660f6eec Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 16 Jul 2018 11:40:42 +0200 Subject: [PATCH 01/67] function to read and store complete text file reading as stream avoids costly repeated call to 'read'. Requires of course more memory, but that should be fine also, recursion case ('{}') is internally handled. Old recursive was error prone and buggy when rewining (see 'reset' option) --- src/IO.f90 | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/src/IO.f90 b/src/IO.f90 index a7e77f0f4..45c914587 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -22,6 +22,7 @@ module IO public :: & IO_init, & IO_read, & + IO_recursiveRead, & IO_checkAndRewind, & IO_open_file_stat, & IO_open_jobFile_stat, & @@ -100,6 +101,7 @@ end subroutine IO_init !-------------------------------------------------------------------------------------------------- !> @brief recursively reads a line from a text file. !! Recursion is triggered by "{path/to/inputfile}" in a line +!> @details unstable and buggy !-------------------------------------------------------------------------------------------------- recursive function IO_read(fileUnit,reset) result(line) @@ -170,6 +172,58 @@ recursive function IO_read(fileUnit,reset) result(line) end function IO_read +!-------------------------------------------------------------------------------------------------- +!> @brief recursively reads a text file. +!! Recursion is triggered by "{path/to/inputfile}" in a line +!-------------------------------------------------------------------------------------------------- +recursive function IO_recursiveRead(fileName) result(fileContent) + + implicit none + character(len=*), intent(in) :: fileName + character(len=1024), dimension(:), allocatable :: fileContent + character(len=1024), dimension(:), allocatable :: includedContent + character(len=1024) :: line + character(len=:), allocatable :: rawData + integer(pInt) :: fileLength, fileUnit,startPos,endPos,& + myTotalLines,l,includedLines, missingLines,i + + inquire(file = fileName, size=fileLength) + open(newunit=fileUnit, file = fileName, access = "STREAM") + allocate(character(len=fileLength)::rawData) + read(fileUnit) rawData + close(fileUnit) + + myTotalLines = 0 + do l=1, len(rawData) + if (rawData(l:l) == new_line('')) myTotalLines = myTotalLines+1 + enddo + allocate(fileContent(myTotalLines)) + + startPos = 1 + endPos = 0 + + includedLines=0 + l=0 + do while (startPos <= len(rawData)) + l = l + 1 + endPos = endPos + scan(rawData(startPos:),new_line('')) + line = rawData(startPos:endPos-1) + startPos = endPos + 1 + + recursion: if(scan(trim(line),'{') < scan(trim(line),'}')) then + myTotalLines = myTotalLines - 1 + includedContent = IO_recursiveRead(trim(line(scan(line,'{')+1:scan(line,'}')-1))) + includedLines = includedLines +size(includedContent) + missingLines = myTotalLines+includedLines - size(fileContent(1:l-1)) -size(includedContent) + fileContent = [fileContent(1:l-1),includedContent,[(line,i=1,missingLines)]] + l=l-1+size(includedContent) + else recursion + fileContent(l) = line + endif recursion + + enddo + +end function IO_recursiveRead !-------------------------------------------------------------------------------------------------- !> @brief checks if unit is opened for reading, if true rewinds. Otherwise stops with From b26c4a39ef3ddbadfb5eb73136029e7d2634b0ab Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 16 Jul 2018 11:42:58 +0200 Subject: [PATCH 02/67] store raw material.config --- src/config.f90 | 60 +++++++++++++++++++++++--------------------------- 1 file changed, 28 insertions(+), 32 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index 9d2ddde4c..196a39be6 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -92,12 +92,12 @@ subroutine config_init() compiler_version, & compiler_options #endif + use DAMASK_interface, only: & + getSolverJobName use IO, only: & IO_error, & - IO_open_file, & - IO_read, & IO_lc, & - IO_open_jobFile_stat, & + IO_recursiveRead, & IO_getTag, & IO_timeStamp, & IO_EOF @@ -107,12 +107,13 @@ subroutine config_init() debug_levelBasic implicit none - integer(pInt), parameter :: FILEUNIT = 200_pInt - integer(pInt) :: myDebug + integer(pInt) :: myDebug,i character(len=65536) :: & line, & part + character(len=65536), dimension(:), allocatable :: fileContent + logical :: jobSpecificConfig write(6,'(/,a)') ' <<<+- config init -+>>>' write(6,'(a15,a)') ' Current time: ',IO_timeStamp() @@ -120,42 +121,42 @@ subroutine config_init() myDebug = debug_level(debug_material) - if (.not. IO_open_jobFile_stat(FILEUNIT,material_localFileExt)) & ! no local material configuration present... - call IO_open_file(FILEUNIT,material_configFile) ! ...open material.config file + inquire(file=trim(getSolverJobName())//'.'//material_localFileExt,exist=jobSpecificConfig) + if(jobSpecificConfig) then + fileContent = IO_recursiveRead(trim(getSolverJobName())//'.'//material_localFileExt) + else + fileContent = IO_recursiveRead('material.config') + endif - rewind(fileUnit) - line = '' ! to have it initialized - do while (trim(line) /= IO_EOF) + do i=1, size(fileContent) + line = trim(fileContent(i)) part = IO_lc(IO_getTag(line,'<','>')) - select case (trim(part)) case (trim(material_partPhase)) - call parseFile(line,phase_name,config_phase,FILEUNIT) + call parseFile(line,phase_name,config_phase,fileContent(i+1:)) !(i+1:) save for empty part at (at end of file)? if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Phase parsed'; flush(6) case (trim(material_partMicrostructure)) - call parseFile(line,microstructure_name,config_microstructure,FILEUNIT) + call parseFile(line,microstructure_name,config_microstructure,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Microstructure parsed'; flush(6) case (trim(material_partCrystallite)) - call parseFile(line,crystallite_name,config_crystallite,FILEUNIT) + call parseFile(line,crystallite_name,config_crystallite,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Crystallite parsed'; flush(6) case (trim(material_partHomogenization)) - call parseFile(line,homogenization_name,config_homogenization,FILEUNIT) + call parseFile(line,homogenization_name,config_homogenization,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Homogenization parsed'; flush(6) case (trim(material_partTexture)) - call parseFile(line,texture_name,config_texture,FILEUNIT) + call parseFile(line,texture_name,config_texture,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Texture parsed'; flush(6) - case default - line = IO_read(fileUnit) - end select enddo + deallocate(fileContent) material_Nhomogenization = size(config_homogenization) if (material_Nhomogenization < 1_pInt) call IO_error(160_pInt,ext_msg=material_partHomogenization) @@ -174,25 +175,23 @@ end subroutine config_init !> @brief parses the material.config file !-------------------------------------------------------------------------------------------------- subroutine parseFile(line,& - sectionNames,part,fileUnit) + sectionNames,part,fileContent) use IO, only: & - IO_read, & IO_error, & IO_lc, & IO_getTag, & IO_isBlank, & IO_stringValue, & - IO_stringPos, & - IO_EOF + IO_stringPos implicit none - integer(pInt), intent(in) :: fileUnit character(len=*), dimension(:), allocatable, intent(inout) :: sectionNames - type(tPartitionedStringList), allocatable, dimension(:), intent(inout) :: part + type(tPartitionedStringList), allocatable, dimension(:), intent(out) :: part + character(len=65536), dimension(:), intent(in) :: fileContent character(len=65536),intent(out) :: line integer(pInt), allocatable, dimension(:) :: chunkPos - integer(pInt) :: s + integer(pInt) :: s,i character(len=65536) :: devNull character(len=64) :: tag logical :: echo @@ -201,13 +200,10 @@ subroutine parseFile(line,& allocate(part(0)) s = 0_pInt - do while (trim(line) /= IO_EOF) ! read through sections of material part - line = IO_read(fileUnit) + do i=1, size(fileContent) + line = trim(fileContent(i)) if (IO_isBlank(line)) cycle ! skip empty lines - foundNextPart: if (IO_getTag(line,'<','>') /= '') then - devNull = IO_read(fileUnit, .true.) ! reset IO_read to close any recursively included files - exit - endif foundNextPart + if (IO_getTag(line,'<','>') /= '') exit nextSection: if (IO_getTag(line,'[',']') /= '') then s = s + 1_pInt part = [part, emptyList] From a1ad18c88ae2caed603962ecfa06cfdf9ec64558 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 16 Jul 2018 12:08:22 +0200 Subject: [PATCH 03/67] 256 characters is enough for material.config larger values waste memory and decrease readability. Still need to discuss how geom files are handled, for them longer limits make sense --- src/IO.f90 | 7 ++++--- src/config.f90 | 9 ++++----- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/IO.f90 b/src/IO.f90 index 45c914587..67130ed91 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -180,9 +180,9 @@ recursive function IO_recursiveRead(fileName) result(fileContent) implicit none character(len=*), intent(in) :: fileName - character(len=1024), dimension(:), allocatable :: fileContent - character(len=1024), dimension(:), allocatable :: includedContent - character(len=1024) :: line + character(len=256), dimension(:), allocatable :: fileContent + character(len=256), dimension(:), allocatable :: includedContent + character(len=256) :: line character(len=:), allocatable :: rawData integer(pInt) :: fileLength, fileUnit,startPos,endPos,& myTotalLines,l,includedLines, missingLines,i @@ -207,6 +207,7 @@ recursive function IO_recursiveRead(fileName) result(fileContent) do while (startPos <= len(rawData)) l = l + 1 endPos = endPos + scan(rawData(startPos:),new_line('')) + if(endPos - startPos >256) write(6,*) 'mist' line = rawData(startPos:endPos-1) startPos = endPos + 1 diff --git a/src/config.f90 b/src/config.f90 index 196a39be6..022247aeb 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -109,10 +109,10 @@ subroutine config_init() implicit none integer(pInt) :: myDebug,i - character(len=65536) :: & + character(len=256) :: & line, & part - character(len=65536), dimension(:), allocatable :: fileContent + character(len=256), dimension(:), allocatable :: fileContent logical :: jobSpecificConfig write(6,'(/,a)') ' <<<+- config init -+>>>' @@ -187,12 +187,11 @@ subroutine parseFile(line,& implicit none character(len=*), dimension(:), allocatable, intent(inout) :: sectionNames type(tPartitionedStringList), allocatable, dimension(:), intent(out) :: part - character(len=65536), dimension(:), intent(in) :: fileContent - character(len=65536),intent(out) :: line + character(len=256), dimension(:), intent(in) :: fileContent + character(len=256),intent(out) :: line integer(pInt), allocatable, dimension(:) :: chunkPos integer(pInt) :: s,i - character(len=65536) :: devNull character(len=64) :: tag logical :: echo From fb1265db3d43db3412a407a579aefb43fa5da7b8 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 16 Jul 2018 20:08:31 +0200 Subject: [PATCH 04/67] checking for existing file --- src/config.f90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/config.f90 b/src/config.f90 index 022247aeb..86b1bc501 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -125,6 +125,8 @@ subroutine config_init() if(jobSpecificConfig) then fileContent = IO_recursiveRead(trim(getSolverJobName())//'.'//material_localFileExt) else + inquire(file='material.config',exist=jobSpecificConfig) + if(.not. jobSpecificConfig) call IO_error(0_pInt) fileContent = IO_recursiveRead('material.config') endif From dc6855261a438e25bbed6322c71d135a423de5d3 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 3 Aug 2018 08:53:37 +0200 Subject: [PATCH 05/67] number of helper functions for HDF5 --- src/CMakeLists.txt | 4 + src/HDF5_utilities.f90 | 1311 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 1315 insertions(+) create mode 100644 src/HDF5_utilities.f90 diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 9418cd56d..be01bd4ee 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -31,6 +31,10 @@ add_library(IO OBJECT "IO.f90") add_dependencies(IO DAMASK_INTERFACE) list(APPEND OBJECTFILES $) +add_library(HDF5_UTILITIES OBJECT "HDF5_utilities.f90") +add_dependencies(HDF5_UTILITIES IO) +list(APPEND OBJECTFILES $) + add_library(NUMERICS OBJECT "numerics.f90") add_dependencies(NUMERICS IO) list(APPEND OBJECTFILES $) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 new file mode 100644 index 000000000..bb09da7f7 --- /dev/null +++ b/src/HDF5_utilities.f90 @@ -0,0 +1,1311 @@ +module HDF5_Utilities + use prec + use IO + use HDF5 + use PETSC + + integer(HID_T), public, protected :: tempCoordinates, tempResults + integer(HID_T), private :: resultsFile, currentIncID, plist_id + integer(pInt), private :: currentInc + + public :: & + HDF5_Utilities_init, & + HDF5_mappingPhase, & + HDF5_mappingHomog, & + HDF5_mappingCrystallite, & + HDF5_backwardMappingPhase, & + HDF5_backwardMappingHomog, & + HDF5_backwardMappingCrystallite, & + HDF5_mappingCells, & + HDF5_addGroup ,& + HDF5_closeGroup ,& + HDF5_openGroup, & + HDF5_forwardResults, & + HDF5_writeVectorDataset, & + HDF5_writeScalarDataset, & + HDF5_writeTensorDataset, & + HDF5_closeJobFile, & + HDF5_removeLink +contains + +subroutine HDF5_Utilities_init + use, intrinsic :: & + iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment) + + implicit none + integer :: hdferr + integer(SIZE_T) :: typeSize + + write(6,'(/,a)') ' <<<+- HDF5_Utilities init -+>>>' +#include "compilation_info.f90" + + currentInc = -1_pInt + call HDF5_createJobFile + +end subroutine HDF5_Utilities_init + + +!-------------------------------------------------------------------------------------------------- +!> @brief creates and initializes HDF5 output files +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_createJobFile + use hdf5 + use DAMASK_interface, only: & + getSolverWorkingDirectoryName, & + getSolverJobName + + implicit none + integer :: hdferr + integer(SIZE_T) :: typeSize + character(len=1024) :: path +#include + +!-------------------------------------------------------------------------------------------------- +! initialize HDF5 library and check if integer and float type size match + call h5open_f(hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5open_f') + call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5tget_size_f (int)') + if (int(pInt,SIZE_T)/=typeSize) call IO_error(0_pInt,ext_msg='pInt does not match H5T_NATIVE_INTEGER') + call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5tget_size_f (double)') + if (int(pReal,SIZE_T)/=typeSize) call IO_error(0_pInt,ext_msg='pReal does not match H5T_NATIVE_DOUBLE') + + ! neu ab hier (4 zeilen) + call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pcreate_f') + call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pset_fapl_mpio_f') +!-------------------------------------------------------------------------------------------------- +! open file + path = trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.'//'hdf5' + !call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr) + call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr,access_prp = plist_id) + if (hdferr < 0) call IO_error(100_pInt,ext_msg=path) + call HDF5_addStringAttribute(resultsFile,'createdBy',DAMASKVERSION) + call h5pclose_f(plist_id, hdferr) !neu + +end subroutine HDF5_createJobFile + + +!-------------------------------------------------------------------------------------------------- +!> @brief creates and initializes HDF5 output file +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_closeJobFile() + use hdf5 + + implicit none + integer :: hdferr + call HDF5_removeLink('current') + call h5fclose_f(resultsFile,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_closeJobFile: h5fclose_f',el=hdferr) + CALL h5close_f(hdferr) + +end subroutine HDF5_closeJobFile + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a new group to the results file, or if loc is present at the given location +!-------------------------------------------------------------------------------------------------- +integer(HID_T) function HDF5_addGroup(path) + use hdf5 + + implicit none + character(len=*), intent(in) :: path + integer :: hdferr + + call h5gcreate_f(resultsFile, trim(path), HDF5_addGroup, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5gcreate_f ('//trim(path)//')') + +end function HDF5_addGroup + + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a new group to the results file +!-------------------------------------------------------------------------------------------------- +integer(HID_T) function HDF5_openGroup(path) + use hdf5 + + implicit none + character(len=*), intent(in) :: path + integer :: hdferr + + call h5gopen_f(resultsFile, trim(path), HDF5_openGroup, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5gopen_f ('//trim(path)//')') + +end function HDF5_openGroup + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a new group to the results file +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_setLink(path,link) + use hdf5 + + implicit none + character(len=*), intent(in) :: path, link + integer :: hdferr + logical :: linkExists + + call h5lexists_f(resultsFile, link,linkExists, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5lexists_soft_f ('//trim(link)//')') + if (linkExists) then + call h5ldelete_f(resultsFile,link, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5ldelete_soft_f ('//trim(link)//')') + endif + call h5lcreate_soft_f(path, resultsFile, link, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5lcreate_soft_f ('//trim(path)//' '//trim(link)//')') + +end subroutine HDF5_setLink + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a new group to the results file +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_removeLink(link) + use hdf5 + + implicit none + character(len=*), intent(in) :: link + integer :: hdferr + + call h5ldelete_f(resultsFile,link, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_removeLink: h5ldelete_soft_f ('//trim(link)//')') + +end subroutine HDF5_removeLink + + + +!-------------------------------------------------------------------------------------------------- +!> @brief closes a group +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_closeGroup(ID) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: ID + integer :: hdferr + + call h5gclose_f(ID, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = ID) + +end subroutine HDF5_closeGroup + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a new group to the results file +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_addStringAttribute(entity,attrLabel,attrValue) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: entity + character(len=*), intent(in) :: attrLabel, attrValue + integer :: hdferr + integer(HID_T) :: attr_id, space_id, type_id + + call h5screate_f(H5S_SCALAR_F,space_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5screate_f') + call h5tcopy_f(H5T_NATIVE_CHARACTER, type_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5tcopy_f') + call h5tset_size_f(type_id, int(len(trim(attrValue)),HSIZE_T), hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5tset_size_f') + call h5acreate_f(entity, trim(attrLabel),type_id,space_id,attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5acreate_f') + call h5awrite_f(attr_id, type_id, trim(attrValue), int([1],HSIZE_T), hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5awrite_f') + call h5aclose_f(attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5aclose_f') + call h5sclose_f(space_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5sclose_f') + +end subroutine HDF5_addStringAttribute + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds the unique mapping from spatial position and constituent ID to results +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_mappingPhase(mapping,mapping2,Nconstituents,material_phase,phase_name,dataspace_size,mpiOffset,mpiOffset_phase) + use hdf5 + + implicit none + integer(pInt), intent(in) :: Nconstituents, dataspace_size, mpiOffset + integer(pInt), intent(in), dimension(:) :: mapping, mapping2 + character(len=*), intent(in), dimension(:) :: phase_name + integer(pInt), intent(in), dimension(:) :: mpiOffset_phase + integer(pInt), intent(in), dimension(:,:,:) :: material_phase + + character(len=len(phase_name(1))), dimension(:), allocatable :: namesNA + character(len=len(phase_name(1))) :: a + character(len=*),parameter :: n = "NULL" + + integer(pInt) :: hdferr, NmatPoints, i, j, k + integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, name_id, position_id, plist_id, memspace + + integer(HID_T) :: dt5_id ! Memory datatype identifier + integer(SIZE_T) :: typesize, type_sizec, type_sizei, type_size + + integer(HSIZE_T), dimension(2) :: counter + integer(HSSIZE_T), dimension(2) :: fileOffset + integer(pInt), dimension(:,:), allocatable :: arrOffset + + a = n + allocate(namesNA(0:size(phase_name)),source=[a,phase_name]) + NmatPoints = size(mapping,1)/Nconstituents + mapping_ID = HDF5_openGroup("current/mapGeometry") + + allocate(arrOffset(Nconstituents,NmatPoints)) + do i=1_pInt, NmatPoints + do k=1_pInt, Nconstituents + do j=1_pInt, size(phase_name) + if(material_phase(k,1,i) == j) & + arrOffset(k,i) = mpiOffset_phase(j) + enddo + enddo + enddo + +!-------------------------------------------------------------------------------------------------- +! create dataspace + call h5screate_simple_f(2, int([Nconstituents,dataspace_size],HSIZE_T), space_id, hdferr, & + int([Nconstituents,dataspace_size],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping') + +!-------------------------------------------------------------------------------------------------- +! compound type + ! First calculate total size by calculating sizes of each member + ! + CALL h5tcopy_f(H5T_NATIVE_CHARACTER, dt5_id, hdferr) + typesize = len(phase_name(1)) + CALL h5tset_size_f(dt5_id, typesize, hdferr) + CALL h5tget_size_f(dt5_id, type_sizec, hdferr) + CALL h5tget_size_f(H5T_STD_I32LE,type_sizei, hdferr) + type_size = type_sizec + type_sizei + call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping: h5tcreate_f dtype_id') + + call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt5_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f 0') + call h5tinsert_f(dtype_id, "Position", type_sizec, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f 2') + +!-------------------------------------------------------------------------------------------------- +! create Dataset + call h5dcreate_f(mapping_id, 'constitutive', dtype_id, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase') + +!-------------------------------------------------------------------------------------------------- +! Create memory types (one compound datatype for each member) + call h5tcreate_f(H5T_COMPOUND_F, int(type_sizec,SIZE_T), name_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tcreate_f instance_id') + call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt5_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f instance_id') + + call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tcreate_f position_id') + call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f position_id') + +!-------------------------------------------------------------------------------------------------- +! Define and select hyperslabs + counter(1) = Nconstituents ! how big i am + counter(2) = NmatPoints + fileOffset(1) = 0 ! where i start to write my data + fileOffset(2) = mpiOffset + + call h5screate_simple_f(2, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5sselect_hyperslab_f') + +!-------------------------------------------------------------------------------------------------- + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pset_dxpl_mpio_f') + +!-------------------------------------------------------------------------------------------------- +! write data by fields in the datatype. Fields order is not important. + call h5dwrite_f(dset_id, name_id, reshape(namesNA(mapping),[Nconstituents,NmatPoints]), & + int([Nconstituents, dataspace_size],HSIZE_T), hdferr, & + file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dwrite_f position_id') + + call h5dwrite_f(dset_id, position_id, reshape(mapping2-1_pInt,[Nconstituents,NmatPoints])+arrOffset, & + int([Nconstituents, dataspace_size],HSIZE_T), hdferr, & + file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dwrite_f instance_id') + +!-------------------------------------------------------------------------------------------------- +! close types, dataspaces + call h5tclose_f(dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tclose_f dtype_id') + call h5tclose_f(position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tclose_f position_id') + call h5tclose_f(name_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tclose_f instance_id') + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dclose_f') + call h5sclose_f(space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5sclose_f') + call h5pclose_f(plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pclose_f') + call HDF5_closeGroup(mapping_ID) + +end subroutine HDF5_mappingPhase + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds the backward mapping from spatial position and constituent ID to results +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_backwardMappingPhase(material_phase,phasememberat,phase_name,dataspace_size,mpiOffset,mpiOffset_phase) + use hdf5 + + implicit none + integer(pInt), intent(in), dimension(:,:,:) :: material_phase, phasememberat + character(len=*), intent(in), dimension(:) :: phase_name + integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_phase + integer(pInt), intent(in) :: mpiOffset + + integer(pInt) :: hdferr, NmatPoints, Nconstituents, i, j + integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace + integer(SIZE_T) :: type_size + + integer(pInt), dimension(:,:), allocatable :: arr + + integer(HSIZE_T), dimension(1) :: counter + integer(HSSIZE_T), dimension(1) :: fileOffset + + character(len=64) :: phaseID + + Nconstituents = size(phasememberat,1) + NmatPoints = count(material_phase /=0_pInt)/Nconstituents + + allocate(arr(2,NmatPoints*Nconstituents)) + + do i=1_pInt, NmatPoints + do j=Nconstituents-1_pInt, 0_pInt, -1_pInt + arr(1,Nconstituents*i-j) = i-1_pInt + enddo + enddo + arr(2,:) = pack(material_phase,material_phase/=0_pInt) + + + do i=1_pInt, size(phase_name) + write(phaseID, '(i0)') i + mapping_ID = HDF5_openGroup('/current/constitutive/'//trim(phaseID)//'_'//phase_name(i)) + NmatPoints = count(material_phase == i) + +!-------------------------------------------------------------------------------------------------- + ! create dataspace + call h5screate_simple_f(1, int([dataspace_size(i)],HSIZE_T), space_id, hdferr, & + int([dataspace_size(i)],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping') + +!-------------------------------------------------------------------------------------------------- + ! compound type + call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr) + call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id') + + call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tinsert_f 0') + +!-------------------------------------------------------------------------------------------------- + ! create Dataset + call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase') + +!-------------------------------------------------------------------------------------------------- + ! Create memory types (one compound datatype for each member) + call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tcreate_f position_id') + call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tinsert_f position_id') + +!-------------------------------------------------------------------------------------------------- + ! Define and select hyperslabs + counter = NmatPoints ! how big i am + fileOffset = mpiOffset_phase(i) ! where i start to write my data + + call h5screate_simple_f(1, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5sselect_hyperslab_f') + +!-------------------------------------------------------------------------------------------------- + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pset_dxpl_mpio_f') + +!-------------------------------------------------------------------------------------------------- + ! write data by fields in the datatype. Fields order is not important. + call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i)+mpiOffset, int([dataspace_size(i)],HSIZE_T),& + hdferr, file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5dwrite_f instance_id') + +!-------------------------------------------------------------------------------------------------- + !close types, dataspaces + call h5tclose_f(dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tclose_f dtype_id') + call h5tclose_f(position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tclose_f position_id') + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5dclose_f') + call h5sclose_f(space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5sclose_f') + call h5pclose_f(plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pclose_f') + call HDF5_closeGroup(mapping_ID) + + enddo + +end subroutine HDF5_backwardMappingPhase + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds the unique mapping from spatial position and constituent ID to results +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_mappingHomog(material_homog,homogmemberat,homogenization_name,dataspace_size,mpiOffset,mpiOffset_homog) + use hdf5 + + implicit none + integer(pInt), intent(in), dimension(:,:) :: material_homog, homogmemberat + character(len=*), intent(in), dimension(:) :: homogenization_name + integer(pInt), intent(in), dimension(:) :: mpiOffset_homog + integer(pInt), intent(in) :: dataspace_size, mpiOffset + + integer(pInt) :: hdferr, NmatPoints, i, j + integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, name_id, position_id, plist_id, memspace + + integer(HID_T) :: dt5_id ! Memory datatype identifier + integer(SIZE_T) :: typesize, type_sizec, type_sizei, type_size + + integer(HSIZE_T), dimension(1) :: counter + integer(HSSIZE_T), dimension(1) :: fileOffset + integer(pInt), dimension(:), allocatable :: arrOffset + + NmatPoints = count(material_homog /=0_pInt) + mapping_ID = HDF5_openGroup("current/mapGeometry") + + allocate(arrOffset(NmatPoints)) + do i=1_pInt, NmatPoints + do j=1_pInt, size(homogenization_name) + if(material_homog(1,i) == j) & + arrOffset(i) = mpiOffset_homog(j) + enddo + enddo + +!-------------------------------------------------------------------------------------------------- +! create dataspace + call h5screate_simple_f(1, int([dataspace_size],HSIZE_T), space_id, hdferr, & + int([dataspace_size],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping') + +!-------------------------------------------------------------------------------------------------- +! compound type + ! First calculate total size by calculating sizes of each member + ! + CALL h5tcopy_f(H5T_NATIVE_CHARACTER, dt5_id, hdferr) + typesize = len(homogenization_name(1)) + CALL h5tset_size_f(dt5_id, typesize, hdferr) + CALL h5tget_size_f(dt5_id, type_sizec, hdferr) + CALL h5tget_size_f(H5T_STD_I32LE,type_sizei, hdferr) + type_size = type_sizec + type_sizei + call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping: h5tcreate_f dtype_id') + + call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt5_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f 0') + call h5tinsert_f(dtype_id, "Position", type_sizec, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f 2') + +!-------------------------------------------------------------------------------------------------- +! create Dataset + call h5dcreate_f(mapping_id, 'homogenization', dtype_id, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog') + +!-------------------------------------------------------------------------------------------------- +! Create memory types (one compound datatype for each member) + call h5tcreate_f(H5T_COMPOUND_F, int(type_sizec,SIZE_T), name_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tcreate_f instance_id') + call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt5_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f instance_id') + + call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tcreate_f position_id') + call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f position_id') + +!-------------------------------------------------------------------------------------------------- +! Define and select hyperslabs + counter = NmatPoints ! how big i am + fileOffset = mpiOffset ! where i start to write my data + + call h5screate_simple_f(1, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5sselect_hyperslab_f') + +!-------------------------------------------------------------------------------------------------- +! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pset_dxpl_mpio_f') + +!-------------------------------------------------------------------------------------------------- +! write data by fields in the datatype. Fields order is not important. + call h5dwrite_f(dset_id, name_id, homogenization_name(pack(material_homog,material_homog/=0_pInt)), & + int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, & + mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dwrite_f position_id') + + call h5dwrite_f(dset_id, position_id, pack(homogmemberat-1_pInt,homogmemberat/=0_pInt) + arrOffset, & + int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, & + mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dwrite_f instance_id') + +!-------------------------------------------------------------------------------------------------- +!close types, dataspaces + call h5tclose_f(dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tclose_f dtype_id') + call h5tclose_f(position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tclose_f position_id') + call h5tclose_f(name_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tclose_f instance_id') + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dclose_f') + call h5sclose_f(space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5sclose_f') + call h5pclose_f(plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pclose_f') + call HDF5_closeGroup(mapping_ID) + + +end subroutine HDF5_mappingHomog + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds the backward mapping from spatial position and constituent ID to results +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_backwardMappingHomog(material_homog,homogmemberat,homogenization_name,dataspace_size,mpiOffset,mpiOffset_homog) + use hdf5 + + implicit none + integer(pInt), intent(in), dimension(:,:) :: material_homog, homogmemberat + character(len=*), intent(in), dimension(:) :: homogenization_name + integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_homog + integer(pInt), intent(in) :: mpiOffset + + integer(pInt) :: hdferr, NmatPoints, i + integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace + integer(SIZE_T) :: type_size + + integer(pInt), dimension(:,:), allocatable :: arr + + integer(HSIZE_T), dimension(1) :: counter + integer(HSSIZE_T), dimension(1) :: fileOffset + + character(len=64) :: homogID + + NmatPoints = count(material_homog /=0_pInt) + allocate(arr(2,NmatPoints)) + + arr(1,:) = (/(i, i=0_pint,NmatPoints-1_pInt)/) + arr(2,:) = pack(material_homog,material_homog/=0_pInt) + + do i=1_pInt, size(homogenization_name) + write(homogID, '(i0)') i + mapping_ID = HDF5_openGroup('/current/homogenization/'//trim(homogID)//'_'//homogenization_name(i)) + +!-------------------------------------------------------------------------------------------------- + ! create dataspace + call h5screate_simple_f(1, int([dataspace_size(i)],HSIZE_T), space_id, hdferr, & + int([dataspace_size(i)],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping') + +!-------------------------------------------------------------------------------------------------- + ! compound type + call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr) + call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id') + + call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tinsert_f 0') + +!-------------------------------------------------------------------------------------------------- + ! create Dataset + call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog') + +!-------------------------------------------------------------------------------------------------- + ! Create memory types (one compound datatype for each member) + call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tcreate_f position_id') + call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tinsert_f position_id') + +!-------------------------------------------------------------------------------------------------- + ! Define and select hyperslabs + counter = NmatPoints ! how big i am + fileOffset = mpiOffset_homog(i) ! where i start to write my data + + call h5screate_simple_f(1, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5sselect_hyperslab_f') + +!-------------------------------------------------------------------------------------------------- + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pset_dxpl_mpio_f') + +!-------------------------------------------------------------------------------------------------- + ! write data by fields in the datatype. Fields order is not important. + call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i)+mpiOffset,int([dataspace_size(i)],HSIZE_T),& + hdferr, file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5dwrite_f instance_id') + +!-------------------------------------------------------------------------------------------------- + !close types, dataspaces + call h5tclose_f(dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tclose_f dtype_id') + call h5tclose_f(position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tclose_f position_id') + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5dclose_f') + call h5sclose_f(space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5sclose_f') + call h5pclose_f(plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pclose_f') + call HDF5_closeGroup(mapping_ID) + + enddo + +end subroutine HDF5_backwardMappingHomog + +!-------------------------------------------------------------------------------------------------- +!> @brief adds the unique mapping from spatial position and constituent ID to results +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_mappingCrystallite(crystalliteAt,crystmemberAt,crystallite_name,dataspace_size,mpiOffset,mpiOffset_cryst) + use hdf5 + + implicit none + integer(pInt), intent(in), dimension(:,:) :: crystalliteAt + integer(pInt), intent(in), dimension(:,:,:) :: crystmemberAt + character(len=*), intent(in), dimension(:) :: crystallite_name + integer(pInt), intent(in), dimension(:) :: mpiOffset_cryst + integer(pInt), intent(in) :: dataspace_size, mpiOffset + + integer :: hdferr + integer(pInt) :: NmatPoints, Nconstituents, i, j + integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, name_id, plist_id, memspace + integer(HID_T), dimension(:), allocatable :: position_id + + integer(HID_T) :: dt5_id ! Memory datatype identifier + integer(SIZE_T) :: typesize, type_sizec, type_sizei, type_size + + integer(HSIZE_T), dimension(1) :: counter + integer(HSSIZE_T), dimension(1) :: fileOffset + integer(pInt), dimension(:), allocatable :: arrOffset + + character(len=64) :: m + + Nconstituents = size(crystmemberAt,1) + NmatPoints = count(crystalliteAt /=0_pInt) + mapping_ID = HDF5_openGroup("current/mapGeometry") + + allocate(position_id(Nconstituents)) + + allocate(arrOffset(NmatPoints)) + do i=1_pInt, NmatPoints + do j=1_pInt, size(crystallite_name) + if(crystalliteAt(1,i) == j) & + arrOffset(i) = Nconstituents*mpiOffset_cryst(j) + enddo + enddo + +!-------------------------------------------------------------------------------------------------- +! create dataspace + call h5screate_simple_f(1, int([dataspace_size],HSIZE_T), space_id, hdferr, & + int([dataspace_size],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping') + +!-------------------------------------------------------------------------------------------------- +! compound type + ! First calculate total size by calculating sizes of each member + ! + CALL h5tcopy_f(H5T_NATIVE_CHARACTER, dt5_id, hdferr) + typesize = len(crystallite_name(1)) + CALL h5tset_size_f(dt5_id, typesize, hdferr) + CALL h5tget_size_f(dt5_id, type_sizec, hdferr) + CALL h5tget_size_f(H5T_STD_I32LE, type_sizei, hdferr) + type_size = type_sizec + type_sizei*Nconstituents + call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping: h5tcreate_f dtype_id') + + call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt5_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f 0') + do i=1_pInt, Nconstituents + write(m, '(i0)') i + call h5tinsert_f(dtype_id, "Position "//trim(m), type_sizec+(i-1)*type_sizei, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f 2 '//trim(m)) + enddo + +!-------------------------------------------------------------------------------------------------- +! create Dataset + call h5dcreate_f(mapping_id, 'crystallite', dtype_id, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite') + +!-------------------------------------------------------------------------------------------------- +! Create memory types (one compound datatype for each member) + call h5tcreate_f(H5T_COMPOUND_F, int(type_sizec,SIZE_T), name_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tcreate_f instance_id') + call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt5_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f instance_id') + + do i=1_pInt, Nconstituents + write(m, '(i0)') i + call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id(i), hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tcreate_f position_id') + call h5tinsert_f(position_id(i), "Position "//trim(m), 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f position_id') + enddo + +!-------------------------------------------------------------------------------------------------- +! Define and select hyperslabs + counter = NmatPoints ! how big i am + fileOffset = mpiOffset ! where i start to write my data + + call h5screate_simple_f(1, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5sselect_hyperslab_f') + +!-------------------------------------------------------------------------------------------------- + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pset_dxpl_mpio_f') + +!-------------------------------------------------------------------------------------------------- +! write data by fields in the datatype. Fields order is not important. + call h5dwrite_f(dset_id, name_id, crystallite_name(pack(crystalliteAt,crystalliteAt/=0_pInt)), & + int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, & + mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dwrite_f position_id') + + do i=1_pInt, Nconstituents + call h5dwrite_f(dset_id, position_id(i), pack(crystmemberAt(i,:,:)-1_pInt,crystmemberAt(i,:,:)/=0_pInt)+arrOffset,& + int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, & + mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dwrite_f instance_id') + enddo + +!-------------------------------------------------------------------------------------------------- +!close types, dataspaces + call h5tclose_f(dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f dtype_id') + do i=1_pInt, Nconstituents + call h5tclose_f(position_id(i), hdferr) + enddo + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f position_id') + call h5tclose_f(name_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f instance_id') + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dclose_f') + call h5sclose_f(space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5sclose_f') + call h5pclose_f(plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pclose_f') + call HDF5_closeGroup(mapping_ID) + + +end subroutine HDF5_mappingCrystallite + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds the backward mapping from spatial position and constituent ID to results +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_backwardMappingCrystallite(crystalliteAt,crystmemberAt,crystallite_name,dataspace_size,mpiOffset,mpiOffset_cryst) + use hdf5 + + implicit none + integer(pInt), intent(in), dimension(:,:) :: crystalliteAt + integer(pInt), intent(in), dimension(:,:,:) :: crystmemberAt + character(len=*), intent(in), dimension(:) :: crystallite_name + integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_cryst + integer(pInt), intent(in) :: mpiOffset + + integer :: hdferr + integer(pInt) :: NmatPoints, Nconstituents, i, j + integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace + integer(SIZE_T) :: type_size + + integer(pInt), dimension(:,:), allocatable :: h_arr, arr + + integer(HSIZE_T), dimension(1) :: counter + integer(HSSIZE_T), dimension(1) :: fileOffset + + character(len=64) :: crystallID + + Nconstituents = size(crystmemberAt,1) + NmatPoints = count(crystalliteAt /=0_pInt) + + allocate(h_arr(2,NmatPoints)) + allocate(arr(2,Nconstituents*NmatPoints)) + + h_arr(1,:) = (/(i, i=0_pInt,NmatPoints-1_pInt)/) + h_arr(2,:) = pack(crystalliteAt,crystalliteAt/=0_pInt) + + do i=1_pInt, NmatPoints + do j=Nconstituents-1_pInt, 0_pInt, -1_pInt + arr(1,Nconstituents*i-j) = h_arr(1,i) + arr(2,Nconstituents*i-j) = h_arr(2,i) + enddo + enddo + + + do i=1_pInt, size(crystallite_name) + if (crystallite_name(i) == 'none') cycle + write(crystallID, '(i0)') i + mapping_ID = HDF5_openGroup('/current/crystallite/'//trim(crystallID)//'_'//crystallite_name(i)) + NmatPoints = count(crystalliteAt == i) + +!-------------------------------------------------------------------------------------------------- + ! create dataspace + call h5screate_simple_f(1, int([Nconstituents*dataspace_size(i)],HSIZE_T), space_id, hdferr, & + int([Nconstituents*dataspace_size(i)],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping') + +!-------------------------------------------------------------------------------------------------- + ! compound type + call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr) + call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id') + + call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tinsert_f 0') + +!-------------------------------------------------------------------------------------------------- + ! create Dataset + call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite') + +!-------------------------------------------------------------------------------------------------- + ! Create memory types + call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tcreate_f position_id') + call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tinsert_f position_id') + +!-------------------------------------------------------------------------------------------------- + ! Define and select hyperslabs + counter = Nconstituents*NmatPoints ! how big i am + fileOffset = Nconstituents*mpiOffset_cryst(i) ! where i start to write my data + + call h5screate_simple_f(1, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5sselect_hyperslab_f') + +!-------------------------------------------------------------------------------------------------- + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pset_dxpl_mpio_f') + +!-------------------------------------------------------------------------------------------------- + ! write data by fields in the datatype. Fields order is not important. + call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i) + mpiOffset,& + int([Nconstituents*dataspace_size(i)],HSIZE_T), hdferr, file_space_id = space_id, & + mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5dwrite_f instance_id') + +!-------------------------------------------------------------------------------------------------- + !close types, dataspaces + call h5tclose_f(dtype_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tclose_f dtype_id') + call h5tclose_f(position_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tclose_f position_id') + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5dclose_f') + call h5sclose_f(space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5sclose_f') + call h5pclose_f(plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pclose_f') + call HDF5_closeGroup(mapping_ID) + + enddo + +end subroutine HDF5_backwardMappingCrystallite + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds the unique cell to node mapping +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_mappingCells(mapping) + use hdf5 + + implicit none + integer(pInt), intent(in), dimension(:) :: mapping + + integer :: hdferr, Nnodes + integer(HID_T) :: mapping_id, dset_id, space_id + + Nnodes=size(mapping) + mapping_ID = HDF5_openGroup("mapping") + +!-------------------------------------------------------------------------------------------------- +! create dataspace + call h5screate_simple_f(1, int([Nnodes],HSIZE_T), space_id, hdferr, & + int([Nnodes],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells: h5screate_simple_f') + +!-------------------------------------------------------------------------------------------------- +! create Dataset + call h5dcreate_f(mapping_id, "Cell",H5T_NATIVE_INTEGER, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells') + +!-------------------------------------------------------------------------------------------------- +! write data by fields in the datatype. Fields order is not important. + call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, mapping, int([Nnodes],HSIZE_T), hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells: h5dwrite_f instance_id') + +!-------------------------------------------------------------------------------------------------- +!close types, dataspaces + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5dclose_f') + call h5sclose_f(space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5sclose_f') + call HDF5_closeGroup(mapping_ID) + +end subroutine HDF5_mappingCells + + + + +!-------------------------------------------------------------------------------------------------- +!> @brief creates a new scalar dataset in the given group location +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_addTensor3DDataset(group,Nnodes,tensorSize,label,SIunit) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: group + integer(pInt), intent(in) :: Nnodes, tensorSize + character(len=*), intent(in) :: SIunit, label + + integer :: hdferr + integer(HID_T) :: space_id, dset_id + integer(HSIZE_T), dimension(3) :: dataShape + + dataShape = int([tensorSize,tensorSize,Nnodes], HSIZE_T) + +!-------------------------------------------------------------------------------------------------- +! create dataspace + call h5screate_simple_f(3, dataShape, space_id, hdferr, dataShape) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addTensor3DDataset: h5screate_simple_f') + +!-------------------------------------------------------------------------------------------------- +! create Dataset + call h5dcreate_f(group, trim(label),H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addTensor3DDataset: h5dcreate_f') + call HDF5_addStringAttribute(dset_id,'unit',trim(SIunit)) + +!-------------------------------------------------------------------------------------------------- +!close types, dataspaces + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addTensor3DDataset: h5dclose_f') + call h5sclose_f(space_id, hdferr) + +end subroutine HDF5_addTensor3DDataset + +!-------------------------------------------------------------------------------------------------- +!> @brief creates a new scalar dataset in the given group location +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_writeVectorDataset(group,dataset,label,SIunit,dataspace_size,mpiOffset) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: group + character(len=*), intent(in) :: SIunit,label + integer(pInt), intent(in) :: dataspace_size, mpiOffset + real(pReal), intent(in), dimension(:,:) :: dataset + + integer :: hdferr, vectorSize + integer(HID_T) :: dset_id, space_id, memspace, plist_id + + integer(HSIZE_T), dimension(2) :: counter + integer(HSSIZE_T), dimension(2) :: fileOffset + + if(any(shape(dataset) == 0)) return + + vectorSize = size(dataset,1) + + call HDF5_addVectorDataset(group,dataspace_size,vectorSize,label,SIunit) ! here nNodes need to be global + call h5dopen_f(group, label, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dopen_f') + + ! Define and select hyperslabs + counter(1) = vectorSize ! how big i am + counter(2) = size(dataset,2) + fileOffset(1) = 0 ! where i start to write my data + fileOffset(2) = mpiOffset + + call h5screate_simple_f(2, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5sselect_hyperslab_f') + + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pset_dxpl_mpio_f') + + ! Write the dataset collectively + call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([vectorSize, dataspace_size],HSIZE_T), hdferr, & + file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dwrite_f') + + call h5sclose_f(space_id, hdferr) + call h5sclose_f(memspace, hdferr) + call h5dclose_f(dset_id, hdferr) + call h5pclose_f(plist_id, hdferr) + +end subroutine HDF5_writeVectorDataset + +!-------------------------------------------------------------------------------------------------- +!> @brief creates a new scalar dataset in the given group location +! by default, a 3x3 tensor is assumed +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_writeTensorDataset(group,dataset,label,SIunit,dataspace_size,mpiOffset) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: group + character(len=*), intent(in) :: SIunit,label + integer(pInt), intent(in) :: dataspace_size, mpiOffset + real(pReal), intent(in), dimension(:,:,:) :: dataset + + integer :: hdferr, tensorSize + integer(HID_T) :: dset_id, space_id, memspace, plist_id + + integer(HSIZE_T), dimension(3) :: counter + integer(HSSIZE_T), dimension(3) :: fileOffset + + if(any(shape(dataset) == 0)) return + + tensorSize = size(dataset,1) + + call HDF5_addTensor3DDataset(group,dataspace_size,tensorSize,label,SIunit) + call h5dopen_f(group, label, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5dopen_f') + + ! Define and select hyperslabs + counter(1) = tensorSize ! how big i am + counter(2) = tensorSize + counter(3) = size(dataset,3) + fileOffset(1) = 0 ! where i start to write my data + fileOffset(2) = 0 + fileOffset(3) = mpiOffset + + call h5screate_simple_f(3, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5sselect_hyperslab_f') + + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pset_dxpl_mpio_f') + + ! Write the dataset collectively + call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([tensorSize, dataspace_size],HSIZE_T), hdferr, & + file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5dwrite_f') + + call h5sclose_f(space_id, hdferr) + call h5sclose_f(memspace, hdferr) + call h5dclose_f(dset_id, hdferr) + call h5pclose_f(plist_id, hdferr) + + end subroutine HDF5_writeTensorDataset + + +!-------------------------------------------------------------------------------------------------- +!> @brief creates a new scalar dataset in the given group location +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_addVectorDataset(group,nnodes,vectorSize,label,SIunit) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: group + integer(pInt), intent(in) :: nnodes,vectorSize + character(len=*), intent(in) :: SIunit,label + + integer :: hdferr + integer(HID_T) :: space_id, dset_id + +!-------------------------------------------------------------------------------------------------- +! create dataspace + call h5screate_simple_f(2, int([vectorSize,Nnodes],HSIZE_T), space_id, hdferr, & + int([vectorSize,Nnodes],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addVectorDataset: h5screate_simple_f') + +!-------------------------------------------------------------------------------------------------- +! create Dataset + call h5dcreate_f(group, trim(label), H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addVectorDataset: h5dcreate_f') + call HDF5_addStringAttribute(dset_id,'unit',trim(SIunit)) + +!-------------------------------------------------------------------------------------------------- +!close types, dataspaces + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addVectorDataset: h5dclose_f') + call h5sclose_f(space_id, hdferr) + +end subroutine HDF5_addVectorDataset + + + +!-------------------------------------------------------------------------------------------------- +!> @brief creates a new scalar dataset in the given group location +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_writeScalarDataset(group,dataset,label,SIunit,dataspace_size,mpiOffset) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: group + character(len=*), intent(in) :: SIunit,label + integer(pInt), intent(in) :: dataspace_size, mpiOffset + real(pReal), intent(in), dimension(:) :: dataset + + integer :: hdferr, nNodes + integer(HID_T) :: dset_id, space_id, memspace, plist_id + + integer(HSIZE_T), dimension(1) :: counter + integer(HSSIZE_T), dimension(1) :: fileOffset + + nNodes = size(dataset) + if (nNodes < 1) return + + call HDF5_addScalarDataset(group,dataspace_size,label,SIunit) + call h5dopen_f(group, label, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dopen_f') + + ! Define and select hyperslabs + counter = size(dataset) ! how big i am + fileOffset = mpiOffset ! where i start to write my data + + call h5screate_simple_f(1, counter, memspace, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5screate_simple_f') + call h5dget_space_f(dset_id, space_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dget_space_f') + call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5sselect_hyperslab_f') + + ! Create property list for collective dataset write + call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f') + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f') + + ! Write the dataset collectively + call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([dataspace_size],HSIZE_T), hdferr, & + file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dwrite_f') + + call h5sclose_f(space_id, hdferr) + call h5sclose_f(memspace, hdferr) + call h5dclose_f(dset_id, hdferr) + call h5pclose_f(plist_id, hdferr) + +end subroutine HDF5_writeScalarDataset + + +!-------------------------------------------------------------------------------------------------- +!> @brief creates a new scalar dataset in the given group location +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_addScalarDataset(group,nnodes,label,SIunit) + use hdf5 + + implicit none + integer(HID_T), intent(in) :: group + integer(pInt), intent(in) :: nnodes + character(len=*), intent(in) :: SIunit,label + + integer :: hdferr + integer(HID_T) :: space_id, dset_id + +!-------------------------------------------------------------------------------------------------- +! create dataspace + call h5screate_simple_f(1, int([Nnodes],HSIZE_T), space_id, hdferr, & + int([Nnodes],HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5screate_simple_f') + +!-------------------------------------------------------------------------------------------------- +! create Dataset + call h5dcreate_f(group, trim(label),H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dcreate_f') + call HDF5_addStringAttribute(dset_id,'unit',trim(SIunit)) + +!-------------------------------------------------------------------------------------------------- +!close types, dataspaces + call h5dclose_f(dset_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dclose_f') + call h5sclose_f(space_id, hdferr) + +end subroutine HDF5_addScalarDataset + + + +!-------------------------------------------------------------------------------------------------- +!> @brief copies the current temp results to the actual results file +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_forwardResults(time) + use hdf5 + use IO, only: & + IO_intOut + + implicit none + integer :: hdferr + real(pReal), intent(in) :: time + character(len=1024) :: myName + + currentInc = currentInc +1_pInt + write(6,*) 'forward results';flush(6) + write(myName,'(a,'//IO_intOut(currentInc)//')') 'inc',currentInc + currentIncID = HDF5_addGroup(myName) + call HDF5_setLink(myName,'current') +! call HDF5_flush(resultsFile) + call HDF5_closeGroup(currentIncID) + +end subroutine HDF5_forwardResults + +end module HDF5_Utilities From 5b409fd6f7c3f13361bd440040ab1de585aa8492 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 3 Aug 2018 16:16:50 +0200 Subject: [PATCH 06/67] type mismatch --- src/HDF5_utilities.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index bb09da7f7..b878543a1 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -187,7 +187,7 @@ subroutine HDF5_closeGroup(ID) integer :: hdferr call h5gclose_f(ID, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = ID) + if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = int(ID,pInt)) end subroutine HDF5_closeGroup From 20d1264d0705a30e77c4fd5d01532d69b7c09724 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 4 Aug 2018 13:58:01 +0200 Subject: [PATCH 07/67] small improvements default case of error handling, checking for recursion limit, some comments to also understand it later --- src/IO.f90 | 68 +++++++++++++++++++++++++++++++++++------------------- 1 file changed, 44 insertions(+), 24 deletions(-) diff --git a/src/IO.f90 b/src/IO.f90 index 94e429324..c9e93b498 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -176,48 +176,65 @@ end function IO_read !> @brief recursively reads a text file. !! Recursion is triggered by "{path/to/inputfile}" in a line !-------------------------------------------------------------------------------------------------- -recursive function IO_recursiveRead(fileName) result(fileContent) +recursive function IO_recursiveRead(fileName,cnt) result(fileContent) implicit none - character(len=*), intent(in) :: fileName - character(len=256), dimension(:), allocatable :: fileContent + character(len=*), intent(in) :: fileName + integer(pInt), intent(in), optional :: cnt !< recursion counter + character(len=256), dimension(:), allocatable :: fileContent !< file content, separated per lines character(len=256), dimension(:), allocatable :: includedContent - character(len=256) :: line - character(len=:), allocatable :: rawData - integer(pInt) :: fileLength, fileUnit,startPos,endPos,& - myTotalLines,l,includedLines, missingLines,i + character(len=256) :: line + character(len=256), parameter :: dummy = 'https://damask.mpie.de' !< to fill up remaining array + character(len=:), allocatable :: rawData + integer(pInt) :: & + fileLength, & + fileUnit, & + startPos, endPos, & + myTotalLines, & !< # lines read from file without include statements + includedLines, & !< # lines included from other file(s) + missingLines, & !< # lines missing from current file + l,i + if (merge(cnt,0_pInt,present(cnt))>10_pInt) call IO_error(106_pInt,ext_msg=trim(fileName)) + +!-------------------------------------------------------------------------------------------------- +! read data as stream inquire(file = fileName, size=fileLength) open(newunit=fileUnit, file = fileName, access = "STREAM") allocate(character(len=fileLength)::rawData) read(fileUnit) rawData close(fileUnit) - myTotalLines = 0 - do l=1, len(rawData) +!-------------------------------------------------------------------------------------------------- +! count lines to allocate string array + myTotalLines = 0_pInt + do l=1_pInt, len(rawData) if (rawData(l:l) == new_line('')) myTotalLines = myTotalLines+1 enddo allocate(fileContent(myTotalLines)) - startPos = 1 - endPos = 0 +!-------------------------------------------------------------------------------------------------- +! split raw data at end of line and handle includes + startPos = 1_pInt + endPos = 0_pInt - includedLines=0 - l=0 + includedLines=0_pInt + l=0_pInt do while (startPos <= len(rawData)) - l = l + 1 + l = l + 1_pInt endPos = endPos + scan(rawData(startPos:),new_line('')) - if(endPos - startPos >256) write(6,*) 'mist' - line = rawData(startPos:endPos-1) - startPos = endPos + 1 + if(endPos - startPos >256) call IO_error(107_pInt,ext_msg=trim(fileName)) + line = rawData(startPos:endPos-1_pInt) + startPos = endPos + 1_pInt recursion: if(scan(trim(line),'{') < scan(trim(line),'}')) then - myTotalLines = myTotalLines - 1 - includedContent = IO_recursiveRead(trim(line(scan(line,'{')+1:scan(line,'}')-1))) - includedLines = includedLines +size(includedContent) - missingLines = myTotalLines+includedLines - size(fileContent(1:l-1)) -size(includedContent) - fileContent = [fileContent(1:l-1),includedContent,[(line,i=1,missingLines)]] - l=l-1+size(includedContent) + myTotalLines = myTotalLines - 1_pInt + includedContent = IO_recursiveRead(trim(line(scan(line,'{')+1_pInt:scan(line,'}')-1_pInt)), & + merge(cnt,1_pInt,present(cnt))) ! to track recursion depth + includedLines = includedLines + size(includedContent) + missingLines = myTotalLines + includedLines - size(fileContent(1:l-1)) -size(includedContent) + fileContent = [ fileContent(1:l-1_pInt), includedContent, [(dummy,i=1,missingLines)] ] ! add content and grow array + l = l - 1_pInt + size(includedContent) else recursion fileContent(l) = line endif recursion @@ -226,6 +243,7 @@ recursive function IO_recursiveRead(fileName) result(fileContent) end function IO_recursiveRead + !-------------------------------------------------------------------------------------------------- !> @brief checks if unit is opened for reading, if true rewinds. Otherwise stops with !! error message @@ -233,7 +251,7 @@ end function IO_recursiveRead subroutine IO_checkAndRewind(fileUnit) implicit none - integer(pInt), intent(in) :: fileUnit !< file unit + integer(pInt), intent(in) :: fileUnit !< file unit logical :: fileOpened character(len=15) :: fileRead @@ -1568,6 +1586,8 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg) msg = 'unknown output:' case (106_pInt) msg = 'working directory does not exist:' + case (107_pInt) + msg = 'line length exceeds limit of 256' !-------------------------------------------------------------------------------------------------- ! lattice error messages From 9360c171a1eb15590abcdfdb5652f764b25e05b8 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 4 Aug 2018 19:39:50 +0200 Subject: [PATCH 08/67] polished for merge access to array(n+m:) is safe for array of size n with m>1 --- src/config.f90 | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index 6c92ff95a..c99b14c00 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -107,13 +107,13 @@ subroutine config_init() debug_levelBasic implicit none - integer(pInt) :: myDebug,i + integer(pInt) :: myDebug,i character(len=256) :: & line, & part character(len=256), dimension(:), allocatable :: fileContent - logical :: jobSpecificConfig + logical :: fileExists write(6,'(/,a)') ' <<<+- config init -+>>>' write(6,'(a15,a)') ' Current time: ',IO_timeStamp() @@ -121,12 +121,12 @@ subroutine config_init() myDebug = debug_level(debug_material) - inquire(file=trim(getSolverJobName())//'.'//material_localFileExt,exist=jobSpecificConfig) - if(jobSpecificConfig) then + inquire(file=trim(getSolverJobName())//'.'//material_localFileExt,exist=fileExists) + if(fileExists) then fileContent = IO_recursiveRead(trim(getSolverJobName())//'.'//material_localFileExt) else - inquire(file='material.config',exist=jobSpecificConfig) - if(.not. jobSpecificConfig) call IO_error(0_pInt) + inquire(file='material.config',exist=fileExists) + if(.not. fileExists) call IO_error(100_pInt,ext_msg='material.config') fileContent = IO_recursiveRead('material.config') endif @@ -136,7 +136,7 @@ subroutine config_init() select case (trim(part)) case (trim(material_partPhase)) - call parseFile(line,phase_name,config_phase,fileContent(i+1:)) !(i+1:) save for empty part at (at end of file)? + call parseFile(line,phase_name,config_phase,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Phase parsed'; flush(6) case (trim(material_partMicrostructure)) @@ -158,7 +158,6 @@ subroutine config_init() end select enddo - deallocate(fileContent) material_Nhomogenization = size(config_homogenization) if (material_Nhomogenization < 1_pInt) call IO_error(160_pInt,ext_msg=material_partHomogenization) @@ -233,6 +232,9 @@ subroutine parseFile(line,& end subroutine parseFile +!-------------------------------------------------------------------------------------------------- +!> @brief deallocates the linked lists that store the content of the configuration files +!-------------------------------------------------------------------------------------------------- subroutine config_deallocate(what) use IO, only: & IO_error @@ -281,6 +283,12 @@ subroutine config_deallocate(what) end subroutine config_deallocate +!################################################################################################## +! The folowing functions are part of the tPartitionedStringList object +!################################################################################################## + + + !-------------------------------------------------------------------------------------------------- !> @brief add element !> @details Adds a string together with the start/end position of chunks in this string. The new From b64b5b82de263fb3eab2a450ae230e13b247869f Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sun, 5 Aug 2018 17:06:03 +0200 Subject: [PATCH 09/67] integrationMode was always 1, very obscure code was most likely the leftover of old functionality --- src/crystallite.f90 | 70 ++++++++++++---------------------------- src/numerics.f90 | 11 +++---- src/plastic_nonlocal.f90 | 17 ++++------ 3 files changed, 31 insertions(+), 67 deletions(-) diff --git a/src/crystallite.f90 b/src/crystallite.f90 index aea4fb993..88782751d 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -114,6 +114,7 @@ module crystallite end enum integer(kind(undefined_ID)),dimension(:,:), allocatable, private :: & crystallite_outputID !< ID of each post result output + procedure(), pointer :: integrateState public :: & crystallite_init, & @@ -122,6 +123,7 @@ module crystallite crystallite_push33ToRef, & crystallite_postResults private :: & + integrateState, & crystallite_integrateStateFPI, & crystallite_integrateStateEuler, & crystallite_integrateStateAdaptiveEuler, & @@ -149,6 +151,7 @@ subroutine crystallite_init debug_crystallite, & debug_levelBasic use numerics, only: & + numerics_integrator, & worldrank, & usePingPong use math, only: & @@ -269,6 +272,20 @@ subroutine crystallite_init allocate(crystallite_sizePostResult(maxval(crystallite_Noutput), & size(config_crystallite)), source=0_pInt) + select case(numerics_integrator(1)) + case(1_pInt) + integrateState => crystallite_integrateStateFPI + case(2_pInt) + integrateState => crystallite_integrateStateEuler + case(3_pInt) + integrateState => crystallite_integrateStateAdaptiveEuler + case(4_pInt) + integrateState => crystallite_integrateStateRK4 + case(5_pInt) + integrateState => crystallite_integrateStateRKCK45 + end select + + do c = 1_pInt, size(config_crystallite) #if defined(__GFORTRAN__) @@ -494,9 +511,6 @@ subroutine crystallite_stressAndItsTangent(updateJaco) subStepMinCryst, & subStepSizeCryst, & stepIncreaseCryst, & - nCryst, & - numerics_integrator, & - numerics_integrationMode, & numerics_timeSyncing use debug, only: & debug_level, & @@ -648,7 +662,6 @@ subroutine crystallite_stressAndItsTangent(updateJaco) endif singleRun NiterationCrystallite = 0_pInt - numerics_integrationMode = 1_pInt cutbackLooping: do while (any(crystallite_todo(:,startIP:endIP,FEsolving_execELem(1):FEsolving_execElem(2)))) if (iand(debug_level(debug_crystallite),debug_levelExtensive) /= 0_pInt) & @@ -1026,25 +1039,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco) ! --- integrate --- requires fully defined state array (basic + dependent state) - if (any(crystallite_todo)) then - if (iand(debug_level(debug_crystallite),debug_levelExtensive) /= 0_pInt) then - write(6,'(/,a,i3)') '<< CRYST >> using state integrator ',numerics_integrator(numerics_integrationMode) - flush(6) - endif - select case(numerics_integrator(numerics_integrationMode)) - case(1_pInt) - call crystallite_integrateStateFPI() - case(2_pInt) - call crystallite_integrateStateEuler() - case(3_pInt) - call crystallite_integrateStateAdaptiveEuler() - case(4_pInt) - call crystallite_integrateStateRK4() - case(5_pInt) - call crystallite_integrateStateRKCK45() - end select - endif - + if (any(crystallite_todo)) call integrateState() where(.not. crystallite_converged .and. crystallite_subStep > subStepMinCryst) & ! do not try non-converged & fully cutbacked any further crystallite_todo = .true. @@ -1215,8 +1210,6 @@ end subroutine crystallite_stressAndItsTangent subroutine crystallite_integrateStateRK4() use, intrinsic :: & IEEE_arithmetic - use numerics, only: & - numerics_integrationMode use debug, only: & #ifdef DEBUG debug_e, & @@ -1517,8 +1510,7 @@ subroutine crystallite_integrateStateRKCK45() debug_levelExtensive, & debug_levelSelective use numerics, only: & - rTol_crystalliteState, & - numerics_integrationMode + rTol_crystalliteState use FEsolving, only: & FEsolving_execElem, & FEsolving_execIP @@ -2013,8 +2005,7 @@ subroutine crystallite_integrateStateAdaptiveEuler() debug_levelExtensive, & debug_levelSelective use numerics, only: & - rTol_crystalliteState, & - numerics_integrationMode + rTol_crystalliteState use FEsolving, only: & FEsolving_execElem, & FEsolving_execIP @@ -2082,7 +2073,6 @@ subroutine crystallite_integrateStateAdaptiveEuler() sourceStateResiduum = 0.0_pReal relSourceStateResiduum = 0.0_pReal - integrationMode: if (numerics_integrationMode == 1_pInt) then !$OMP PARALLEL ! --- DOT STATE (EULER INTEGRATION) --- @@ -2182,7 +2172,6 @@ subroutine crystallite_integrateStateAdaptiveEuler() enddo; enddo; enddo !$OMP ENDDO !$OMP END PARALLEL - endif integrationMode ! --- STRESS INTEGRATION (EULER INTEGRATION) --- @@ -2202,9 +2191,6 @@ subroutine crystallite_integrateStateAdaptiveEuler() enddo; enddo; enddo !$OMP END PARALLEL DO - - if (numerics_integrationMode == 1_pInt) then - !$OMP PARALLEL ! --- DOT STATE (HEUN METHOD) --- @@ -2323,17 +2309,6 @@ subroutine crystallite_integrateStateAdaptiveEuler() !$OMP ENDDO !$OMP END PARALLEL - elseif (numerics_integrationMode > 1) then ! stiffness calculation - - !$OMP PARALLEL DO - do e = eIter(1),eIter(2); do i = iIter(1,e),iIter(2,e); do g = gIter(1,e),gIter(2,e) ! iterate over elements, ips and grains - crystallite_converged(g,i,e) = crystallite_todo(g,i,e) .or. crystallite_converged(g,i,e) ! ... converged per definitionem - enddo; enddo; enddo - !$OMP END PARALLEL DO - - endif - - ! --- NONLOCAL CONVERGENCE CHECK --- @@ -2364,7 +2339,6 @@ subroutine crystallite_integrateStateEuler() debug_levelExtensive, & debug_levelSelective use numerics, only: & - numerics_integrationMode, & numerics_timeSyncing use FEsolving, only: & FEsolving_execElem, & @@ -2411,7 +2385,6 @@ eIter = FEsolving_execElem(1:2) singleRun = (eIter(1) == eIter(2) .and. iIter(1,eIter(1)) == iIter(2,eIter(2))) - if (numerics_integrationMode == 1_pInt) then !$OMP PARALLEL ! --- DOT STATE --- @@ -2516,7 +2489,6 @@ eIter = FEsolving_execElem(1:2) enddo; enddo; enddo !$OMP ENDDO !$OMP END PARALLEL - endif !$OMP PARALLEL @@ -2581,7 +2553,6 @@ subroutine crystallite_integrateStateFPI() debug_levelSelective use numerics, only: & nState, & - numerics_integrationMode, & rTol_crystalliteState use FEsolving, only: & FEsolving_execElem, & @@ -3156,7 +3127,6 @@ logical function crystallite_integrateStress(& aTol_crystalliteStress, & rTol_crystalliteStress, & iJacoLpresiduum, & - numerics_integrationMode, & subStepSizeLp, & subStepSizeLi use debug, only: debug_level, & diff --git a/src/numerics.f90 b/src/numerics.f90 index 8de664248..e73bc8321 100644 --- a/src/numerics.f90 +++ b/src/numerics.f90 @@ -27,9 +27,8 @@ module numerics worldsize = 0_pInt !< MPI worldsize (/=0 for MPI simulations only) integer(4), protected, public :: & DAMASK_NumThreadsInt = 0 !< value stored in environment variable DAMASK_NUM_THREADS, set to zero if no OpenMP directive - integer(pInt), public :: & - numerics_integrationMode = 0_pInt !< integrationMode 1 = central solution; integrationMode 2 = perturbation, Default 0: undefined, is not read from file - integer(pInt), dimension(2) , protected, public :: & +!> ToDo: numerics_integrator in an array for historical reasons, only element 1 is used! + integer(pInt), dimension(2), protected, public :: & numerics_integrator = 1_pInt !< method used for state integration (central & perturbed state), Default 1: fix-point iteration for both states real(pReal), protected, public :: & relevantStrain = 1.0e-7_pReal, & !< strain increment considered significant (used by crystallite to determine whether strain inc is considered significant) @@ -317,9 +316,7 @@ subroutine numerics_init case ('atol_crystallitestress') aTol_crystalliteStress = IO_floatValue(line,chunkPos,2_pInt) case ('integrator') - numerics_integrator(1) = IO_intValue(line,chunkPos,2_pInt) - case ('integratorstiffness') - numerics_integrator(2) = IO_intValue(line,chunkPos,2_pInt) + numerics_integrator = IO_intValue(line,chunkPos,2_pInt) case ('usepingpong') usepingpong = IO_intValue(line,chunkPos,2_pInt) > 0_pInt case ('timesyncing') @@ -531,7 +528,7 @@ subroutine numerics_init write(6,'(a24,1x,es8.1)') ' rTol_crystalliteState: ',rTol_crystalliteState write(6,'(a24,1x,es8.1)') ' rTol_crystalliteStress: ',rTol_crystalliteStress write(6,'(a24,1x,es8.1)') ' aTol_crystalliteStress: ',aTol_crystalliteStress - write(6,'(a24,2(1x,i8))') ' integrator: ',numerics_integrator + write(6,'(a24,1x,es8.1)') ' integtator: ',numerics_integrator write(6,'(a24,1x,L8)') ' timeSyncing: ',numerics_timeSyncing write(6,'(a24,1x,L8)') ' use ping pong scheme: ',usepingpong write(6,'(a24,1x,es8.1,/)')' unitlength: ',numerics_unitlength diff --git a/src/plastic_nonlocal.f90 b/src/plastic_nonlocal.f90 index 41666a34c..e1355da8f 100644 --- a/src/plastic_nonlocal.f90 +++ b/src/plastic_nonlocal.f90 @@ -2382,8 +2382,7 @@ use, intrinsic :: & use prec, only: dNeq0, & dNeq, & dEq0 -use numerics, only: numerics_integrationMode, & - numerics_timeSyncing +use numerics, only: numerics_timeSyncing use IO, only: IO_error use debug, only: debug_level, & debug_constitutive, & @@ -2942,14 +2941,12 @@ rhoDot = rhoDotFlux & + rhoDotAthermalAnnihilation & + rhoDotThermalAnnihilation -if (numerics_integrationMode == 1_pInt) then ! save rates for output if in central integration mode - rhoDotFluxOutput(1:ns,1:8,1_pInt,ip,el) = rhoDotFlux(1:ns,1:8) - rhoDotMultiplicationOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotMultiplication(1:ns,[1,3]) - rhoDotSingle2DipoleGlideOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotSingle2DipoleGlide(1:ns,9:10) - rhoDotAthermalAnnihilationOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotAthermalAnnihilation(1:ns,9:10) - rhoDotThermalAnnihilationOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotThermalAnnihilation(1:ns,9:10) - rhoDotEdgeJogsOutput(1:ns,1_pInt,ip,el) = 2.0_pReal * rhoDotThermalAnnihilation(1:ns,1) -endif +rhoDotFluxOutput(1:ns,1:8,1_pInt,ip,el) = rhoDotFlux(1:ns,1:8) +rhoDotMultiplicationOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotMultiplication(1:ns,[1,3]) +rhoDotSingle2DipoleGlideOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotSingle2DipoleGlide(1:ns,9:10) +rhoDotAthermalAnnihilationOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotAthermalAnnihilation(1:ns,9:10) +rhoDotThermalAnnihilationOutput(1:ns,1:2,1_pInt,ip,el) = rhoDotThermalAnnihilation(1:ns,9:10) +rhoDotEdgeJogsOutput(1:ns,1_pInt,ip,el) = 2.0_pReal * rhoDotThermalAnnihilation(1:ns,1) #ifdef DEBUG From 67314fc204f010e955443eb63b524c9c2d680846 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 18 Aug 2018 16:40:13 +0200 Subject: [PATCH 10/67] leftover from reducing numerics_integrator to scalar postponed simplification to scalar because of heavy modification in plastic constitutive laws --- src/numerics.f90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/numerics.f90 b/src/numerics.f90 index 05abc0198..146961b86 100644 --- a/src/numerics.f90 +++ b/src/numerics.f90 @@ -26,7 +26,7 @@ module numerics worldsize = 0_pInt !< MPI worldsize (/=0 for MPI simulations only) integer(4), protected, public :: & DAMASK_NumThreadsInt = 0 !< value stored in environment variable DAMASK_NUM_THREADS, set to zero if no OpenMP directive -!> ToDo: numerics_integrator in an array for historical reasons, only element 1 is used! + !< ToDo: numerics_integrator is an array for historical reasons, only element 1 is used! integer(pInt), dimension(2), protected, public :: & numerics_integrator = 1_pInt !< method used for state integration (central & perturbed state), Default 1: fix-point iteration for both states real(pReal), protected, public :: & @@ -525,7 +525,7 @@ subroutine numerics_init write(6,'(a24,1x,es8.1)') ' rTol_crystalliteState: ',rTol_crystalliteState write(6,'(a24,1x,es8.1)') ' rTol_crystalliteStress: ',rTol_crystalliteStress write(6,'(a24,1x,es8.1)') ' aTol_crystalliteStress: ',aTol_crystalliteStress - write(6,'(a24,1x,es8.1)') ' integtator: ',numerics_integrator + write(6,'(a24,2(1x,i8))') ' integrator: ',numerics_integrator write(6,'(a24,1x,L8)') ' timeSyncing: ',numerics_timeSyncing write(6,'(a24,1x,L8)') ' use ping pong scheme: ',usepingpong write(6,'(a24,1x,es8.1,/)')' unitlength: ',numerics_unitlength From 3b3e0bc06851363062efce0d02619f2fa7d0cdf3 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 18 Aug 2018 17:11:50 +0200 Subject: [PATCH 11/67] forgotten use --- src/crystallite.f90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/crystallite.f90 b/src/crystallite.f90 index cdb112a48..88782751d 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -511,8 +511,6 @@ subroutine crystallite_stressAndItsTangent(updateJaco) subStepMinCryst, & subStepSizeCryst, & stepIncreaseCryst, & - numerics_integrator, & - numerics_integrationMode, & numerics_timeSyncing use debug, only: & debug_level, & From 4ba5bdd87c1d4d7f34ae2b91da558ab8ad4f18bc Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 3 Aug 2018 18:33:26 +0200 Subject: [PATCH 12/67] merged private --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 50eb21714..85ce83964 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 50eb21714e2f501b111bb62096ebb6a5bfc6708a +Subproject commit 85ce83964904324d4e6ce93e14b0b4e1946dc04a From 97659c359a71bcfa49d07611abd4fa5caee4e2a8 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sun, 5 Aug 2018 06:41:35 +0200 Subject: [PATCH 13/67] MPI write only in case that PETSc is used --- src/HDF5_utilities.f90 | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index b878543a1..37ddc4ad8 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -2,7 +2,9 @@ module HDF5_Utilities use prec use IO use HDF5 +#ifdef PETSc use PETSC +#endif integer(HID_T), public, protected :: tempCoordinates, tempResults integer(HID_T), private :: resultsFile, currentIncID, plist_id @@ -58,7 +60,9 @@ subroutine HDF5_createJobFile integer :: hdferr integer(SIZE_T) :: typeSize character(len=1024) :: path +#ifdef PETSc #include +#endif !-------------------------------------------------------------------------------------------------- ! initialize HDF5 library and check if integer and float type size match @@ -71,11 +75,13 @@ subroutine HDF5_createJobFile if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5tget_size_f (double)') if (int(pReal,SIZE_T)/=typeSize) call IO_error(0_pInt,ext_msg='pReal does not match H5T_NATIVE_DOUBLE') - ! neu ab hier (4 zeilen) +#ifdef PETSC call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pcreate_f') call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pset_fapl_mpio_f') +#endif + !-------------------------------------------------------------------------------------------------- ! open file path = trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.'//'hdf5' @@ -321,10 +327,12 @@ subroutine HDF5_mappingPhase(mapping,mapping2,Nconstituents,material_phase,phase !-------------------------------------------------------------------------------------------------- ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pset_dxpl_mpio_f') +#endif !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -439,10 +447,12 @@ subroutine HDF5_backwardMappingPhase(material_phase,phasememberat,phase_name,dat !-------------------------------------------------------------------------------------------------- ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pset_dxpl_mpio_f') +#ifdef PETSC !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -557,10 +567,12 @@ subroutine HDF5_mappingHomog(material_homog,homogmemberat,homogenization_name,da !-------------------------------------------------------------------------------------------------- ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pset_dxpl_mpio_f') +#ifdef PETSC !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -668,10 +680,12 @@ subroutine HDF5_backwardMappingHomog(material_homog,homogmemberat,homogenization !-------------------------------------------------------------------------------------------------- ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pset_dxpl_mpio_f') +#ifdef PETSC !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -799,10 +813,12 @@ subroutine HDF5_mappingCrystallite(crystalliteAt,crystmemberAt,crystallite_name, !-------------------------------------------------------------------------------------------------- ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pset_dxpl_mpio_f') +#ifdef PETSC !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -929,10 +945,12 @@ subroutine HDF5_backwardMappingCrystallite(crystalliteAt,crystmemberAt,crystalli !-------------------------------------------------------------------------------------------------- ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pset_dxpl_mpio_f') +#ifdef PETSC !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -1080,10 +1098,12 @@ subroutine HDF5_writeVectorDataset(group,dataset,label,SIunit,dataspace_size,mpi if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5sselect_hyperslab_f') ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pset_dxpl_mpio_f') +#ifdef PETSC ! Write the dataset collectively call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([vectorSize, dataspace_size],HSIZE_T), hdferr, & @@ -1140,10 +1160,12 @@ subroutine HDF5_writeTensorDataset(group,dataset,label,SIunit,dataspace_size,mpi if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5sselect_hyperslab_f') ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pset_dxpl_mpio_f') +#ifdef PETSC ! Write the dataset collectively call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([tensorSize, dataspace_size],HSIZE_T), hdferr, & @@ -1231,10 +1253,12 @@ subroutine HDF5_writeScalarDataset(group,dataset,label,SIunit,dataspace_size,mpi if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5sselect_hyperslab_f') ! Create property list for collective dataset write +#ifdef PETSC call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f') +#ifdef PETSC ! Write the dataset collectively call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([dataspace_size],HSIZE_T), hdferr, & From 0bdfae1a4bdce258972c168fa6f5e3f17ce78d9d Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 18 Aug 2018 21:12:55 +0200 Subject: [PATCH 14/67] using newer Intel Compiler --- .gitlab-ci.yml | 15 ++++++++------- PRIVATE | 2 +- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 0721f1374..c3aa1c2d1 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -47,6 +47,7 @@ variables: # =============================================================================================== # ++++++++++++ Compiler ++++++++++++++++++++++++++++++++++++++++++++++ IntelCompiler16_0: "Compiler/Intel/16.0 Libraries/IMKL/2016" + IntelCompiler16_4: "Compiler/Intel/16.4" IntelCompiler17_0: "Compiler/Intel/17.0 Libraries/IMKL/2017" IntelCompiler18_1: "Compiler/Intel/18.1 Libraries/IMKL/2018" GNUCompiler7_3: "Compiler/GNU/7.3" @@ -329,7 +330,7 @@ TextureComponents: Marc_compileIfort2017: stage: compileMarc2017 script: - - module load $IntelCompiler17_0 $MSC2017 + - module load $IntelCompiler16_4 $MSC2017 - Marc_compileIfort/test.py -m 2017 except: - master @@ -339,7 +340,7 @@ Marc_compileIfort2017: Hex_elastic: stage: marc script: - - module load $IntelCompiler17_0 $MSC + - module load $IntelCompiler16_4 $MSC - Hex_elastic/test.py except: - master @@ -348,7 +349,7 @@ Hex_elastic: CubicFCC_elastic: stage: marc script: - - module load $IntelCompiler17_0 $MSC + - module load $IntelCompiler16_4 $MSC - CubicFCC_elastic/test.py except: - master @@ -357,7 +358,7 @@ CubicFCC_elastic: CubicBCC_elastic: stage: marc script: - - module load $IntelCompiler17_0 $MSC + - module load $IntelCompiler16_4 $MSC - CubicBCC_elastic/test.py except: - master @@ -366,7 +367,7 @@ CubicBCC_elastic: J2_plasticBehavior: stage: marc script: - - module load $IntelCompiler17_0 $MSC + - module load $IntelCompiler16_4 $MSC - J2_plasticBehavior/test.py except: - master @@ -376,7 +377,7 @@ J2_plasticBehavior: Abaqus_compile2017: stage: compileAbaqus2017 script: - - module load $IntelCompiler16_0 $Abaqus2017 + - module load $IntelCompiler16_4 $Abaqus2017 - Abaqus_compileIfort/test.py -a 2017 except: - master @@ -392,7 +393,7 @@ SpectralExample: AbaqusExample: stage: example script: - - module load $IntelCompiler16_0 $Abaqus + - module load $IntelCompiler16_4 $Abaqus - Abaqus_example/test.py only: - development diff --git a/PRIVATE b/PRIVATE index 85ce83964..737427a96 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 85ce83964904324d4e6ce93e14b0b4e1946dc04a +Subproject commit 737427a967e098e1cc82f69f5447fd1a02ffa855 From 85358bae1becff0d703def4c8c84976bdd179bd8 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 18 Aug 2018 21:30:57 +0200 Subject: [PATCH 15/67] copy and paste error --- src/HDF5_utilities.f90 | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index 37ddc4ad8..ca75d6aff 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -452,7 +452,7 @@ subroutine HDF5_backwardMappingPhase(material_phase,phasememberat,phase_name,dat if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -572,7 +572,7 @@ subroutine HDF5_mappingHomog(material_homog,homogmemberat,homogenization_name,da if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -685,7 +685,7 @@ subroutine HDF5_backwardMappingHomog(material_homog,homogmemberat,homogenization if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -818,7 +818,7 @@ subroutine HDF5_mappingCrystallite(crystalliteAt,crystmemberAt,crystallite_name, if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -950,7 +950,7 @@ subroutine HDF5_backwardMappingCrystallite(crystalliteAt,crystmemberAt,crystalli if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif !-------------------------------------------------------------------------------------------------- ! write data by fields in the datatype. Fields order is not important. @@ -1103,7 +1103,7 @@ subroutine HDF5_writeVectorDataset(group,dataset,label,SIunit,dataspace_size,mpi if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif ! Write the dataset collectively call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([vectorSize, dataspace_size],HSIZE_T), hdferr, & @@ -1165,7 +1165,7 @@ subroutine HDF5_writeTensorDataset(group,dataset,label,SIunit,dataspace_size,mpi if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif ! Write the dataset collectively call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([tensorSize, dataspace_size],HSIZE_T), hdferr, & @@ -1258,7 +1258,7 @@ subroutine HDF5_writeScalarDataset(group,dataset,label,SIunit,dataspace_size,mpi if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f') call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f') -#ifdef PETSC +#endif ! Write the dataset collectively call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([dataspace_size],HSIZE_T), hdferr, & From 031c59954f80a7113023d119ea52ff2adb817c65 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 20 Aug 2018 17:45:34 +0200 Subject: [PATCH 16/67] working directory is changed automatically --- src/HDF5_utilities.f90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index ca75d6aff..e2b0c2450 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -53,7 +53,6 @@ end subroutine HDF5_Utilities_init subroutine HDF5_createJobFile use hdf5 use DAMASK_interface, only: & - getSolverWorkingDirectoryName, & getSolverJobName implicit none @@ -84,7 +83,7 @@ subroutine HDF5_createJobFile !-------------------------------------------------------------------------------------------------- ! open file - path = trim(getSolverWorkingDirectoryName())//trim(getSolverJobName())//'.'//'hdf5' + path = trim(getSolverJobName())//'.'//'hdf5' !call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr) call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr,access_prp = plist_id) if (hdferr < 0) call IO_error(100_pInt,ext_msg=path) From c78396dd781c4009525d77f280a49b7808f8e1a4 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 20 Aug 2018 22:11:53 +0200 Subject: [PATCH 17/67] randomized FILEUNIT matrix inversion error when numerics.config is not there or not present very strange --- src/constitutive.f90 | 2 +- src/debug.f90 | 2 +- src/material.f90 | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/constitutive.f90 b/src/constitutive.f90 index 7833f70cf..ce09c86a0 100644 --- a/src/constitutive.f90 +++ b/src/constitutive.f90 @@ -138,7 +138,7 @@ subroutine constitutive_init() use kinematics_hydrogen_strain implicit none - integer(pInt), parameter :: FILEUNIT = 200_pInt + integer(pInt), parameter :: FILEUNIT = 204_pInt integer(pInt) :: & o, & !< counter in output loop ph, & !< counter in phase loop diff --git a/src/debug.f90 b/src/debug.f90 index 55cc62ca0..2a4edf28e 100644 --- a/src/debug.f90 +++ b/src/debug.f90 @@ -102,7 +102,7 @@ subroutine debug_init IO_EOF implicit none - integer(pInt), parameter :: FILEUNIT = 300_pInt + integer(pInt), parameter :: FILEUNIT = 330_pInt integer(pInt) :: i, what integer(pInt), allocatable, dimension(:) :: chunkPos diff --git a/src/material.f90 b/src/material.f90 index c2c52aaa6..4c5a9ed74 100644 --- a/src/material.f90 +++ b/src/material.f90 @@ -370,7 +370,7 @@ subroutine material_init() FE_geomtype implicit none - integer(pInt), parameter :: FILEUNIT = 200_pInt + integer(pInt), parameter :: FILEUNIT = 210_pInt integer(pInt) :: m,c,h, myDebug, myPhase, myHomog integer(pInt) :: & g, & !< grain number From 69ad600916f44a701c5d1777dfe7f818c8e0b7b3 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 20 Aug 2018 22:36:55 +0200 Subject: [PATCH 18/67] more explicit file opening still having trouble with Gfortran 7.3 and no numerics.config --- src/IO.f90 | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/src/IO.f90 b/src/IO.f90 index c9e93b498..4a61f25c1 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -153,7 +153,7 @@ recursive function IO_read(fileUnit,reset) result(line) pathOn(stack) = path(1:scan(path,SEP,.true.))//input ! glue include to current file's dir endif - open(newunit=unitOn(stack),iostat=myStat,file=pathOn(stack),action='read') ! open included file + open(newunit=unitOn(stack),iostat=myStat,file=pathOn(stack),action='read',status='old',position='rewind') ! open included file if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=pathOn(stack)) line = IO_read(fileUnit) @@ -193,14 +193,17 @@ recursive function IO_recursiveRead(fileName,cnt) result(fileContent) myTotalLines, & !< # lines read from file without include statements includedLines, & !< # lines included from other file(s) missingLines, & !< # lines missing from current file - l,i + l,i, & + myStat if (merge(cnt,0_pInt,present(cnt))>10_pInt) call IO_error(106_pInt,ext_msg=trim(fileName)) !-------------------------------------------------------------------------------------------------- ! read data as stream inquire(file = fileName, size=fileLength) - open(newunit=fileUnit, file = fileName, access = "STREAM") + open(newunit=fileUnit, file=fileName, access='stream',& + status='old', position='rewind', action='read',iostat=myStat) + if(myStat /= 0_pInt) call IO_error(100_pInt,ext_msg=trim(fileName)) allocate(character(len=fileLength)::rawData) read(fileUnit) rawData close(fileUnit) @@ -276,7 +279,7 @@ subroutine IO_open_file(fileUnit,path) integer(pInt) :: myStat - open(fileUnit,status='old',iostat=myStat,file=path) + open(fileUnit,status='old',iostat=myStat,file=path,action='read',position='rewind') if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=path) end subroutine IO_open_file @@ -295,7 +298,8 @@ logical function IO_open_file_stat(fileUnit,path) integer(pInt) :: myStat - open(fileUnit,status='old',iostat=myStat,file=path) + open(fileUnit,status='old',iostat=myStat,file=path,action='read',position='rewind') + if (myStat /= 0_pInt) close(fileUnit) IO_open_file_stat = (myStat == 0_pInt) end function IO_open_file_stat @@ -319,7 +323,7 @@ subroutine IO_open_jobFile(fileUnit,ext) character(len=1024) :: path path = trim(getSolverJobName())//'.'//ext - open(fileUnit,status='old',iostat=myStat,file=path) + open(fileUnit,status='old',iostat=myStat,file=path,action='read',position='rewind') if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=path) end subroutine IO_open_jobFile @@ -343,7 +347,8 @@ logical function IO_open_jobFile_stat(fileUnit,ext) character(len=1024) :: path path = trim(getSolverJobName())//'.'//ext - open(fileUnit,status='old',iostat=myStat,file=path) + open(fileUnit,status='old',iostat=myStat,file=path,action='read',position='rewind') + if (myStat /= 0_pInt) close(fileUnit) IO_open_jobFile_stat = (myStat == 0_pInt) end function IO_open_JobFile_stat @@ -369,11 +374,11 @@ subroutine IO_open_inputFile(fileUnit,modelName) fileType = 1_pInt ! assume .pes path = trim(modelName)//inputFileExtension(fileType) ! attempt .pes, if it exists: it should be used - open(fileUnit+1,status='old',iostat=myStat,file=path) + open(fileUnit+1,status='old',iostat=myStat,file=path,action='read',position='rewind') if(myStat /= 0_pInt) then ! if .pes does not work / exist; use conventional extension, i.e.".inp" fileType = 2_pInt path = trim(modelName)//inputFileExtension(fileType) - open(fileUnit+1,status='old',iostat=myStat,file=path) + open(fileUnit+1,status='old',iostat=myStat,file=path,action='read',position='rewind') endif if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=path) @@ -408,7 +413,7 @@ subroutine IO_open_logFile(fileUnit) character(len=1024) :: path path = trim(getSolverJobName())//LogFileExtension - open(fileUnit,status='old',iostat=myStat,file=path) + open(fileUnit,status='old',iostat=myStat,file=path,action='read',position='rewind') if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=path) end subroutine IO_open_logFile From 465d950ab173b6a3ceeb372b1e62298a20f6c2b5 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 21 Aug 2018 07:09:50 +0200 Subject: [PATCH 19/67] gfortran 7.3 and optimized code still gives 'terminally ill' --- src/plastic_phenopowerlaw.f90 | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/plastic_phenopowerlaw.f90 b/src/plastic_phenopowerlaw.f90 index bdc6e12a6..59a106435 100644 --- a/src/plastic_phenopowerlaw.f90 +++ b/src/plastic_phenopowerlaw.f90 @@ -241,29 +241,29 @@ subroutine plastic_phenopowerlaw_init select case(outputs(i)) case ('resistance_slip') outputID = resistance_slip_ID - outputSize = sum(prm%Nslip) + outputSize = prm%totalNslip case ('accumulatedshear_slip') outputID = accumulatedshear_slip_ID - outputSize = sum(prm%Nslip) + outputSize = prm%totalNslip case ('shearrate_slip') outputID = shearrate_slip_ID - outputSize = sum(prm%Nslip) + outputSize = prm%totalNslip case ('resolvedstress_slip') outputID = resolvedstress_slip_ID - outputSize = sum(prm%Nslip) + outputSize = prm%totalNslip case ('resistance_twin') outputID = resistance_twin_ID - outputSize = sum(prm%Ntwin) + outputSize = prm%totalNtwin case ('accumulatedshear_twin') outputID = accumulatedshear_twin_ID - outputSize = sum(prm%Ntwin) + outputSize = prm%totalNtwin case ('shearrate_twin') outputID = shearrate_twin_ID - outputSize = sum(prm%Ntwin) + outputSize = prm%totalNtwin case ('resolvedstress_twin') outputID = resolvedstress_twin_ID - outputSize = sum(prm%Ntwin) + outputSize = prm%totalNtwin case ('totalvolfrac_twin') outputID = totalvolfrac_twin_ID From d146417abec3b9fc46d572d2fd51e3067d581c8e Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 21 Aug 2018 07:41:10 +0200 Subject: [PATCH 20/67] hot fix for terminally ill with gfortran 7.3 might be a bug in the compiler or in the linked list. waste some memory at the moment... check linked list carefully before enabling again and blaming gfortran --- src/config.f90 | 75 +++++++++++++++++++++++++------------------------- 1 file changed, 38 insertions(+), 37 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index c99b14c00..08d1ace5a 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -234,6 +234,7 @@ end subroutine parseFile !-------------------------------------------------------------------------------------------------- !> @brief deallocates the linked lists that store the content of the configuration files +! commenting out removes erratic errors with gfortran 7.3 !-------------------------------------------------------------------------------------------------- subroutine config_deallocate(what) use IO, only: & @@ -243,42 +244,42 @@ subroutine config_deallocate(what) character(len=*), intent(in) :: what integer(pInt) :: i - select case(what) - - case('material.config/phase') - do i=1, size(config_phase) - call config_phase(i)%free - enddo - deallocate(config_phase) - - case('material.config/microstructure') - do i=1, size(config_microstructure) - call config_microstructure(i)%free - enddo - deallocate(config_microstructure) - - case('material.config/crystallite') - do i=1, size(config_crystallite) - call config_crystallite(i)%free - enddo - deallocate(config_crystallite) - - case('material.config/homogenization') - do i=1, size(config_homogenization) - call config_homogenization(i)%free - enddo - deallocate(config_homogenization) - - case('material.config/texture') - do i=1, size(config_texture) - call config_texture(i)%free - enddo - deallocate(config_texture) - - case default - call IO_error(0_pInt,ext_msg='config_deallocate') - - end select +! select case(what) +! +! case('material.config/phase') +! do i=1, size(config_phase) +! call config_phase(i)%free +! enddo +! deallocate(config_phase) +! +! case('material.config/microstructure') +! do i=1, size(config_microstructure) +! call config_microstructure(i)%free +! enddo +! deallocate(config_microstructure) +! +! case('material.config/crystallite') +! do i=1, size(config_crystallite) +! call config_crystallite(i)%free +! enddo +! deallocate(config_crystallite) +! +! case('material.config/homogenization') +! do i=1, size(config_homogenization) +! call config_homogenization(i)%free +! enddo +! deallocate(config_homogenization) +! +! case('material.config/texture') +! do i=1, size(config_texture) +! call config_texture(i)%free +! enddo +! deallocate(config_texture) +! +! case default +! call IO_error(0_pInt,ext_msg='config_deallocate') +! +! end select end subroutine config_deallocate @@ -342,7 +343,7 @@ end subroutine show !-------------------------------------------------------------------------------------------------- !> @brief cleans entire list -!> @details list head is remains alive +!> @details list head remains alive !-------------------------------------------------------------------------------------------------- subroutine free(this) From 8de321382f94c36a66f58189c634aab81fbf35ba Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 21 Aug 2018 08:14:59 +0200 Subject: [PATCH 21/67] using final seems to be the better approach http://www.training.prace-ri.eu/uploads/tx_pracetmo/AdvFTN_handout.pdf still needs in-depth analysis, even though I cannot reproduce 'terminally ill' --- src/config.f90 | 78 +++++++++++++++++++++++++------------------------- 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index 08d1ace5a..05da341d4 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -20,11 +20,10 @@ module config type, public :: tPartitionedStringList type(tPartitionedString) :: string type(tPartitionedStringList), pointer :: next => null() - contains procedure :: add => add procedure :: show => show - procedure :: free => free + !procedure :: free => free procedure :: keyExists => keyExists procedure :: countKeys => countKeys @@ -36,6 +35,7 @@ module config procedure :: getFloats => getFloats procedure :: getInts => getInts procedure :: getStrings => getStrings + final :: free end type tPartitionedStringList @@ -244,42 +244,42 @@ subroutine config_deallocate(what) character(len=*), intent(in) :: what integer(pInt) :: i -! select case(what) -! -! case('material.config/phase') -! do i=1, size(config_phase) -! call config_phase(i)%free -! enddo -! deallocate(config_phase) -! -! case('material.config/microstructure') -! do i=1, size(config_microstructure) -! call config_microstructure(i)%free -! enddo -! deallocate(config_microstructure) -! -! case('material.config/crystallite') -! do i=1, size(config_crystallite) -! call config_crystallite(i)%free -! enddo -! deallocate(config_crystallite) -! -! case('material.config/homogenization') -! do i=1, size(config_homogenization) -! call config_homogenization(i)%free -! enddo -! deallocate(config_homogenization) -! -! case('material.config/texture') -! do i=1, size(config_texture) -! call config_texture(i)%free -! enddo -! deallocate(config_texture) -! -! case default -! call IO_error(0_pInt,ext_msg='config_deallocate') -! -! end select + select case(what) + + case('material.config/phase') + !do i=1, size(config_phase) + ! call config_phase(i)%free + !enddo + deallocate(config_phase) + + case('material.config/microstructure') + !do i=1, size(config_microstructure) + ! call config_microstructure(i)%free + !enddo + deallocate(config_microstructure) + + case('material.config/crystallite') + !do i=1, size(config_crystallite) + ! call config_crystallite(i)%free + !enddo + deallocate(config_crystallite) + + case('material.config/homogenization') + !do i=1, size(config_homogenization) + ! call config_homogenization(i)%free + !enddo + deallocate(config_homogenization) + + case('material.config/texture') + !do i=1, size(config_texture) + ! call config_texture(i)%free + !enddo + deallocate(config_texture) + + case default + call IO_error(0_pInt,ext_msg='config_deallocate') + + end select end subroutine config_deallocate @@ -348,7 +348,7 @@ end subroutine show subroutine free(this) implicit none - class(tPartitionedStringList), target, intent(in) :: this + type(tPartitionedStringList), target, intent(in) :: this type(tPartitionedStringList), pointer :: new, item if (.not. associated(this%next)) return From 179a23f55b8f026ad14f1680633a4ad33cc12722 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 21 Aug 2018 22:49:56 +0200 Subject: [PATCH 22/67] IMKL needed for MSC.Marc --- .gitlab-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d3068c454..be8eb3465 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -47,7 +47,7 @@ variables: # =============================================================================================== # ++++++++++++ Compiler ++++++++++++++++++++++++++++++++++++++++++++++ IntelCompiler16_0: "Compiler/Intel/16.0 Libraries/IMKL/2016" - IntelCompiler16_4: "Compiler/Intel/16.4" + IntelCompiler16_4: "Compiler/Intel/16.4 Libraries/IMKL/2016-4" IntelCompiler17_0: "Compiler/Intel/17.0 Libraries/IMKL/2017" IntelCompiler18_1: "Compiler/Intel/18.1 Libraries/IMKL/2018" GNUCompiler7_3: "Compiler/GNU/7.3" From 52002f654e512acd2366f374f28fabae05e927b1 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 09:14:16 +0200 Subject: [PATCH 23/67] to converge at one point to one (or two) string lenth values --- src/prec.f90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/prec.f90 b/src/prec.f90 index caf59cfe8..959ee77ba 100644 --- a/src/prec.f90 +++ b/src/prec.f90 @@ -23,6 +23,7 @@ module prec NO SUITABLE PRECISION FOR INTEGER SELECTED, STOPPING COMPILATION #endif + integer, parameter, public :: pStringLen = 256 !< default string lenth integer, parameter, public :: pLongInt = 8 !< integer representation 64 bit (was selected_int_kind(12), number with at least up to +- 1e12) real(pReal), parameter, public :: tol_math_check = 1.0e-8_pReal !< tolerance for internal math self-checks (rotation) From 52088691d1d441bfbc0bc83fc9fda91a1c688408 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 11:51:23 +0200 Subject: [PATCH 24/67] improved linked list and fixed solution for strange bug Bug: Using automated LHS re-allocation for a string array that with global scope seems to cause trouble Hence, "parse_file" works with a local string and assings only once to it Linked_List: Now storing data in the list head also and last element is always empty. Finalize allows simple handling of deallocation --- src/config.f90 | 223 ++++++++++++++++++++++------------------- src/constitutive.f90 | 4 +- src/crystallite.f90 | 5 +- src/homogenization.f90 | 3 +- src/material.f90 | 10 +- 5 files changed, 131 insertions(+), 114 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index 05da341d4..a22acbff9 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -23,7 +23,13 @@ module config contains procedure :: add => add procedure :: show => show - !procedure :: free => free + procedure :: free => free + +! currently, a finalize is needed for all shapes of tPartitionedStringList. +! with Fortran 2015, we can define one recursive elemental function +! https://software.intel.com/en-us/forums/intel-visual-fortran-compiler-for-windows/topic/543326 + final :: finalize, & + finalizeArray procedure :: keyExists => keyExists procedure :: countKeys => countKeys @@ -35,13 +41,13 @@ module config procedure :: getFloats => getFloats procedure :: getInts => getInts procedure :: getStrings => getStrings - final :: free + end type tPartitionedStringList type(tPartitionedStringList), public :: emptyList - type(tPartitionedStringList), public, protected, allocatable, dimension(:) :: & ! QUESTION: rename to config_XXX? + type(tPartitionedStringList), public, allocatable, dimension(:) :: & config_phase, & config_microstructure, & config_homogenization, & @@ -78,8 +84,7 @@ module config public :: & - config_init, & - config_deallocate + config_init contains @@ -92,6 +97,8 @@ subroutine config_init() compiler_version, & compiler_options #endif + use prec, only: & + pStringLen use DAMASK_interface, only: & getSolverJobName use IO, only: & @@ -109,10 +116,10 @@ subroutine config_init() implicit none integer(pInt) :: myDebug,i - character(len=256) :: & + character(len=pStringLen) :: & line, & part - character(len=256), dimension(:), allocatable :: fileContent + character(len=pStringLen), dimension(:), allocatable :: fileContent logical :: fileExists write(6,'(/,a)') ' <<<+- config init -+>>>' @@ -175,8 +182,10 @@ end subroutine config_init !-------------------------------------------------------------------------------------------------- !> @brief parses the material.config file !-------------------------------------------------------------------------------------------------- -subroutine parseFile(line,& - sectionNames,part,fileContent) +subroutine parseFile(line,sectionNames,part,& + fileContent) + use prec, only: & + pStringLen use IO, only: & IO_error, & IO_lc, & @@ -186,11 +195,12 @@ subroutine parseFile(line,& IO_stringPos implicit none - character(len=*), dimension(:), allocatable, intent(inout) :: sectionNames + character(len=pStringLen), intent(out) :: line + character(len=64), allocatable, dimension(:), intent(out) :: sectionNames type(tPartitionedStringList), allocatable, dimension(:), intent(out) :: part - character(len=256), dimension(:), intent(in) :: fileContent - character(len=256),intent(out) :: line + character(len=pStringLen), dimension(:), intent(in) :: fileContent + character(len=64), allocatable, dimension(:) :: sectionNamesTemp ! Circumvent Gfortran bug integer(pInt), allocatable, dimension(:) :: chunkPos integer(pInt) :: s,i character(len=64) :: tag @@ -198,6 +208,8 @@ subroutine parseFile(line,& echo = .false. allocate(part(0)) + tag='' + allocate(sectionNamesTemp(0),source=tag) s = 0_pInt do i=1, size(fileContent) @@ -208,11 +220,7 @@ subroutine parseFile(line,& s = s + 1_pInt part = [part, emptyList] tag = IO_getTag(line,'[',']') - GfortranBug86033: if (.not. allocated(sectionNames)) then - allocate(sectionNames(1),source=tag) - else GfortranBug86033 - sectionNames = [sectionNames,tag] - endif GfortranBug86033 + sectionNamesTemp = [sectionNamesTemp,tag] cycle endif nextSection chunkPos = IO_stringPos(line) @@ -224,8 +232,11 @@ subroutine parseFile(line,& endif inSection enddo + sectionNames = sectionNamesTemp + if (echo) then do s = 1, size(sectionNames) + write(6,*) 'section',s, '"'//trim(sectionNames(i))//'"' call part(s)%show() end do end if @@ -234,7 +245,6 @@ end subroutine parseFile !-------------------------------------------------------------------------------------------------- !> @brief deallocates the linked lists that store the content of the configuration files -! commenting out removes erratic errors with gfortran 7.3 !-------------------------------------------------------------------------------------------------- subroutine config_deallocate(what) use IO, only: & @@ -244,36 +254,21 @@ subroutine config_deallocate(what) character(len=*), intent(in) :: what integer(pInt) :: i - select case(what) + select case(trim(what)) case('material.config/phase') - !do i=1, size(config_phase) - ! call config_phase(i)%free - !enddo deallocate(config_phase) case('material.config/microstructure') - !do i=1, size(config_microstructure) - ! call config_microstructure(i)%free - !enddo deallocate(config_microstructure) case('material.config/crystallite') - !do i=1, size(config_crystallite) - ! call config_crystallite(i)%free - !enddo deallocate(config_crystallite) case('material.config/homogenization') - !do i=1, size(config_homogenization) - ! call config_homogenization(i)%free - !enddo deallocate(config_homogenization) case('material.config/texture') - !do i=1, size(config_texture) - ! call config_texture(i)%free - !enddo deallocate(config_texture) case default @@ -294,7 +289,7 @@ end subroutine config_deallocate !> @brief add element !> @details Adds a string together with the start/end position of chunks in this string. The new !! element is added at the end of the list. Empty strings are not added. All strings are converted -!! to lower case +!! to lower case. The data is not stored in the new element but in the current. !-------------------------------------------------------------------------------------------------- subroutine add(this,string) use IO, only: & @@ -305,19 +300,18 @@ subroutine add(this,string) implicit none class(tPartitionedStringList), target, intent(in) :: this character(len=*), intent(in) :: string - type(tPartitionedStringList), pointer :: new, item + type(tPartitionedStringList), pointer :: new, temp if (IO_isBlank(string)) return allocate(new) - new%string%val = IO_lc (trim(string)) - new%string%pos = IO_stringPos(trim(string)) - - item => this - do while (associated(item%next)) - item => item%next + temp => this + do while (associated(temp%next)) + temp => temp%next enddo - item%next => new + temp%string%val = IO_lc (trim(string)) + temp%string%pos = IO_stringPos(trim(string)) + temp%next => new end subroutine add @@ -329,11 +323,11 @@ end subroutine add subroutine show(this) implicit none - class(tPartitionedStringList) :: this - type(tPartitionedStringList), pointer :: item + class(tPartitionedStringList), target, intent(in) :: this + type(tPartitionedStringList), pointer :: item - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) write(6,'(a)') trim(item%string%val) item => item%next end do @@ -343,27 +337,54 @@ end subroutine show !-------------------------------------------------------------------------------------------------- !> @brief cleans entire list -!> @details list head remains alive +!> @details explicit interface to reset list. Triggers final statement (and following chain reaction) !-------------------------------------------------------------------------------------------------- subroutine free(this) implicit none - type(tPartitionedStringList), target, intent(in) :: this - type(tPartitionedStringList), pointer :: new, item + class(tPartitionedStringList), intent(inout) :: this - if (.not. associated(this%next)) return - - item => this%next - do while (associated(item%next)) - new => item - deallocate(item) - item => new%next - enddo - deallocate(item) + if(associated(this%next)) deallocate(this%next) end subroutine free +!-------------------------------------------------------------------------------------------------- +!> @brief cleans entire list +!> @details called when variable goes out of scope. Triggers chain reaction. +!-------------------------------------------------------------------------------------------------- +recursive subroutine finalize(this) + + implicit none + type(tPartitionedStringList), intent(inout) :: this + + if(associated(this%next)) deallocate(this%next) + +end subroutine finalize + + +!-------------------------------------------------------------------------------------------------- +!> @brief cleans entire list +!> @details called when variable goes out of scope. Triggers chain reaction. +!-------------------------------------------------------------------------------------------------- +subroutine finalizeArray(this) + + implicit none + integer :: i + type(tPartitionedStringList), intent(inout), dimension(:) :: this + type(tPartitionedStringList), pointer :: temp ! bug in Gfortran + + do i=1, size(this) + if (associated(this(i)%next)) then + temp => this(i)%next + !deallocate(this(i)) !internal compiler error: in gfc_build_final_call, at fortran/trans.c:975 + deallocate(temp) + endif + enddo + +end subroutine finalizeArray + + !-------------------------------------------------------------------------------------------------- !> @brief reports wether a given key (string value at first position) exists in the list !-------------------------------------------------------------------------------------------------- @@ -372,14 +393,14 @@ logical function keyExists(this,key) IO_stringValue implicit none - class(tPartitionedStringList), intent(in) :: this - character(len=*), intent(in) :: key - type(tPartitionedStringList), pointer :: item + class(tPartitionedStringList), target, intent(in) :: this + character(len=*), intent(in) :: key + type(tPartitionedStringList), pointer :: item keyExists = .false. - item => this%next - do while (associated(item) .and. .not. keyExists) + item => this + do while (associated(item%next) .and. .not. keyExists) keyExists = trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key) item => item%next end do @@ -397,14 +418,14 @@ integer(pInt) function countKeys(this,key) implicit none - class(tPartitionedStringList), intent(in) :: this - character(len=*), intent(in) :: key - type(tPartitionedStringList), pointer :: item + class(tPartitionedStringList), target, intent(in) :: this + character(len=*), intent(in) :: key + type(tPartitionedStringList), pointer :: item countKeys = 0_pInt - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) if (trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key)) & countKeys = countKeys + 1_pInt item => item%next @@ -425,17 +446,17 @@ real(pReal) function getFloat(this,key,defaultVal) IO_FloatValue implicit none - class(tPartitionedStringList), intent(in) :: this - character(len=*), intent(in) :: key - real(pReal), intent(in), optional :: defaultVal - type(tPartitionedStringList), pointer :: item - logical :: found + class(tPartitionedStringList), target, intent(in) :: this + character(len=*), intent(in) :: key + real(pReal), intent(in), optional :: defaultVal + type(tPartitionedStringList), pointer :: item + logical :: found found = present(defaultVal) if (found) getFloat = defaultVal - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) if (trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key)) then found = .true. if (item%string%pos(1) < 2_pInt) call IO_error(143_pInt,ext_msg=key) @@ -461,17 +482,17 @@ integer(pInt) function getInt(this,key,defaultVal) IO_IntValue implicit none - class(tPartitionedStringList), intent(in) :: this - character(len=*), intent(in) :: key - integer(pInt), intent(in), optional :: defaultVal - type(tPartitionedStringList), pointer :: item - logical :: found + class(tPartitionedStringList), target, intent(in) :: this + character(len=*), intent(in) :: key + integer(pInt), intent(in), optional :: defaultVal + type(tPartitionedStringList), pointer :: item + logical :: found found = present(defaultVal) if (found) getInt = defaultVal - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) if (trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key)) then found = .true. if (item%string%pos(1) < 2_pInt) call IO_error(143_pInt,ext_msg=key) @@ -497,13 +518,13 @@ character(len=65536) function getString(this,key,defaultVal,raw) IO_stringValue implicit none - class(tPartitionedStringList), intent(in) :: this - character(len=*), intent(in) :: key - character(len=65536), intent(in), optional :: defaultVal - logical, intent(in), optional :: raw - type(tPartitionedStringList), pointer :: item - logical :: found, & - whole + class(tPartitionedStringList), target, intent(in) :: this + character(len=*), intent(in) :: key + character(len=65536), intent(in), optional :: defaultVal + logical, intent(in), optional :: raw + type(tPartitionedStringList), pointer :: item + logical :: found, & + whole whole = merge(raw,.false.,present(raw)) ! whole string or white space splitting found = present(defaultVal) @@ -512,8 +533,8 @@ character(len=65536) function getString(this,key,defaultVal,raw) if (len_trim(getString) /= len_trim(defaultVal)) call IO_error(0_pInt,ext_msg='getString') endif - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) if (trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key)) then found = .true. if (item%string%pos(1) < 2_pInt) call IO_error(143_pInt,ext_msg=key) @@ -545,7 +566,7 @@ function getFloats(this,key,defaultVal,requiredShape) implicit none real(pReal), dimension(:), allocatable :: getFloats - class(tPartitionedStringList), intent(in) :: this + class(tPartitionedStringList), target, intent(in) :: this character(len=*), intent(in) :: key real(pReal), dimension(:), intent(in), optional :: defaultVal integer(pInt), dimension(:), intent(in), optional :: requiredShape @@ -559,8 +580,8 @@ function getFloats(this,key,defaultVal,requiredShape) allocate(getFloats(0)) - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) if (trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key)) then found = .true. if (.not. cumulative) getFloats = [real(pReal)::] @@ -592,7 +613,7 @@ function getInts(this,key,defaultVal,requiredShape) implicit none integer(pInt), dimension(:), allocatable :: getInts - class(tPartitionedStringList), intent(in) :: this + class(tPartitionedStringList), target, intent(in) :: this character(len=*), intent(in) :: key integer(pInt), dimension(:), intent(in), optional :: defaultVal, & requiredShape @@ -606,8 +627,8 @@ function getInts(this,key,defaultVal,requiredShape) allocate(getInts(0)) - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) if (trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key)) then found = .true. if (.not. cumulative) getInts = [integer(pInt)::] @@ -639,7 +660,7 @@ function getStrings(this,key,defaultVal,requiredShape,raw) implicit none character(len=65536),dimension(:), allocatable :: getStrings - class(tPartitionedStringList), intent(in) :: this + class(tPartitionedStringList), target, intent(in) :: this character(len=*), intent(in) :: key character(len=65536),dimension(:), intent(in), optional :: defaultVal integer(pInt), dimension(:), intent(in), optional :: requiredShape @@ -655,8 +676,8 @@ function getStrings(this,key,defaultVal,requiredShape,raw) whole = merge(raw,.false.,present(raw)) found = .false. - item => this%next - do while (associated(item)) + item => this + do while (associated(item%next)) if (trim(IO_stringValue(item%string%val,item%string%pos,1)) == trim(key)) then found = .true. if (allocated(getStrings) .and. .not. cumulative) deallocate(getStrings) diff --git a/src/constitutive.f90 b/src/constitutive.f90 index ce09c86a0..f27edcc07 100644 --- a/src/constitutive.f90 +++ b/src/constitutive.f90 @@ -58,7 +58,7 @@ subroutine constitutive_init() IO_write_jobIntFile, & IO_timeStamp use config, only: & - config_deallocate + config_phase use mesh, only: & FE_geomtype use config, only: & @@ -192,7 +192,7 @@ subroutine constitutive_init() if (any(phase_kinematics == KINEMATICS_hydrogen_strain_ID)) call kinematics_hydrogen_strain_init(FILEUNIT) close(FILEUNIT) - call config_deallocate('material.config/phase') + deallocate(config_phase) write(6,'(/,a)') ' <<<+- constitutive init -+>>>' write(6,'(a15,a)') ' Current time: ',IO_timeStamp() diff --git a/src/crystallite.f90 b/src/crystallite.f90 index 0ee71b5de..6601fe29e 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -173,8 +173,7 @@ subroutine crystallite_init use material use config, only: & config_crystallite, & - crystallite_name, & - config_deallocate + crystallite_name use constitutive, only: & constitutive_initialFi, & constitutive_microstructure ! derived (shortcut) quantities of given state @@ -376,7 +375,7 @@ subroutine crystallite_init close(FILEUNIT) endif - call config_deallocate('material.config/crystallite') + deallocate(config_crystallite) !-------------------------------------------------------------------------------------------------- ! initialize diff --git a/src/homogenization.f90 b/src/homogenization.f90 index 3565999a8..de195f18a 100644 --- a/src/homogenization.f90 +++ b/src/homogenization.f90 @@ -101,7 +101,6 @@ subroutine homogenization_init crystallite_maxSizePostResults #endif use config, only: & - config_deallocate, & material_configFile, & material_localFileExt, & config_homogenization, & @@ -375,7 +374,7 @@ subroutine homogenization_init close(FILEUNIT) endif mainProcess2 - call config_deallocate('material.config/homogenization') + deallocate(config_homogenization) !-------------------------------------------------------------------------------------------------- ! allocate and initialize global variables diff --git a/src/material.f90 b/src/material.f90 index 4c5a9ed74..73edc8281 100644 --- a/src/material.f90 +++ b/src/material.f90 @@ -360,8 +360,7 @@ subroutine material_init() homogenization_name, & microstructure_name, & phase_name, & - texture_name, & - config_deallocate + texture_name use mesh, only: & mesh_maxNips, & mesh_NcpElems, & @@ -469,7 +468,6 @@ subroutine material_init() endif debugOut call material_populateGrains - call config_deallocate('material.config/microstructure') allocate(phaseAt ( homogenization_maxNgrains,mesh_maxNips,mesh_NcpElems),source=0_pInt) allocate(phasememberAt ( homogenization_maxNgrains,mesh_maxNips,mesh_NcpElems),source=0_pInt) @@ -921,8 +919,7 @@ subroutine material_parseTexture IO_floatValue, & IO_stringValue use config, only: & - config_texture, & - config_deallocate + config_texture use math, only: & inRad, & math_sampleRandomOri, & @@ -1061,7 +1058,7 @@ subroutine material_parseTexture endif enddo - call config_deallocate('material.config/texture') + deallocate(config_texture) end subroutine material_parseTexture @@ -1429,6 +1426,7 @@ subroutine material_populateGrains deallocate(texture_transformation) deallocate(Nelems) deallocate(elemsOfHomogMicro) + deallocate(config_microstructure) end subroutine material_populateGrains From 037ab3d081f3389ac774e29a97c484d3cdf9bb5d Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 13:10:59 +0200 Subject: [PATCH 25/67] getTag works now for tags with the same start and close tag needed for '/echo/'. Still suggest to rather use /echo\ --- src/IO.f90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/IO.f90 b/src/IO.f90 index 4a61f25c1..6777fd6c7 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -833,16 +833,16 @@ pure function IO_getTag(string,openChar,closeChar) character(len=*), intent(in) :: string !< string to check for tag character(len=len_trim(string)) :: IO_getTag - character(len=*), intent(in) :: openChar, & !< indicates beginning of tag - closeChar !< indicates end of tag + character, intent(in) :: openChar, & !< indicates beginning of tag + closeChar !< indicates end of tag character(len=*), parameter :: SEP=achar(32)//achar(9)//achar(10)//achar(13) ! whitespaces integer :: left,right ! no pInt IO_getTag = '' - left = scan(string,openChar) - right = scan(string,closeChar) + left = scan(string,openChar) + right = merge(scan(string,closeChar), scan(string(left:),closeChar),openChar /= closeChar) if (left == verify(string,SEP) .and. right > left) & ! openChar is first and closeChar occurs IO_getTag = string(left+1:right-1) From 1b5623ad6cfa55d4c409bd97245bc15593c67c30 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 13:57:43 +0200 Subject: [PATCH 26/67] avoid out of bound access, removed unneeded stuff --- src/IO.f90 | 183 +++-------------------------------------------------- 1 file changed, 9 insertions(+), 174 deletions(-) diff --git a/src/IO.f90 b/src/IO.f90 index 6777fd6c7..0358785f6 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -36,10 +36,6 @@ module IO IO_hybridIA, & IO_isBlank, & IO_getTag, & - IO_countSections, & - IO_countTagInPart, & - IO_spotTagInPart, & - IO_globalTagInPart, & IO_stringPos, & IO_stringValue, & IO_fixedStringValue ,& @@ -837,12 +833,18 @@ pure function IO_getTag(string,openChar,closeChar) closeChar !< indicates end of tag character(len=*), parameter :: SEP=achar(32)//achar(9)//achar(10)//achar(13) ! whitespaces - integer :: left,right ! no pInt IO_getTag = '' - left = scan(string,openChar) - right = merge(scan(string,closeChar), scan(string(left:),closeChar),openChar /= closeChar) + + + if (openChar /= closeChar) then + left = scan(string,openChar) + right = scan(string,closeChar) + else + left = scan(string,openChar) + right = left + merge(scan(string(left+1:),openChar),0_pInt,len(string) > left) + endif if (left == verify(string,SEP) .and. right > left) & ! openChar is first and closeChar occurs IO_getTag = string(left+1:right-1) @@ -850,173 +852,6 @@ pure function IO_getTag(string,openChar,closeChar) end function IO_getTag -!-------------------------------------------------------------------------------------------------- -!> @brief count number of [sections] in for given file handle -!-------------------------------------------------------------------------------------------------- -integer(pInt) function IO_countSections(fileUnit,part) - - implicit none - integer(pInt), intent(in) :: fileUnit !< file handle - character(len=*), intent(in) :: part !< part name in which sections are counted - - character(len=65536) :: line - - line = '' - IO_countSections = 0_pInt - rewind(fileUnit) - - do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= part) ! search for part - line = IO_read(fileUnit) - enddo - - do while (trim(line) /= IO_EOF) - line = IO_read(fileUnit) - if (IO_isBlank(line)) cycle ! skip empty lines - if (IO_getTag(line,'<','>') /= '') then ! stop at next part - line = IO_read(fileUnit, .true.) ! reset IO_read - exit - endif - if (IO_getTag(line,'[',']') /= '') & ! found [section] identifier - IO_countSections = IO_countSections + 1_pInt - enddo - -end function IO_countSections - - -!-------------------------------------------------------------------------------------------------- -!> @brief returns array of tag counts within for at most N [sections] -!-------------------------------------------------------------------------------------------------- -function IO_countTagInPart(fileUnit,part,tag,Nsections) - - implicit none - integer(pInt), intent(in) :: Nsections !< maximum number of sections in which tag is searched for - integer(pInt), dimension(Nsections) :: IO_countTagInPart - integer(pInt), intent(in) :: fileUnit !< file handle - character(len=*),intent(in) :: part, & !< part in which tag is searched for - tag !< tag to search for - - - integer(pInt), dimension(Nsections) :: counter - integer(pInt), allocatable, dimension(:) :: chunkPos - integer(pInt) :: section - character(len=65536) :: line - - line = '' - counter = 0_pInt - section = 0_pInt - - rewind(fileUnit) - do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= part) ! search for part - line = IO_read(fileUnit) - enddo - - do while (trim(line) /= IO_EOF) - line = IO_read(fileUnit) - if (IO_isBlank(line)) cycle ! skip empty lines - if (IO_getTag(line,'<','>') /= '') then ! stop at next part - line = IO_read(fileUnit, .true.) ! reset IO_read - exit - endif - if (IO_getTag(line,'[',']') /= '') section = section + 1_pInt ! found [section] identifier - if (section > 0) then - chunkPos = IO_stringPos(line) - if (tag == trim(IO_lc(IO_stringValue(line,chunkPos,1_pInt)))) & ! match - counter(section) = counter(section) + 1_pInt - endif - enddo - - IO_countTagInPart = counter - -end function IO_countTagInPart - - -!-------------------------------------------------------------------------------------------------- -!> @brief returns array of tag presence within for at most N [sections] -!-------------------------------------------------------------------------------------------------- -function IO_spotTagInPart(fileUnit,part,tag,Nsections) - - implicit none - integer(pInt), intent(in) :: Nsections !< maximum number of sections in which tag is searched for - logical, dimension(Nsections) :: IO_spotTagInPart - integer(pInt), intent(in) :: fileUnit !< file handle - character(len=*),intent(in) :: part, & !< part in which tag is searched for - tag !< tag to search for - - - integer(pInt), allocatable, dimension(:) :: chunkPos - integer(pInt) :: section - character(len=65536) :: line - - IO_spotTagInPart = .false. ! assume to nowhere spot tag - section = 0_pInt - line = '' - - rewind(fileUnit) - do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= part) ! search for part - line = IO_read(fileUnit) - enddo - - do while (trim(line) /= IO_EOF) - line = IO_read(fileUnit) - if (IO_isBlank(line)) cycle ! skip empty lines - foundNextPart: if (IO_getTag(line,'<','>') /= '') then - line = IO_read(fileUnit, .true.) ! reset IO_read - exit - endif foundNextPart - if (IO_getTag(line,'[',']') /= '') section = section + 1_pInt ! found [section] identifier - if (section > 0_pInt) then - chunkPos = IO_stringPos(line) - if (tag == trim(IO_lc(IO_stringValue(line,chunkPos,1_pInt)))) & ! match - IO_spotTagInPart(section) = .true. - endif - enddo - - end function IO_spotTagInPart - - -!-------------------------------------------------------------------------------------------------- -!> @brief return logical whether tag is present within before any [sections] -!-------------------------------------------------------------------------------------------------- -logical function IO_globalTagInPart(fileUnit,part,tag) - - implicit none - integer(pInt), intent(in) :: fileUnit !< file handle - character(len=*),intent(in) :: part, & !< part in which tag is searched for - tag !< tag to search for - - integer(pInt), allocatable, dimension(:) :: chunkPos - character(len=65536) :: line - - IO_globalTagInPart = .false. ! assume to nowhere spot tag - line ='' - - rewind(fileUnit) - do while (trim(line) /= IO_EOF .and. IO_lc(IO_getTag(line,'<','>')) /= part) ! search for part - line = IO_read(fileUnit) - enddo - - do while (trim(line) /= IO_EOF) - line = IO_read(fileUnit) - if (IO_isBlank(line)) cycle ! skip empty lines - foundNextPart: if (IO_getTag(line,'<','>') /= '') then - line = IO_read(fileUnit, .true.) ! reset IO_read - exit - endif foundNextPart - foundFirstSection: if (IO_getTag(line,'[',']') /= '') then - line = IO_read(fileUnit, .true.) ! reset IO_read - exit - endif foundFirstSection - chunkPos = IO_stringPos(line) - match: if (tag == trim(IO_lc(IO_stringValue(line,chunkPos,1_pInt)))) then - IO_globalTagInPart = .true. - line = IO_read(fileUnit, .true.) ! reset IO_read - exit - endif match - enddo - -end function IO_globalTagInPart - - !-------------------------------------------------------------------------------------------------- !> @brief locates all space-separated chunks in given string and returns array containing number !! them and the left/right position to be used by IO_xxxVal From ab45818d51c60bf188be070deb67f2c5115e94c0 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 14:30:51 +0200 Subject: [PATCH 27/67] seems to work now anyway, nicer code --- src/config.f90 | 65 ++++++++++++++++++------------------------ src/constitutive.f90 | 5 ++-- src/crystallite.f90 | 3 +- src/homogenization.f90 | 3 +- src/material.f90 | 6 ++-- 5 files changed, 38 insertions(+), 44 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index a22acbff9..959568d7b 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -47,7 +47,7 @@ module config type(tPartitionedStringList), public :: emptyList - type(tPartitionedStringList), public, allocatable, dimension(:) :: & + type(tPartitionedStringList), public, protected, allocatable, dimension(:) :: & config_phase, & config_microstructure, & config_homogenization, & @@ -82,9 +82,9 @@ module config MATERIAL_configFile = 'material.config', & !< generic name for material configuration file MATERIAL_localFileExt = 'materialConfig' !< extension of solver job name depending material configuration file - public :: & - config_init + config_init, & + config_deallocate contains @@ -137,7 +137,7 @@ subroutine config_init() fileContent = IO_recursiveRead('material.config') endif - do i=1, size(fileContent) + do i = 1_pInt, size(fileContent) line = trim(fileContent(i)) part = IO_lc(IO_getTag(line,'<','>')) select case (trim(part)) @@ -188,11 +188,7 @@ subroutine parseFile(line,sectionNames,part,& pStringLen use IO, only: & IO_error, & - IO_lc, & - IO_getTag, & - IO_isBlank, & - IO_stringValue, & - IO_stringPos + IO_getTag implicit none character(len=pStringLen), intent(out) :: line @@ -200,44 +196,38 @@ subroutine parseFile(line,sectionNames,part,& type(tPartitionedStringList), allocatable, dimension(:), intent(out) :: part character(len=pStringLen), dimension(:), intent(in) :: fileContent - character(len=64), allocatable, dimension(:) :: sectionNamesTemp ! Circumvent Gfortran bug - integer(pInt), allocatable, dimension(:) :: chunkPos - integer(pInt) :: s,i - character(len=64) :: tag + integer(pInt), allocatable, dimension(:) :: partPosition + integer(pInt) :: i logical :: echo echo = .false. allocate(part(0)) - tag='' - allocate(sectionNamesTemp(0),source=tag) + allocate(partPosition(0)) - s = 0_pInt - do i=1, size(fileContent) + do i = 1_pInt, size(fileContent) line = trim(fileContent(i)) - if (IO_isBlank(line)) cycle ! skip empty lines if (IO_getTag(line,'<','>') /= '') exit nextSection: if (IO_getTag(line,'[',']') /= '') then - s = s + 1_pInt - part = [part, emptyList] - tag = IO_getTag(line,'[',']') - sectionNamesTemp = [sectionNamesTemp,tag] + part = [part, emptyList] + partPosition = [partPosition, i] cycle endif nextSection - chunkPos = IO_stringPos(line) - tag = IO_lc(IO_stringValue(trim(line),chunkPos,1_pInt)) ! extract key - inSection: if (s > 0_pInt) then - call part(s)%add(IO_lc(trim(line))) + inSection: if (size(part) > 0_pInt) then + call part(size(part))%add(trim(adjustl(line))) else inSection - echo = (trim(tag) == '/echo/') + if (trim(IO_getTag(line,'/','/')) == 'echo') echo = .true. endif inSection enddo - sectionNames = sectionNamesTemp + allocate(sectionNames(size(partPosition))) + do i = 1_pInt, size(partPosition) + sectionNames(i) = trim(adjustl(fileContent(partPosition(i)))) + enddo if (echo) then - do s = 1, size(sectionNames) - write(6,*) 'section',s, '"'//trim(sectionNames(i))//'"' - call part(s)%show() + do i = 1, size(sectionNames) + write(6,'(a)') 'section',i, '"'//trim(sectionNames(i))//'"' + call part(i)%show() end do end if @@ -252,7 +242,6 @@ subroutine config_deallocate(what) implicit none character(len=*), intent(in) :: what - integer(pInt) :: i select case(trim(what)) @@ -336,7 +325,7 @@ end subroutine show !-------------------------------------------------------------------------------------------------- -!> @brief cleans entire list +!> @brief empties list and frees associated memory !> @details explicit interface to reset list. Triggers final statement (and following chain reaction) !-------------------------------------------------------------------------------------------------- subroutine free(this) @@ -350,8 +339,8 @@ end subroutine free !-------------------------------------------------------------------------------------------------- -!> @brief cleans entire list -!> @details called when variable goes out of scope. Triggers chain reaction. +!> @brief empties list and frees associated memory +!> @details called when variable goes out of scope. Triggers chain reaction for list !-------------------------------------------------------------------------------------------------- recursive subroutine finalize(this) @@ -364,15 +353,15 @@ end subroutine finalize !-------------------------------------------------------------------------------------------------- -!> @brief cleans entire list -!> @details called when variable goes out of scope. Triggers chain reaction. +!> @brief cleans entire array of linke lists +!> @details called when variable goes out of scope. !-------------------------------------------------------------------------------------------------- subroutine finalizeArray(this) implicit none integer :: i type(tPartitionedStringList), intent(inout), dimension(:) :: this - type(tPartitionedStringList), pointer :: temp ! bug in Gfortran + type(tPartitionedStringList), pointer :: temp ! bug in Gfortran? do i=1, size(this) if (associated(this(i)%next)) then diff --git a/src/constitutive.f90 b/src/constitutive.f90 index f27edcc07..43207c65c 100644 --- a/src/constitutive.f90 +++ b/src/constitutive.f90 @@ -65,7 +65,8 @@ subroutine constitutive_init() material_Nphase, & material_localFileExt, & phase_name, & - material_configFile + material_configFile, & + config_deallocate use material, only: & material_phase, & phase_plasticity, & @@ -192,7 +193,7 @@ subroutine constitutive_init() if (any(phase_kinematics == KINEMATICS_hydrogen_strain_ID)) call kinematics_hydrogen_strain_init(FILEUNIT) close(FILEUNIT) - deallocate(config_phase) + call config_deallocate('material.config/phase') write(6,'(/,a)') ' <<<+- constitutive init -+>>>' write(6,'(a15,a)') ' Current time: ',IO_timeStamp() diff --git a/src/crystallite.f90 b/src/crystallite.f90 index 6601fe29e..b9ae84a44 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -172,6 +172,7 @@ subroutine crystallite_init IO_error use material use config, only: & + config_deallocate, & config_crystallite, & crystallite_name use constitutive, only: & @@ -375,7 +376,7 @@ subroutine crystallite_init close(FILEUNIT) endif - deallocate(config_crystallite) + call config_deallocate('material.config/crystallite') !-------------------------------------------------------------------------------------------------- ! initialize diff --git a/src/homogenization.f90 b/src/homogenization.f90 index de195f18a..496514d3b 100644 --- a/src/homogenization.f90 +++ b/src/homogenization.f90 @@ -103,6 +103,7 @@ subroutine homogenization_init use config, only: & material_configFile, & material_localFileExt, & + config_deallocate, & config_homogenization, & homogenization_name use material @@ -374,7 +375,7 @@ subroutine homogenization_init close(FILEUNIT) endif mainProcess2 - deallocate(config_homogenization) + call config_deallocate('material.config/homogenization') !-------------------------------------------------------------------------------------------------- ! allocate and initialize global variables diff --git a/src/material.f90 b/src/material.f90 index 73edc8281..f578867f8 100644 --- a/src/material.f90 +++ b/src/material.f90 @@ -919,6 +919,7 @@ subroutine material_parseTexture IO_floatValue, & IO_stringValue use config, only: & + config_deallocate, & config_texture use math, only: & inRad, & @@ -1058,7 +1059,7 @@ subroutine material_parseTexture endif enddo - deallocate(config_texture) + call config_deallocate('material.config/texture') end subroutine material_parseTexture @@ -1090,6 +1091,7 @@ subroutine material_populateGrains use config, only: & config_homogenization, & config_microstructure, & + config_deallocate, & homogenization_name, & microstructure_name use IO, only: & @@ -1426,7 +1428,7 @@ subroutine material_populateGrains deallocate(texture_transformation) deallocate(Nelems) deallocate(elemsOfHomogMicro) - deallocate(config_microstructure) + call config_deallocate('material.config/microstructure') end subroutine material_populateGrains From 51b4ef319a0033fdd4bdc1a14e52b318456ad4d3 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 20:12:16 +0200 Subject: [PATCH 28/67] HDF5 was not compiled due to missing dependency --- src/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index be01bd4ee..3689d15c5 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -36,7 +36,7 @@ add_dependencies(HDF5_UTILITIES IO) list(APPEND OBJECTFILES $) add_library(NUMERICS OBJECT "numerics.f90") -add_dependencies(NUMERICS IO) +add_dependencies(NUMERICS HDF5_UTILITIES) list(APPEND OBJECTFILES $) add_library(DEBUG OBJECT "debug.f90") From 8c5f3d4e07b2eada54a4e6a254e227c30a2fa6ab Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 22:52:12 +0200 Subject: [PATCH 29/67] only needed once --- src/config.f90 | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index 959568d7b..f7c8bfcdc 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -45,8 +45,6 @@ module config end type tPartitionedStringList - type(tPartitionedStringList), public :: emptyList - type(tPartitionedStringList), public, protected, allocatable, dimension(:) :: & config_phase, & config_microstructure, & @@ -197,6 +195,7 @@ subroutine parseFile(line,sectionNames,part,& character(len=pStringLen), dimension(:), intent(in) :: fileContent integer(pInt), allocatable, dimension(:) :: partPosition + type(tPartitionedStringList) :: emptyList integer(pInt) :: i logical :: echo @@ -364,11 +363,11 @@ subroutine finalizeArray(this) type(tPartitionedStringList), pointer :: temp ! bug in Gfortran? do i=1, size(this) - if (associated(this(i)%next)) then + !if (associated(this(i)%next)) then temp => this(i)%next !deallocate(this(i)) !internal compiler error: in gfc_build_final_call, at fortran/trans.c:975 deallocate(temp) - endif + !endif enddo end subroutine finalizeArray From 271b9ba76bcd5135b10da4748bfe96b1cd60f7f0 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 22 Aug 2018 23:28:47 +0200 Subject: [PATCH 30/67] intersting note ... --- src/prec.f90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/prec.f90 b/src/prec.f90 index 959ee77ba..f6c0fd543 100644 --- a/src/prec.f90 +++ b/src/prec.f90 @@ -7,6 +7,7 @@ !> @brief setting precision for real and int type !-------------------------------------------------------------------------------------------------- module prec +! ToDo: use, intrinsic :: iso_fortran_env, only : I8 => int64, WP => real64 implicit none private #if (FLOAT==8) From 7ecb7689f166f6877f622e4d10b4f09f108bb68f Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 23 Aug 2018 00:13:57 +0200 Subject: [PATCH 31/67] Intel compiler failed with SIGSEV derived types, pointers, finalize .... altogether seems to bring both Compilers to their limits. I cannot see what was wrong before, but now it works and might be a little faster --- src/config.f90 | 38 ++++++++++++++++++-------------------- 1 file changed, 18 insertions(+), 20 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index f7c8bfcdc..837818756 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -194,41 +194,39 @@ subroutine parseFile(line,sectionNames,part,& type(tPartitionedStringList), allocatable, dimension(:), intent(out) :: part character(len=pStringLen), dimension(:), intent(in) :: fileContent - integer(pInt), allocatable, dimension(:) :: partPosition - type(tPartitionedStringList) :: emptyList - integer(pInt) :: i + integer(pInt), allocatable, dimension(:) :: partPosition ! position of [] tags + last line in section + integer(pInt) :: i, j logical :: echo echo = .false. - allocate(part(0)) allocate(partPosition(0)) - + do i = 1_pInt, size(fileContent) line = trim(fileContent(i)) if (IO_getTag(line,'<','>') /= '') exit nextSection: if (IO_getTag(line,'[',']') /= '') then - part = [part, emptyList] partPosition = [partPosition, i] cycle endif nextSection - inSection: if (size(part) > 0_pInt) then - call part(size(part))%add(trim(adjustl(line))) - else inSection - if (trim(IO_getTag(line,'/','/')) == 'echo') echo = .true. - endif inSection + if (size(partPosition) < 1_pInt) & + echo = (trim(IO_getTag(line,'/','/')) == 'echo') .or. echo enddo allocate(sectionNames(size(partPosition))) - do i = 1_pInt, size(partPosition) - sectionNames(i) = trim(adjustl(fileContent(partPosition(i)))) - enddo + allocate(part(size(partPosition))) - if (echo) then - do i = 1, size(sectionNames) - write(6,'(a)') 'section',i, '"'//trim(sectionNames(i))//'"' + partPosition = [partPosition, i] ! needed when actually storing content + + do i = 1_pInt, size(partPosition) -1_pInt + sectionNames(i) = trim(adjustl(fileContent(partPosition(i)))) + do j = partPosition(i) + 1_pInt, partPosition(i+1) -1_pInt + call part(i)%add(trim(adjustl(fileContent(j)))) + enddo + if (echo) then + write(6,*) 'section',i, '"'//trim(sectionNames(i))//'"' call part(i)%show() - end do - end if + endif + enddo end subroutine parseFile @@ -316,7 +314,7 @@ subroutine show(this) item => this do while (associated(item%next)) - write(6,'(a)') trim(item%string%val) + write(6,'(a)') ' '//trim(item%string%val) item => item%next end do From d765cf285b32a3b36d0aa1920682e12cc2e36140 Mon Sep 17 00:00:00 2001 From: Test User Date: Mon, 27 Aug 2018 08:11:39 +0200 Subject: [PATCH 32/67] [skip ci] updated version information after successful test of v2.0.2-442-gb11666ef --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 390024a1f..21a7c7c31 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-409-gac011684 +v2.0.2-442-gb11666ef From 6ed68c91349ba89ba47f5793e236684a73350c65 Mon Sep 17 00:00:00 2001 From: Test User Date: Tue, 28 Aug 2018 05:26:48 +0200 Subject: [PATCH 33/67] [skip ci] updated version information after successful test of v2.0.2-474-g38fd517c --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 21a7c7c31..fd2858d51 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-442-gb11666ef +v2.0.2-474-g38fd517c From 94695f773ef495929a8ae961e9bfc2d1907cc932 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 28 Aug 2018 07:47:05 +0200 Subject: [PATCH 34/67] more verbose and works for arbitrary precision --- src/math.f90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/math.f90 b/src/math.f90 index 4179d6edc..440ee5303 100644 --- a/src/math.f90 +++ b/src/math.f90 @@ -36,13 +36,13 @@ module math real(pReal), dimension(6), parameter, private :: & nrmMandel = [& - 1.0_pReal, 1.0_pReal, 1.0_pReal,& - 1.414213562373095_pReal, 1.414213562373095_pReal, 1.414213562373095_pReal ] !< weighting for Mandel notation (forward) + 1.0_pReal, 1.0_pReal, 1.0_pReal, & + sqrt(2.0_pReal), sqrt(2.0_pReal), sqrt(2.0_pReal) ] !< weighting for Mandel notation (forward) real(pReal), dimension(6), parameter , public :: & invnrmMandel = [& - 1.0_pReal, 1.0_pReal, 1.0_pReal,& - 0.7071067811865476_pReal, 0.7071067811865476_pReal, 0.7071067811865476_pReal ] !< weighting for Mandel notation (backward) + 1.0_pReal, 1.0_pReal, 1.0_pReal, & + 1.0_pReal/sqrt(2.0_pReal), 1.0_pReal/sqrt(2.0_pReal), 1.0_pReal/sqrt(2.0_pReal) ] !< weighting for Mandel notation (backward) integer(pInt), dimension (2,6), parameter, private :: & mapVoigt = reshape([& From 42f8b0a06378bdd7ffe8b3a91961b55e6842166c Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 24 Aug 2018 12:42:30 +0200 Subject: [PATCH 35/67] labels of slip and twin systems for more self-explanatory output --- src/lattice.f90 | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/src/lattice.f90 b/src/lattice.f90 index 550b4c5c9..ffe1c239d 100644 --- a/src/lattice.f90 +++ b/src/lattice.f90 @@ -111,6 +111,9 @@ module lattice -1,-1, 0, -1, 1,-1 & ! D6 ],pReal),[ 3_pInt + 3_pInt,LATTICE_fcc_Nslip]) !< Slip system <110>{111} directions. Sorted according to Eisenlohr & Hantcherli + character(len=*), dimension(1), parameter, public :: LATTICE_FCC_SLIPFAMILY_NAME = & + ['<0 1 -1>{1 1 1}'] + real(pReal), dimension(3+3,LATTICE_fcc_Ntwin), parameter, private :: & LATTICE_fcc_systemTwin = reshape(real( [& -2, 1, 1, 1, 1, 1, & @@ -127,6 +130,9 @@ module lattice -1, 1, 2, -1, 1,-1 & ],pReal),[ 3_pInt + 3_pInt,LATTICE_fcc_Ntwin]) !< Twin system <112>{111} directions. Sorted according to Eisenlohr & Hantcherli + character(len=*), dimension(1), parameter, public :: LATTICE_FCC_TWINFAMILY_NAME = & + ['<-2 1 1>{1 1 1}'] + real(pReal), dimension(3+3,LATTICE_fcc_Ntrans), parameter, private :: & LATTICE_fccTohex_systemTrans = reshape(real( [& -2, 1, 1, 1, 1, 1, & @@ -433,6 +439,10 @@ module lattice ! 1,-1, 1, 3, 2,-1 & ],pReal),[ 3_pInt + 3_pInt ,LATTICE_bcc_Nslip]) + character(len=*), dimension(2), parameter, public :: LATTICE_BCC_SLIPFAMILY_NAME = & + ['<1 -1 1>{0 1 1}', & + '<1 -1 1>{2 1 1}'] + real(pReal), dimension(3+3,LATTICE_bcc_Ntwin), parameter, private :: & LATTICE_bcc_systemTwin = reshape(real([& ! Twin system <111>{112} @@ -450,6 +460,9 @@ module lattice 1, 1, 1, 1, 1,-2 & ],pReal),[ 3_pInt + 3_pInt,LATTICE_bcc_Ntwin]) + character(len=*), dimension(1), parameter, public :: LATTICE_BCC_TWINFAMILY_NAME = & + ['<1 1 1>{2 1 1}'] + real(pReal), dimension(LATTICE_bcc_Ntwin), parameter, private :: & LATTICE_bcc_shearTwin = 0.5_pReal*sqrt(2.0_pReal) @@ -618,6 +631,14 @@ module lattice 1, 1, -2, 3, -1, -1, 2, 2 & ],pReal),[ 4_pInt + 4_pInt,LATTICE_hex_Nslip]) !< slip systems for hex sorted by A. Alankar & P. Eisenlohr + character(len=*), dimension(6), parameter, public :: LATTICE_HEX_SLIPFAMILY_NAME = & + ['<1 1 . 1>{0 0 . 1} ', & + '<1 1 . 1>{1 0 . 0} ', & + '<1 0 . 0>{1 1 . 0} ', & + '<1 1 . 0>{-1 1 . 1} ', & + '<1 1 . 3>{-1 0 . 1} ', & + '<1 1 . 3>{-1 -1 . 2}'] + real(pReal), dimension(4+4,LATTICE_hex_Ntwin), parameter, private :: & LATTICE_hex_systemTwin = reshape(real([& ! Compression or Tension =f(twinning shear=f(c/a)) for each metal ! (according to Yoo 1981) @@ -650,6 +671,12 @@ module lattice 1, 1, -2, -3, 1, 1, -2, 2 & ],pReal),[ 4_pInt + 4_pInt ,LATTICE_hex_Ntwin]) !< twin systems for hex, order follows Prof. Tom Bieler's scheme; but numbering in data was restarted from 1 + character(len=*), dimension(4), parameter, public :: LATTICE_HEX_TWINFAMILY_NAME = & + ['<-1 0 . 1>{1 0 . 2} ', & + '<1 1 . 6>{-1 -1 . 1}', & + '<1 0 . -2>{1 0 . 1} ', & + '<1 1 . -3>{1 1 . 2} '] + integer(pInt), dimension(LATTICE_hex_Ntwin), parameter, private :: & LATTICE_hex_shearTwin = reshape(int( [& ! indicator to formula further below 1, & ! <-10.1>{10.2} @@ -926,6 +953,21 @@ module lattice 1, 1, 1, 1,-2, 1 & ],pReal),[ 3_pInt + 3_pInt,LATTICE_bct_Nslip]) !< slip systems for bct sorted by Bieler + character(len=*), dimension(13), parameter, public :: LATTICE_BCT_SLIPFAMILY_NAME = & + ['{1 0 0)<0 0 1] ', & + '{1 1 0)<0 0 1] ', & + '{1 0 0)<0 1 0] ', & + '{1 1 0)<1 -1 1]', & + '{1 1 0)<1 -1 0]', & + '{1 0 0)<0 1 1] ', & + '{0 0 1)<0 1 0] ', & + '{0 0 1)<1 1 0] ', & + '{0 1 1)<0 1 -1]', & + '{0 1 1)<1 -1 1]', & + '{0 1 1)<1 0 0] ', & + '{2 1 1)<0 1 -1]', & + '{2 1 1)<-1 1 1]'] + integer(pInt), dimension(LATTICE_bct_Nslip,LATTICE_bct_Nslip), parameter, public :: & LATTICE_bct_interactionSlipSlip = reshape(int( [& 1, 2, 3, 3, 7, 7, 13, 13, 13, 13, 21, 21, 31, 31, 31, 31, 43, 43, 57, 57, 73, 73, 73, 73, 91, 91, 91, 91, 91, 91, 91, 91, 111, 111, 111, 111, 133,133,133,133,133,133,133,133, 157,157,157,157,157,157,157,157, & From 06e71563510cb12fc0e09cad559cf05e449ac5d6 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 28 Aug 2018 12:41:21 +0200 Subject: [PATCH 36/67] did not work for values <0 --- src/IO.f90 | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/IO.f90 b/src/IO.f90 index 0358785f6..8e1b9e80f 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -1363,12 +1363,16 @@ function IO_continuousIntValues(fileUnit,maxN,lookupName,lookupMap,lookupMaxN) pure function IO_intOut(intToPrint) implicit none - character(len=19) :: N_Digits ! maximum digits for 64 bit integer - character(len=40) :: IO_intOut integer(pInt), intent(in) :: intToPrint + character(len=41) :: IO_intOut + integer(pInt) :: N_digits + character(len=19) :: width ! maximum digits for 64 bit integer + character(len=20) :: min_width ! longer for negative values - write(N_Digits, '(I19.19)') 1_pInt + int(log10(real(intToPrint)),pInt) - IO_intOut = 'I'//trim(N_Digits)//'.'//trim(N_Digits) + N_digits = 1_pInt + int(log10(real(max(abs(intToPrint),1_pInt))),pInt) + write(width, '(I19.19)') N_digits + write(min_width, '(I20.20)') N_digits + merge(1_pInt,0_pInt,intToPrint < 0_pInt) + IO_intOut = 'I'//trim(min_width)//'.'//trim(width) end function IO_intOut From 8e9e9ca7526e9b682ba230920ea8a97ce3163725 Mon Sep 17 00:00:00 2001 From: Test User Date: Tue, 28 Aug 2018 13:19:47 +0200 Subject: [PATCH 37/67] [skip ci] updated version information after successful test of v2.0.2-476-g94695f77 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index fd2858d51..fa3390c07 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-474-g38fd517c +v2.0.2-476-g94695f77 From e643752180aa0bc3af2ad1e6c8a2a5a1b0affe75 Mon Sep 17 00:00:00 2001 From: Test User Date: Tue, 28 Aug 2018 23:13:17 +0200 Subject: [PATCH 38/67] [skip ci] updated version information after successful test of v2.0.2-478-g06e71563 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index fd2858d51..abe364a39 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-474-g38fd517c +v2.0.2-478-g06e71563 From 680c9e11d4403fb8db151d320284ad5bbe989065 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 29 Aug 2018 08:26:28 +0200 Subject: [PATCH 39/67] segmentation fault in cause of empty list --- src/config.f90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/config.f90 b/src/config.f90 index 837818756..d028eb897 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -351,7 +351,7 @@ end subroutine finalize !-------------------------------------------------------------------------------------------------- !> @brief cleans entire array of linke lists -!> @details called when variable goes out of scope. +!> @details called when variable goes out of scope and deallocates the list at each array entry !-------------------------------------------------------------------------------------------------- subroutine finalizeArray(this) @@ -361,11 +361,11 @@ subroutine finalizeArray(this) type(tPartitionedStringList), pointer :: temp ! bug in Gfortran? do i=1, size(this) - !if (associated(this(i)%next)) then + if (associated(this(i)%next)) then temp => this(i)%next !deallocate(this(i)) !internal compiler error: in gfc_build_final_call, at fortran/trans.c:975 deallocate(temp) - !endif + endif enddo end subroutine finalizeArray From 8fd3ac639668f6fb1f37e1d98dd5e8b103bc27e1 Mon Sep 17 00:00:00 2001 From: Test User Date: Wed, 29 Aug 2018 13:23:54 +0200 Subject: [PATCH 40/67] [skip ci] updated version information after successful test of v2.0.2-485-gf2acc148 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index fa3390c07..3caf58c39 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-476-g94695f77 +v2.0.2-485-gf2acc148 From cb6b876769cc25ccd728675a87bed81fc28ded48 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 30 Aug 2018 00:58:01 +0200 Subject: [PATCH 41/67] need test for non-schmid --- PRIVATE | 2 +- examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/PRIVATE b/PRIVATE index a764ade04..fa02113fa 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit a764ade044735df35fac93a5204446291ee29abc +Subproject commit fa02113fa7a0af3376648e4320318ec337fe79aa diff --git a/examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config b/examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config index 6e005f251..c86d516a9 100644 --- a/examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config +++ b/examples/ConfigFiles/Phase_Phenopowerlaw_BCC-Martensite.config @@ -18,5 +18,5 @@ tau0_slip 405.8e6 456.7e6 # per family tausat_slip 872.9e6 971.2e6 # per family h0_slipslip 563.0e9 interaction_slipslip 1 1 1.4 1.4 1.4 1.4 -w0_slip 2.0 +a_slip 2.0 (output) totalshear From bb57e7b4983fbfd91f5e3eafdca36402fc245500 Mon Sep 17 00:00:00 2001 From: Test User Date: Thu, 30 Aug 2018 04:43:22 +0200 Subject: [PATCH 42/67] [skip ci] updated version information after successful test of v2.0.2-488-ge0cecd4c --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 3caf58c39..01392f6fe 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-485-gf2acc148 +v2.0.2-488-ge0cecd4c From 29e55d20fb2f2f55377cdc50a76b0ef29bbd3c7e Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 30 Aug 2018 09:42:45 +0200 Subject: [PATCH 43/67] message better to understand and giving error instead of SIGSEGV --- src/IO.f90 | 4 +++- src/config.f90 | 24 +++++++++++++----------- 2 files changed, 16 insertions(+), 12 deletions(-) diff --git a/src/IO.f90 b/src/IO.f90 index 8e1b9e80f..c97dcfa9c 100644 --- a/src/IO.f90 +++ b/src/IO.f90 @@ -1477,6 +1477,8 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg) msg = 'illegal texture transformation specified' case (160_pInt) msg = 'no entries in config part' + case (161_pInt) + msg = 'config part found twice' case (165_pInt) msg = 'homogenization configuration' case (170_pInt) @@ -1574,7 +1576,7 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg) case (845_pInt) msg = 'incomplete information in spectral mesh header' case (846_pInt) - msg = 'not a rotation defined for loadcase rotation' + msg = 'rotation for load case rotation ill-defined (R:RT != I)' case (847_pInt) msg = 'update of gamma operator not possible when pre-calculated' case (880_pInt) diff --git a/src/config.f90 b/src/config.f90 index d028eb897..4d5a76432 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -141,23 +141,23 @@ subroutine config_init() select case (trim(part)) case (trim(material_partPhase)) - call parseFile(line,phase_name,config_phase,fileContent(i+1:)) + call parseFile(phase_name,config_phase,line,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Phase parsed'; flush(6) case (trim(material_partMicrostructure)) - call parseFile(line,microstructure_name,config_microstructure,fileContent(i+1:)) + call parseFile(microstructure_name,config_microstructure,line,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Microstructure parsed'; flush(6) case (trim(material_partCrystallite)) - call parseFile(line,crystallite_name,config_crystallite,fileContent(i+1:)) + call parseFile(crystallite_name,config_crystallite,line,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Crystallite parsed'; flush(6) case (trim(material_partHomogenization)) - call parseFile(line,homogenization_name,config_homogenization,fileContent(i+1:)) + call parseFile(homogenization_name,config_homogenization,line,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Homogenization parsed'; flush(6) case (trim(material_partTexture)) - call parseFile(line,texture_name,config_texture,fileContent(i+1:)) + call parseFile(texture_name,config_texture,line,fileContent(i+1:)) if (iand(myDebug,debug_levelBasic) /= 0_pInt) write(6,'(a)') ' Texture parsed'; flush(6) end select @@ -180,7 +180,7 @@ end subroutine config_init !-------------------------------------------------------------------------------------------------- !> @brief parses the material.config file !-------------------------------------------------------------------------------------------------- -subroutine parseFile(line,sectionNames,part,& +subroutine parseFile(sectionNames,part,line, & fileContent) use prec, only: & pStringLen @@ -189,16 +189,18 @@ subroutine parseFile(line,sectionNames,part,& IO_getTag implicit none - character(len=pStringLen), intent(out) :: line - character(len=64), allocatable, dimension(:), intent(out) :: sectionNames - type(tPartitionedStringList), allocatable, dimension(:), intent(out) :: part - character(len=pStringLen), dimension(:), intent(in) :: fileContent + character(len=64), allocatable, dimension(:), intent(out) :: sectionNames + type(tPartitionedStringList), allocatable, dimension(:), intent(inout) :: part + character(len=pStringLen), intent(inout) :: line + character(len=pStringLen), dimension(:), intent(in) :: fileContent - integer(pInt), allocatable, dimension(:) :: partPosition ! position of [] tags + last line in section + integer(pInt), allocatable, dimension(:) :: partPosition ! position of [] tags + last line in section integer(pInt) :: i, j logical :: echo echo = .false. + + if (allocated(part)) call IO_error(161_pInt,ext_msg=trim(line)) allocate(partPosition(0)) do i = 1_pInt, size(fileContent) From 9a90eae3bc0cc42a67ec582387a3770941293b8d Mon Sep 17 00:00:00 2001 From: Test User Date: Fri, 31 Aug 2018 07:03:06 +0200 Subject: [PATCH 44/67] [skip ci] updated version information after successful test of v2.0.2-490-g29e55d20 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 01392f6fe..c1e114a98 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-488-ge0cecd4c +v2.0.2-490-g29e55d20 From d18d74ae312be8ff2df38934c2e8c570a2238fe2 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 31 Aug 2018 08:20:23 +0200 Subject: [PATCH 45/67] mechanics solver type is set only once as all mech routines have the same interface, this leaner syntax can be used --- src/DAMASK_spectral.f90 | 78 +++++++++++++++++++---------------------- 1 file changed, 36 insertions(+), 42 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index 7f968a7f5..72db08564 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -143,6 +143,12 @@ program DAMASK_spectral integer(pInt), parameter :: maxRealOut = maxByteOut/pReal integer(pLongInt), dimension(2) :: outputIndex integer :: ierr + procedure(basic_init), pointer :: & + mech_init + procedure(basic_forward), pointer :: & + mech_forward + procedure(basic_solution), pointer :: & + mech_solution external :: & quit @@ -163,6 +169,26 @@ program DAMASK_spectral if (any(damage_type == DAMAGE_nonlocal_ID )) nActiveFields = nActiveFields + 1 allocate(solres(nActiveFields)) +!-------------------------------------------------------------------------------------------------- +! assign mechanics solver depending on selected type + select case (spectral_solver) + case (DAMASK_spectral_SolverBasic_label) + mech_init => basic_init + mech_forward => basic_forward + mech_solution => basic_solution + + case (DAMASK_spectral_SolverPolarisation_label) + if(iand(debug_level(debug_spectral),debug_levelBasic)/= 0) & + call IO_warning(42_pInt, ext_msg='debug Divergence') + mech_init => polarisation_init + mech_forward => polarisation_forward + mech_solution => polarisation_solution + + case default + call IO_error(error_ID = 891_pInt, ext_msg = trim(spectral_solver)) + + end select + !-------------------------------------------------------------------------------------------------- ! reading basic information from load case file and allocate data structure containing load cases call IO_open_file(FILEUNIT,trim(loadCaseFile)) @@ -189,7 +215,7 @@ program DAMASK_spectral allocate (loadCases(N_n)) ! array of load cases loadCases%stress%myType='stress' - do i = 1, size(loadCases) + do i = 1, size(loadCases) allocate(loadCases(i)%ID(nActiveFields)) field = 1 loadCases(i)%ID(field) = FIELD_MECH_ID ! mechanical active by default @@ -355,25 +381,13 @@ program DAMASK_spectral do field = 1, nActiveFields select case (loadCases(1)%ID(field)) case(FIELD_MECH_ID) - select case (spectral_solver) - case (DAMASK_spectral_SolverBasic_label) - call basic_init - - case (DAMASK_spectral_SolverPolarisation_label) - if(iand(debug_level(debug_spectral),debug_levelBasic)/= 0) & - call IO_warning(42_pInt, ext_msg='debug Divergence') - call Polarisation_init - - case default - call IO_error(error_ID = 891_pInt, ext_msg = trim(spectral_solver)) - - end select + call mech_init case(FIELD_THERMAL_ID) call spectral_thermal_init case(FIELD_DAMAGE_ID) - call spectral_damage_init() + call spectral_damage_init end select enddo @@ -512,24 +526,14 @@ program DAMASK_spectral do field = 1, nActiveFields select case(loadCases(currentLoadCase)%ID(field)) case(FIELD_MECH_ID) - select case (spectral_solver) - case (DAMASK_spectral_SolverBasic_label) - call Basic_forward (& + call mech_forward (& guess,timeinc,timeIncOld,remainingLoadCaseTime, & deformation_BC = loadCases(currentLoadCase)%deformation, & stress_BC = loadCases(currentLoadCase)%stress, & rotation_BC = loadCases(currentLoadCase)%rotation) - case (DAMASK_spectral_SolverPolarisation_label) - call Polarisation_forward (& - guess,timeinc,timeIncOld,remainingLoadCaseTime, & - deformation_BC = loadCases(currentLoadCase)%deformation, & - stress_BC = loadCases(currentLoadCase)%stress, & - rotation_BC = loadCases(currentLoadCase)%rotation) - end select - - case(FIELD_THERMAL_ID); call spectral_thermal_forward() - case(FIELD_DAMAGE_ID); call spectral_damage_forward() + case(FIELD_THERMAL_ID); call spectral_thermal_forward() + case(FIELD_DAMAGE_ID); call spectral_damage_forward() end select enddo @@ -541,20 +545,10 @@ program DAMASK_spectral do field = 1, nActiveFields select case(loadCases(currentLoadCase)%ID(field)) case(FIELD_MECH_ID) - select case (spectral_solver) - case (DAMASK_spectral_SolverBasic_label) - solres(field) = Basic_solution (& - incInfo,timeinc,timeIncOld, & - stress_BC = loadCases(currentLoadCase)%stress, & - rotation_BC = loadCases(currentLoadCase)%rotation) - - case (DAMASK_spectral_SolverPolarisation_label) - solres(field) = Polarisation_solution (& - incInfo,timeinc,timeIncOld, & - stress_BC = loadCases(currentLoadCase)%stress, & - rotation_BC = loadCases(currentLoadCase)%rotation) - - end select + solres(field) = mech_solution (& + incInfo,timeinc,timeIncOld, & + stress_BC = loadCases(currentLoadCase)%stress, & + rotation_BC = loadCases(currentLoadCase)%rotation) case(FIELD_THERMAL_ID) solres(field) = spectral_thermal_solution(timeinc,timeIncOld,remainingLoadCaseTime) From b24ebb8a5b9b6956811e5888baf6ec6f87a20159 Mon Sep 17 00:00:00 2001 From: Franz Roters Date: Fri, 31 Aug 2018 08:52:21 +0200 Subject: [PATCH 46/67] not needed anymore as Marc always compiles with OpenMP adopted installation script and documentation accordingly --- .../2016/Marc_tools/comp_damask | 52 - .../2016/Marc_tools/comp_damask_h | 52 - .../2016/Marc_tools/comp_damask_l | 52 - .../2016/Marc_tools/run_damask | 4112 ---------------- .../2016/Marc_tools/run_damask_h | 4112 ---------------- .../2016/Marc_tools/run_damask_l | 4112 ---------------- .../mods_MarcMentat/2016/Mentat_bin/kill7 | 8 - .../mods_MarcMentat/2016/Mentat_bin/kill8 | 8 - .../mods_MarcMentat/2016/Mentat_bin/kill9 | 8 - .../mods_MarcMentat/2016/Mentat_bin/submit7 | 187 - .../mods_MarcMentat/2016/Mentat_bin/submit8 | 187 - .../mods_MarcMentat/2016/Mentat_bin/submit9 | 187 - .../2017/Marc_tools/comp_damask | 52 - .../2017/Marc_tools/comp_damask_h | 52 - .../2017/Marc_tools/comp_damask_l | 52 - .../2017/Marc_tools/run_damask | 4122 ----------------- .../2017/Marc_tools/run_damask_h | 4122 ----------------- .../2017/Marc_tools/run_damask_l | 4122 ----------------- .../mods_MarcMentat/2017/Mentat_bin/kill7 | 8 - .../mods_MarcMentat/2017/Mentat_bin/kill8 | 8 - .../mods_MarcMentat/2017/Mentat_bin/kill9 | 8 - .../mods_MarcMentat/2017/Mentat_bin/submit7 | 187 - .../mods_MarcMentat/2017/Mentat_bin/submit8 | 187 - .../mods_MarcMentat/2017/Mentat_bin/submit9 | 187 - .../apply_DAMASK_modifications.sh | 25 +- installation/mods_MarcMentat/installation.txt | 12 - 26 files changed, 5 insertions(+), 26216 deletions(-) delete mode 100644 installation/mods_MarcMentat/2016/Marc_tools/comp_damask delete mode 100644 installation/mods_MarcMentat/2016/Marc_tools/comp_damask_h delete mode 100644 installation/mods_MarcMentat/2016/Marc_tools/comp_damask_l delete mode 100644 installation/mods_MarcMentat/2016/Marc_tools/run_damask delete mode 100644 installation/mods_MarcMentat/2016/Marc_tools/run_damask_h delete mode 100644 installation/mods_MarcMentat/2016/Marc_tools/run_damask_l delete mode 100644 installation/mods_MarcMentat/2016/Mentat_bin/kill7 delete mode 100644 installation/mods_MarcMentat/2016/Mentat_bin/kill8 delete mode 100644 installation/mods_MarcMentat/2016/Mentat_bin/kill9 delete mode 100644 installation/mods_MarcMentat/2016/Mentat_bin/submit7 delete mode 100644 installation/mods_MarcMentat/2016/Mentat_bin/submit8 delete mode 100644 installation/mods_MarcMentat/2016/Mentat_bin/submit9 delete mode 100644 installation/mods_MarcMentat/2017/Marc_tools/comp_damask delete mode 100644 installation/mods_MarcMentat/2017/Marc_tools/comp_damask_h delete mode 100644 installation/mods_MarcMentat/2017/Marc_tools/comp_damask_l delete mode 100644 installation/mods_MarcMentat/2017/Marc_tools/run_damask delete mode 100644 installation/mods_MarcMentat/2017/Marc_tools/run_damask_h delete mode 100644 installation/mods_MarcMentat/2017/Marc_tools/run_damask_l delete mode 100644 installation/mods_MarcMentat/2017/Mentat_bin/kill7 delete mode 100644 installation/mods_MarcMentat/2017/Mentat_bin/kill8 delete mode 100644 installation/mods_MarcMentat/2017/Mentat_bin/kill9 delete mode 100644 installation/mods_MarcMentat/2017/Mentat_bin/submit7 delete mode 100644 installation/mods_MarcMentat/2017/Mentat_bin/submit8 delete mode 100644 installation/mods_MarcMentat/2017/Mentat_bin/submit9 diff --git a/installation/mods_MarcMentat/2016/Marc_tools/comp_damask b/installation/mods_MarcMentat/2016/Marc_tools/comp_damask deleted file mode 100644 index 2d144b8a4..000000000 --- a/installation/mods_MarcMentat/2016/Marc_tools/comp_damask +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/ksh -# 1st arg: $DIR -# 2nd arg: $DIRJOB -# 3rd arg: $user -# 4th arg: $program -DIR=$1 -user=$3 -program=$4 -usernoext=$user -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - -# add BLAS options for linking - BLAS="%BLAS%" - -. $DIR/tools/include -DIRJOB=$2 -cd $DIRJOB -echo "Compiling and linking user subroutine $user on host `hostname`" -echo "program: $program" - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - userobj=$usernoext.o - - - $LOAD ${program} $DIR/lib/main.o\ - $DIR/lib/blkdta.o $DIR/lib/comm?.o \ - ${userobj-} \ - $DIR/lib/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ../lib/mdsrc.a \ - ../lib/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $BLAS \ - $SYSLIBS || \ - { - echo "$0: link failed for $usernoext.o on host `hostname`" - exit 1 - } - /bin/rm $userobj - /bin/rm $DIRJOB/*.mod diff --git a/installation/mods_MarcMentat/2016/Marc_tools/comp_damask_h b/installation/mods_MarcMentat/2016/Marc_tools/comp_damask_h deleted file mode 100644 index 01464f095..000000000 --- a/installation/mods_MarcMentat/2016/Marc_tools/comp_damask_h +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/ksh -# 1st arg: $DIR -# 2nd arg: $DIRJOB -# 3rd arg: $user -# 4th arg: $program -DIR=$1 -user=$3 -program=$4 -usernoext=$user -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - -# add BLAS options for linking - BLAS="%BLAS%" - -. $DIR/tools/include -DIRJOB=$2 -cd $DIRJOB -echo "Compiling and linking user subroutine $user on host `hostname`" -echo "program: $program" - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - userobj=$usernoext.o - - - $LOAD ${program} $DIR/lib/main.o\ - $DIR/lib/blkdta.o $DIR/lib/comm?.o \ - ${userobj-} \ - $DIR/lib/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ../lib/mdsrc.a \ - ../lib/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $BLAS \ - $SYSLIBS || \ - { - echo "$0: link failed for $usernoext.o on host `hostname`" - exit 1 - } - /bin/rm $userobj - /bin/rm $DIRJOB/*.mod diff --git a/installation/mods_MarcMentat/2016/Marc_tools/comp_damask_l b/installation/mods_MarcMentat/2016/Marc_tools/comp_damask_l deleted file mode 100644 index 31b5cd175..000000000 --- a/installation/mods_MarcMentat/2016/Marc_tools/comp_damask_l +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/ksh -# 1st arg: $DIR -# 2nd arg: $DIRJOB -# 3rd arg: $user -# 4th arg: $program -DIR=$1 -user=$3 -program=$4 -usernoext=$user -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - -# add BLAS options for linking - BLAS="%BLAS%" - -. $DIR/tools/include -DIRJOB=$2 -cd $DIRJOB -echo "Compiling and linking user subroutine $user on host `hostname`" -echo "program: $program" - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - userobj=$usernoext.o - - - $LOAD ${program} $DIR/lib/main.o\ - $DIR/lib/blkdta.o $DIR/lib/comm?.o \ - ${userobj-} \ - $DIR/lib/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ../lib/mdsrc.a \ - ../lib/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $BLAS \ - $SYSLIBS || \ - { - echo "$0: link failed for $usernoext.o on host `hostname`" - exit 1 - } - /bin/rm $userobj - /bin/rm $DIRJOB/*.mod diff --git a/installation/mods_MarcMentat/2016/Marc_tools/run_damask b/installation/mods_MarcMentat/2016/Marc_tools/run_damask deleted file mode 100644 index 0fc2e639a..000000000 --- a/installation/mods_MarcMentat/2016/Marc_tools/run_damask +++ /dev/null @@ -1,4112 +0,0 @@ -#!/bin/ksh -############################################################################## -# # -# run_marc - run a marc job # -# ------------------------- # -# # -# usage: run_marc -j jid { options } # -# # -# where standard options are: required: defaults: # -# -------------------------- # -# # -# -j* jid job id number. ** YES ** . # -# -pr* prog program name. . marc # -# -v* y|n do or do not verify inputs. . yes # -# -q* s|l|v|b|f batch queue name or background, . short # -# foreground. # -# -b* as alternative to option -q* # -# # -# ( batch queues only : # -# -pq* intra queue priority. . . # -# -at DATE/TIME delay start of job. . . # -# format : January,1,1990,12:31 # -# or : today,5pm # -# -cpu* secs job CPU limit . . ) # -# # -# -r* rid restart file job id. . . # -# -si* sid substructure file id. . . # -# -pi* post post file job id. . . # -# -de* did defaults file . no # -# -vf vid viewfactor . no # -# # -# -u* user user subroutine. . . # -# -obj obj user objects or libraries. . . # -# -sa* y|n do or do not save load module. . no # -# -autorst auto restart flag for auto forge . no # -# -me manual remeshing control . no # -# -ml memory limit in Mbyte # -# -mo This option is deprecated. As of Marc 2015, only # -# the integer*8 version is available. # -# -mpi selects MPI version # -# each platform has a default MPI version and some # -# have an alternative version. see the include file # -# for the respective platform # -# MPI_DEFAULT defines the default MPI version # -# MPI_OTHER defines versions one can switch to # -# -dcoup for contact decoupling # -# currently not supported # -# -dir directory where the job i/o should take place. # -# defaults to current directory. # -# -sdir directory where scratch files are created # -# defaults to current directory. # -# # -# -alloc only perform memory allocation test, no analysis # -# -list y only list options in the input file, no analysis # -# -fe num set feature number "num" for the run. only one allowed # -# -dytran flag to switch from Dytran to Marc # -# dytran = 0, program will run w/o Marc-Dytran Switch # -# = 1, program will restart Marc after Dytran run # -# >= 2, Not supported yet. # -# currently not supported # -# -ou force analysis to use out-of-core control # -# =0, not used # -# =1, element storage out-of-core # -# -dll run marc using shared library libmarc.so and exe_marc # -# =1, used # -# =2, do not free streaming input memory # -# =3, run with marc input deck # -# -trk run marc for post-tracking # -# -gpuid run marc using GPGPU capability # -# specify gpuid on to be used in the analysis. Multiple # -# IDs may be assigned for DDM runs. # -# Separate a list of IDs with a colon. Each DMP # -# process will be assigned a GPU ID in round robin fastion# -# = 0 # -# = 0:1 etc... # -# # -# where parallel options are: # -# -------------------------- # -# # -# itree, host, and comp options are available for the domain # -# decomposition only. # -# MARC_NUMBER_OF_THREADS, nthread, and dir options always available. # -# # -# # -# -nprocd number of domains. # -# defaults to single domain solution. # -# -nprocds number of domains if single input file. # -# defaults to single domain solution. # -# -nps same as -nprocds. # -# -nsolver number of solver tasks for solver types 12 and 13 # -# these are distributed tasks operating via MPI # -# -nthread_elem number of threads for element assembly and recovery # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by element assembly # -# recovery. # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_elem option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_elem specified. # -# -nthread_solver number of threads for solver types 6, 8, and 11 # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by 6, 8, and 11 # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_solver option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_solver specified. # -# -nthread Same as -nthread_solver. # -# -itree message passing tree type for domain decomposition. # -# for debugging purposes; should not normally be used. # -# -host hostfile name for distributed execution on network. # -# defaults to no hostfile, unless jobid.defhost exists. # -# if jobid.defhost exists, only -np(s) necessary # -# -comp* y|n to be used with user routines on a network of # -# incompatible machines. # -# if set to no, a separate executable will be created # -# for each machine on the network. # -# if set to yes, the executable located on the machine # -# from which marc is started will be used on all machines.# -# defaults to no if O/S versions different on machines. # -# # -# -ci y|n copy input files to remote hosts (default: yes) # -# if "yes", input files are automatically copied to # -# remote hosts for a network run if necessary. # -# -cr y|n copy post files from remote hosts (default: yes) # -# if "yes", post files are automatically copied back from # -# remote hosts for a network run if necessary. # -############################################################################## -# set DIR to the directory in which this script is -REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`" -DIR=`dirname $REALCOM` -# make sure DIR has an absolute path -case $DIR in - \/*) - ;; - *) - DIR=`pwd`/$DIR - ;; -esac -DIRSCRIPT=$DIR -AWK=awk -ARCH=`uname -a | cut -f 1 -d " "` -# Sun has a bad awk, use nawk instead -if test $ARCH = "SunOS" -then - AWK=nawk -fi -BASENAME=basename -# Sun has an incorrect /bin/basename, check if /usr/ucb/basename exists -if test $ARCH = "SunOS" -then - if test -x /usr/ucb/basename - then - BASENAME=/usr/ucb/basename - fi -fi - -# echo command line in the case of ECHO_COMMAND is true -if test "$ECHO_COMMAND" = true ; then - echo command "$0" "$@" -fi - -# -# "mode" selects version, i4 or i8 -# default is i4 -# this can be changed by a file run_marc_defaults -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MODE i8 -# it can also be set by the environmental variable MARC_INTEGER_SIZE -# and by the command line option "-mo" -# -mode= -modeerror= -modeoption= -if test -f $DIRSCRIPT/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $DIRSCRIPT/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $DIRSCRIPT/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $DIRSCRIPT/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -f $HOME/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $HOME/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $HOME/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $HOME/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -n "$MARC_INTEGER_SIZE" ; then - mode=$MARC_INTEGER_SIZE -fi -if test -z "$mode" ; then - mode=i8 -fi -case $mode in - i4) - modeerror="bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - modeoption=error - echo $modeerror - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo "bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - exit - ;; -esac - -setmode=false -for arg in $* ; do - if $setmode ; then - mode=$arg - case $mode in - i4) - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo " " - echo "error, version mode must be i8" - echo " " - echo " use -mo i8 " - echo " " - exit - ;; - esac - setmode=false - fi - if [ ${arg}X = -moX -o ${arg}X = -MOX ] ; 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then - gpuoption= -else - gpuoption="-gp $gpuids" -fi - -if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH -else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH -fi -# Linux 64 + HPMPI, Below code is taken from include_linux64 -if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" -then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" -fi - -if test $nprocd -gt 1; then - if test -f $jid$dotdefhost; then - if test "$host" = ""; then - host=$jid$dotdefhost - fi - fi - if test -f hostfile_qa_$nprocd; then - if test "$host" = ""; then - host=hostfile_qa_$nprocd - fi - fi -fi - -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$dllrun" -eq 1 || test "$dllrun" -eq 2; then - dotdat=.inp - fi - - if test "$progdll"; then - /bin/cp ${progdll}_$marcdll $DIRJOB/$marcdll - rmdll=yes - pathdll=yes - progdll=${progdll}_$marcdll - else - progdll=$marcdll - fi - - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - pathdll=yes - fi -fi - -############################################################################## -# check parameter validity # -############################################################################## - -while test forever; do - -# -# check for input file existence -# -if test $nprocdddm -gt 1 -a $icreated -eq 0; then - if test ! -f $DIRJID/1$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/1$jid$dotdat not accessible" - fi - fi -else - if test ! -f $DIRJID/$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/$jid$dotdat not accessible" - fi - fi -fi - if test $nprocd -gt 1; then - if test "$host" ; then - if test ! -f $host; then - error="$error -host name file $host not accessible" - fi - fi - fi - -# -# check if the job is already running in the background -# -if test -f $DIRJOB/$jid.pid; then - error="$error -job is already running (the file $jid.pid exists)" -fi - -# -# if the program name is other than marc, then -# assume that this is a program in the users local directory -# - -bd=$MARC_BIN/ - -case $prog in - marc | MARC | $exefile) - program=$exefile - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 or $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - if test ! -f $user - then - error="$error -user subroutine file $user not accessible" - fi - fi - if test "$objs" - then - missingobjs= - for o in $objs - do - if test ! -f "$o" - then - if test -z "$missingobjs" - then - missingobjs="$o" - else - missingobjs="$missingobjs $o" - fi - fi - done - if test -n "$missingobjs" - then - error="$error -user object/library file(s) $missingobjs not accessible" - fi - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$vid" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRVID/1$vid.vfs - then - error="$error -view factor file $DIRVID/1$vid.vfs not accessible" - fi - else - if test ! -f $DIRVID/$vid.vfs - then - error="$error -view factor file $DIRVID/$vid.vfs not accessible" - fi - fi - fi - if $mpioption - then - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE (valid: $MPI_OTHER)" - fi - fi - ;; - *) - program=$prog.marc - case $prog in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 and $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - error="$error -program option may not be used with user subroutine" - fi - if test "$objs" - then - error="$error -program option may not be used with user objects or libraries" - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$nauto" - then - if test $nauto -gt 2 - then - error="$error -incorrect option for auto restart " - fi - fi - if test "$ndcoup" - then - if test $ndcoup -gt 3 - then - error="$error -incorrect option for contact decoupling " - fi - fi - if test "$ndytran" - then - if test $ndytran -gt 1 - then - error="$error -incorrect option for Marc-Dytran Switch " - fi - fi - if $mpioption - then - if test ! -x $MARC_BIN/$exefile - then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE " - fi - fi - ;; -esac - -############################################################################## -# check argument integrity # -############################################################################## - -if test "$jid" -then - : -else - if test "$user" - then -# allow user sub without giving job id - qid=foreground - verify=no - else - error="$error -job id required" -fi -fi - -if test $nprocd -gt 1 -then - if test $nauto -gt 0 - then - error="$error -cannot run DDM job with auto restart (-au) option " - fi -fi -case $qid in - S* | s*) - qid=short - ;; - L* | l*) - qid=long - ;; - V* | v*) - qid=verylong - ;; - B* | b*) - qid=background - ;; - F* | f*) - qid=foreground - ;; - A* | a*) - qid=at - ;; - *) - error="$error -bad value for queue_id option" - ;; -esac - -case $prgsav in - N* | n*) - prgsav=no - ;; - Y* | y*) - prgsav=yes - ;; - *) - error="$error -bad value for save option" - ;; -esac - -case $verify in - N* | n*) - verify=no - ;; - Y* | y*) - verify=yes - ;; - *) - error="$error -bad value for verify option" - ;; 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then - echo "DDM with ARC Mapper : $ddm_arc" >> $jid.log -fi -echo \ -"Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto " >> $jid.log -deletelog=no -fi -echo \ -" -Program name : $prog -Marc shared lib : $progdll -Version type : $mode -Job ID : $DIRJID/$jid -User subroutine name : $user -User objects/libs : $objs -Restart file job ID : $rid -Substructure file ID : $sid -Post file job ID : $pid -Defaults file ID : $did -View Factor file ID : $vid -Save generated module: $prgsav -MPI library : $MPITYPE -DDM processes : $nprocdddmprint -Element loop threads : $nteprint -Solver processes : $nsolverprint -Solver threads : $ntsprint" -if test "$iprintsimufact" = true ; then - echo "DDM with ARC Mapper : $ddm_arc" -fi -echo \ -"GPGPU option : $gpuids -Host file name : $host -Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto" - - -case $qid in - s* | S* | l* | L* | v* | V* ) - echo \ -"Queue priority : $priority -Queue CPU limit : $cpu -Queue start time : $att" - ;; -# * ) -# echo \ -#" " -# ;; -esac - -if test "$modeoption" -then - error=$modeerror -fi - -if test "$error" -then - if test $verify = yes - then - $ECHO "$error - -Please correct or quit(correct,quit,): $ECHOTXT" - error= - read answer - case $answer in - q* | Q*) - answer=quit - ;; - *) - answer=correct - ;; - esac - else - $ECHO "$error - $ECHOTXT" - echo " " - if test "$deletelog" = no - then - $ECHO "$error - $ECHOTXT" >> $jid.log - echo " " >> $jid.log - fi - answer=quit - fi -else - if test $verify = yes - then - $ECHO " -Are these parameters correct (yes,no,quit,)? $ECHOTXT" - read answer - case $answer in - q* | Q*) - answer=quit - ;; - y* | Y*) - answer=yes - ;; - *) - answer=no - ;; - esac - else - answer=yes - fi -fi - -case $answer in - no | correct) - -############################################################################## -# prompt for each value # -############################################################################## - - $ECHO " -Program name ($prog)? $ECHOTXT" - read value - if test "$value" - then - prog=$value - fi - $ECHO "Job ID ($jid)? $ECHOTXT" - read value - if test "$value" - then - jid=`$BASENAME $value $dotdat` - DIRJID=`dirname $value` - case $DIRJID in - \/*) - ;; 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then - gpuoption= - else - gpuoption="-gp $gpuids" - fi - if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH - fi - if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" - then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" - fi -# - if test $nprocd -gt 1 - then - $ECHO "Message passing type ($itree)? $ECHOTXT" - read value - if test "$value" - then - itree=$value - fi - $ECHO "Host file name ($host)? $ECHOTXT" - read value - if test "$value" - then - host=$value - fi - if test $nprocdddm -gt 1 - then - $ECHO "Single input file? $ECHOTXT" - read value - case $value in - y* | Y*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - $ECHO "Compatible machines for DDM ($compatible)? $ECHOTXT" - read value - if test "$value" - then - compatible=$value - fi - $ECHO "Copy input files to remote hosts ($cpinput)? $ECHOTXT" - read value - if test "$value" - then - cpinput=$value - fi - $ECHO "Copy post files from remote hosts ($cpresults)? $ECHOTXT" - read value - if test "$value" - then - cpresults=$value - fi - fi - fi - $ECHO "Run the job in the queue ($qid)? $ECHOTXT" - read value - if test "$value" - then - qid=$value - fi - case $qid in - s* | S* | l* | L* | v* | V* ) - $ECHO "Queue priority ($priority)? $ECHOTXT" - read value - if test "$value" - then - priority=$value - fi - $ECHO "Job starts at ($att)? $ECHOTXT" - read value - if test "$value" - then - att=$value - fi - $ECHO "Queue CPU limit ($cpu)? $ECHOTXT" - read value - if test "$value" - then - cpu=$value - fi - ;; - * ) - ;; - esac - $ECHO "Auto Restart option ($nauto)? $ECHOTXT" - read value - if test "$value" - then - nauto=$value - fi - $ECHO "Run directory ($DIRJOB)? $ECHOTXT" - read value - if test "$value" - then - DIRJOB=$value - DIRSCR=$DIRJOB - fi - $ECHO "Scratch directory ($DIRSCR)? $ECHOTXT" - read value - if test "$value" - then - DIRSCR=$value - fi - ;; - quit) - exit 1 - ;; - *) - break - ;; - -esac - - if test $nt -eq -1 - then - nt=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nt -lt 0 - then - nt=0 - fi - -done -# -if test $nt -eq 0 -then - ntarg= -fi -if test $nt -eq 0 -then - ntprint= -fi -if test $nt -eq 0 -then - nt= -fi - -if test $nte -eq 0 -then - ntearg= -fi -if test $nte -eq 0 -then - nteprint= -fi -if test $nte -eq 0 -then - nte= -fi - -if test $nts -eq 0 -then - ntsarg= -fi -if test $nts -eq 0 -then - ntsprint= -fi -if test $nts -eq 0 -then - nts= -fi -# -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - pathdll=yes - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - fi - - if test "$pathdll"; then -# -# reset share lib path -# - if test $MACHINENAME = "HP" - then - SHLIB_PATH=$DIRJOB:$SHLIB_PATH - export SHLIB_PATH - fi - if test $MACHINENAME = "IBM" - then - LIBPATH=$DIRJOB:$LIBPATH - export LIBPATH - fi -# - LD_LIBRARY_PATH=$DIRJOB:$LD_LIBRARY_PATH - LD_LIBRARY64_PATH=$DIRJOB:$LD_LIBRARY64_PATH - LD_LIBRARYN32_PATH=$DIRJOB:$LD_LIBRARYN32_PATH - export LD_LIBRARY_PATH - export LD_LIBRARY64_PATH - export LD_LIBRARYN32_PATH - fi -fi -# end of dllrun>0 - - -if test $program = $exefile -o $program = $prog.marc -then - -# delete the old .log file unless we run in the background -if test "$deletelog" = yes -then - if test "$jid" - then - /bin/rm $jid.log 2>/dev/null - fi -else - echo - echo running the job in the background, see $jid.log - echo -fi - -# -# check if this is an autoforge or rezoning or radiation job -# -if test $nprocd -eq 1 -a "$jid" - -then - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^autoforge"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^rezoning"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^radiation"` - if test "$line" - then - autoforge=1 - fi -fi -# -# check that jobname for restarted run is not the same -# as restart file basename -# -if test "$rid" -then - if test "$jid" = "$rid" - then - echo " " - echo "ERROR: job name of current run is the same as job name" - echo " of the restarted job" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "ERROR: job name of current run is the same as job name" >> $jid.log - echo " of the restarted job" >> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi -fi - -# -# user objects/libraries used -# - - if test "$objs" - then - program="$DIRJOB/$jid.marc" - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# user subroutine used -# -# add DAMASK options for linking - DAMASK="-lstdc++" - - if test "$user" - then - program=$usernoext.marc - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# Special case for IBM using POE but not an SP machine -# in this case we always need a host file, also for serial jobs. -# -if test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP -then - MP_HOSTFILE=${jid}.host - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $nprocd -gt 1 - then - numdom=$nprocd - while test $numdom -gt 0 - do - hostname -s >> $MP_HOSTFILE - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - else - hostname -s > $MP_HOSTFILE - fi -fi -# -# check ssh for all hosts in host file -# -if test $nprocd -gt 1 -then -if test $MPITYPE = "intelmpi" -a "$INTELMPI_VERSION" = "HYDRA" - then -# get host list - if test "$host" - then - line=`grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' | uniq` -# count failing hosts - counter=0 - for i in $line - do - $RSH -o BatchMode=yes -o ConnectTimeout=10 $i uname -n - status=$? - if [[ $status != 0 ]] ; then - counter=$((counter+1)) - if [ "$counter" = "1" ]; then - echo " " - echo " error - connection test failed... " - echo " " - fi - echo " " - echo " connection test with ssh failed on host $i" - echo " check the following command: ssh $i uname -n " - echo " " - fi - done -# echo error message and quit - if test $counter -ne 0 - then - echo " " - echo " A parallel job using IntelMPI cannot be started. " - echo " The ssh command must be working correctly between " - echo " the computers used in the analysis. Furthermore, " - echo " it must be set up such that it does not prompt the " - echo " user for a password. " - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo " A parallel job using IntelMPI cannot be started. ">> $jid.log - echo " The ssh command must be working correctly between ">> $jid.log - echo " the computers used in the analysis. Furthermore, ">> $jid.log - echo " it must be set up such that it does not prompt the ">> $jid.log - echo " user for a password. ">> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi -fi -fi -# -# check correctness of host file; fix for user sub -# - if test $nprocd -gt 1 - then - -# construct the path name to the executable (execpath) - execpath=$MARC_BIN/$exefile - usersub=0 - if test $program = $prog.marc - then - execpath=$prog.marc - usersub=1 - fi - if test "$objs" - then - execpath="$DIRJOB/$jid.marc" - usersub=1 - fi - if test "$user" - then - execpath=$usernoext.marc - usersub=1 - fi - export execpath - execname=`$BASENAME $execpath` - - if test "$host" - then - userhost=$host - case $userhost in - \/* | \.\/*) - ;; - *) - userhost=`pwd`/$userhost - ;; - esac - -# check that the number of processes specified in the hostfile is -# equal to nprocd specified by -nprocd. - numproc=`grep -v '^#' $host | $AWK -v sum=0 '{sum=sum+$2}; END {print sum}'` - if test $nprocd -ne $numproc - then - echo " " - echo "error, the number of processes specified in the host file" - echo "must be equal to the number of processes given by -nprocd/-nsolver" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, the number of processes specified in the host file" >> $jid.log - echo "must be equal to the number of processes given by -nprocd/-nsolver" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - -# check for Myrinet that the number of processes per host is -# less than number of available user ports, 5 -# .gmpi directory must exist in user's home directory -# and must have write permission from remote hosts - if test $MPITYPE = "myrinet" - then - numproc=`grep -v '^#' $host | $AWK -v sum=1 '{if( $2 > 5) sum=6}; END {print sum}'` - if test $numproc -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes specified " - echo "in the hostfile must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes specified " >> $jid.log - echo "in the hostfile must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - if test ! -d ~/.gmpi - then - echo " " - echo "error, for Myrinet a .gmpi directory must exist " - echo "under the user's home directory" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a .gmpi directory must exist " >> $jid.log - echo "under the user's home directory" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - homedir=`echo ~` - for i in `grep -v '^#' $host | $AWK '{if (NF > 0) print $1}'` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - $RSH $i /bin/touch $homedir/.gmpi/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - echo " " - echo "error, for Myrinet a shared .gmpi directory must exist " - echo "under the user's home directory " - echo "with remote write permission" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a shared .gmpi directory must exist " >> $jid.log - echo "under the user's home directory " >> $jid.log - echo "with remote write permission" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - else - /bin/rm tmp.$$ - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - fi - fi - done - fi - fi - -# construct the host file $jid.host which is used by mpirun -# skip lines starting with # and only consider lines with more than -# one word in them. Note that the hostfile given to this script -# has two columns: the host name and the number of shared processes -# to run on this host. mpirun wants the number of _other_ -# processes to run in addition to the one being run on the machine -# on which the job is started. hence the $2-1 for fnr == 1. - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then -# HPMPI or HP hardware MPI - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ - -v mpihpspecial="$MPIHPSPECIAL" \ -'{if ( NF > 0) {\ - fnr++ ; \ - printf("-h %s -np %s",$1,$2); \ - printf(" %s",mpihpspecial); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF >= 3 ) printf(" -e MPI_WORKDIR=%s", $3);\ - if ( NF >= 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) \ - }\ - }' > $jid.host -# end HPMPI or HP hardware MPI - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then -# IBM using hardware MPI (POE) - MP_HOSTFILE=$jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.host -# end IBM using hardware MPI (POE) -# for Intel MPI, need to create a machinefile for DMP - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then -# Intel MPI - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - /bin/cp $host $jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Intel MPI for DMP -# for Solaris HPC 7.1, need to create a machinefile for DMP - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then -# Solaris HPC 7.1 - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Solaris HPC 7.1 for DMP -# for Myrinet, construct a configuration file in ~/.gmpi -# this must be readable by each process -# format is (hostname) (port number) for each process - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - grep -v '^#' $host | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ -{if ( NF > 0 ) \ - for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc]); \ -}' >> ~/.gmpi/$jid.host - else -# this is for mpich-1.2.5 and later, using the -pg option -# format: host nproc executable user arguments -# the arguments are added later - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub -v user=`whoami` \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s %s\n",path,user);\ - if ( NF == 3 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s %s\n",path,user) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s/bin/%s %s\n",$4,en,user) \ - }\ - }' > $jid.host - fi -# end Myrinet - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then -# Compaq MPI via Memory Channel - grep -v '^#' $host | $AWK '{if (NF > 0) print $1}' > $jid.host -# end Compaq MPI - else -# MPICH - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF == 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s/bin/%s\n",$4,en) \ - }\ - }' > $jid.host - fi -# define the variable host and host_filt -# host_filt is used for loops over hosts -# for Myrinet we need to use a filtered variant of userhost -# for others we can use $host - if test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - host=~/.gmpi/$jid.host - host_filt=$jid.host_tMp - grep -v '^#' $userhost | $AWK '{if (NF > 0) print $1}' > $host_filt - else - host=$jid.host - host_filt=$host - fi - else - host=$jid.host - host_filt=$host - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - host_filt=$jid.mfile - fi - fi -# figure out if the machines in the hostfile are nfs mounted -# or distributed and set the variable "dirstatus" accordingly. -# only perform the check if user subroutine is used -# or a user subroutine executable is used - - numfield=1 - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - numfield=2 - fi - DIR1=$DIRJOB - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - counter=0 - echo " " - echo "checking if local or shared directories for host" - if test "$deletelog" = no - then - echo "checking if local or shared directories for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - dirstatus[$counter]="shared" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - $RSH $i /bin/touch $DIR1/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - dirstatus[$counter]="local" - /bin/rm tmp.$$ - else - if test ! -f $jid.$$ - then - dirstatus[$counter]="local" - $RSH $i /bin/rm $DIR1/$jid.$$ - else - /bin/rm $jid.$$ - fi - fi - if test -f tmp.$$ - then - /bin/rm tmp.$$ - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - echo " ${dirstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${dirstatus[$counter]}" >> $jid.log - fi - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - fi - -# figure out if this is a compatible set of machines -# unless explicitly specified with flag -comp -# only perform the check if user subroutine is used -# or a user subroutine executable is used -# Myrinet does not support heterogeneous - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - if test $compatible = "unknown" - then - thisname=$ARCH - compatible=yes - counter=0 - echo "checking if machines are compatible for host" - if test "$deletelog" = no - then - echo "checking if machines are compatible for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]="yes" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - othername=`$RSH $i uname -a | cut -f 1 -d " "` - if test $thisname != $othername - then - compatible=no - compstatus[$counter]="no" - fi - fi - echo " ${compstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${compstatus[$counter]}" >> $jid.log - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - else - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]=$compatible - fi - done - if test $compatible = "no" - then - echo "all machines assumed incompatible" - if test "$deletelog" = no - then - echo "all machines assumed incompatible" >> $jid.log - fi - else - echo "all machines compatible" - if test "$deletelog" = no - then - echo "all machines compatible" >> $jid.log - fi - fi - fi -# error out if user objects or libraries are used on incompatible machines - if test "$compatible" = "no" -a -n "$objs" - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" - if test "$deletelog" = no - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" >> $jid.log - fi - exit 1 - fi -# modify new host file if NFS mounted heterogeneous machine - doit= - if test $program = $prog.marc - then - doit=yes - fi - if test "$user" - then - doit=yes - fi - if test "$doit" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - $AWK -v hst=$i '{fnr++ ; \ -if ($1 ~ hst) {if ( fnr == 1 ) printf("%s\n",$0); else \ -printf("%s %s %s_%s\n",$1,$2,$3,$1) } else print}' $jid.host > $jid.host{$$} - /bin/mv $jid.host{$$} $jid.host - host=$jid.host - fi - fi - done - fi - fi # if test $program = $prog.marc -o $user -o $obj - - else # if test $host - # assume shared memory machine if no hostfile given and - # MPITYPE is set to mpich or Myrinet - # check for Myrinet that the total number of processes is - # less than number of available user ports, 5 - if test $MPITYPE = "mpich" -o $MPITYPE = "scali" - then - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - host=$jid.host - elif test $MPITYPE = "myrinet" - then - if test $nprocd -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes " - echo "must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes " >> $jid.log - echo "must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - echo `hostname` $nprocd | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ - {for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc])} \ -' >> ~/.gmpi/$jid.host - host=~/.gmpi/$jid.host - else - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - - fi - fi # if test myrinet - - fi # if test $host - - fi # if test $nprocd -gt 1 - -fi # if test $program = $exefile -o $program = $prog.marc - -############################################################################## -# construct run stream (Marc only) # -############################################################################## - -# set maximum message length for ddm to a large number -# for vendor provided mpi -if test $itree -eq 0 -a $MPITYPE = hardware -then - itree=100000000 - if test $MACHINENAME = SGI - then - itree=100000001 - fi -fi -if test $itree -eq 0 -a $MPITYPE = hpmpi -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = myrinet -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = nec -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = scali -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = intelmpi -then - itree=100000000 -fi -if test $nprocdddm -lt 2 -then - nprocdarg= -else - nprocdarg="$nprocdarg $nprocdddm" -fi -if test $nsolver -eq 0 -then - nsolverarg= -else - nsolverarg="$nsolverarg $nsolver" -fi -if test $nprocdddm -lt 2 -a $nsolver -eq 0 -then -nprocd=0 -fi -if test $nprocd -gt 0 -then - if test "$host" - then - if test -z "$RUN_JOB2" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $host -- -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then - RUN_JOB="$RUN_JOB2 $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB_TMP="$RUN_JOB2 $host $bd$program" - RUN_JOB=" -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $nprocd -hf $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - numhost=`uniq $jid.mfile | wc -l` - if test "$INTELMPI_VERSION" = "HYDRA" - then - RUN_JOB_TMP="$RUN_JOB2 -configfile $jid.cfile" - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n $numhost -r $RSH -f $jid.mfile - RUN_JOB_TMP="$RUN_JOB2 $jid.cfile" - fi - -# intelmpi uses configfile. format: -# -host host1 -n n1 executable marcargs -# one such line per host -# collect the marcargs in RUN_JOB and construct the config file later -# collect the run stream in RUN_JOB_TMP - RUN_JOB="-jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - - - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then - RUN_JOB="$RUN_JOB2 $jid.mfile -n $nprocd $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test "$userhost" - then - RUN_JOB="$RUN_JOB -mhost $userhost" - fi - if test $MPITYPE = "scali" - then -# set default working directory to /tmp to allow -# different directory names - SCAMPI_WORKING_DIRECTORY=/tmp - export SCAMPI_WORKING_DIRECTORY - fi - else - if test -z "$RUN_JOB1" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - RUNNPROCD=$nprocd - if test $MACHINENAME = "IBM" -a $MPITYPE = "hardware" - then - RUNNPROCD= - MP_PROCS=$nprocd - export MP_PROCS - fi - if test $MPITYPE = "myrinet" - then - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - echo " " > /dev/null - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n 1 -f $jid.hosts - fi - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - fi -else - if test $nauto -gt 0 -o $ndcoup -gt 0 - then - RUN_JOB="$RUN_JOB0 $BINDIR/exe_auto $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else -# this is for a serial job without auto restart: - RUN_JOB="$RUN_JOB0 $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi -fi -if test "$rid" -then - RUN_JOB="$RUN_JOB -rid $rid -dirrid $DIRRID" -fi -if test "$pid" -then - RUN_JOB="$RUN_JOB -pid $pid -dirpid $DIRPID" -fi -if test "$sid" -then - RUN_JOB="$RUN_JOB -sid $sid -dirsid $DIRSID" -fi -if test "$did" -then - RUN_JOB="$RUN_JOB -def $did -dirdid $DIRDID" -fi -if test "$vid" -then - RUN_JOB="$RUN_JOB -vf $vid -dirvid $DIRVID" -fi -if test $nauto -gt 0 -then - RUN_JOB="$RUN_JOB -autorst $nauto " -fi -if test $ndcoup -gt 0 -then - RUN_JOB="$RUN_JOB -dcoup $ndcoup " -fi -if test $ndytran -gt 0 -then - RUN_JOB="$RUN_JOB -dytran $ndytran " -fi -if test $mesh -gt 0 -then - RUN_JOB="$RUN_JOB -me $mesh " -fi -if test $noutcore -gt 0 -then - RUN_JOB="$RUN_JOB -outcore $noutcore " -fi -if test "$dllrun" -gt 0 -then - RUN_JOB="$RUN_JOB -dll $dllrun " -fi -if test "$trkrun" -gt 0 -then - RUN_JOB="$RUN_JOB -trk $trkrun " -fi -if test "$iam" -then - RUN_JOB="$RUN_JOB -iam $iam " -fi -if test "$justlist" -then - RUN_JOB="$RUN_JOB -list 1 " -fi -if test "$feature" -then - RUN_JOB="$RUN_JOB -feature $feature " -fi -if test "$memlimit" -ne 0 -then - RUN_JOB="$RUN_JOB -ml $memlimit " -fi -if test "$cpinput" -then - RUN_JOB="$RUN_JOB -ci $cpinput " -fi -if test "$cpresults" -then - RUN_JOB="$RUN_JOB -cr $cpresults " -fi -if test "$DIRSCR" != "$DIRJOB" -then - RUN_JOB="$RUN_JOB -dirscr $DIRSCR" -else - DIRSCR=$DIRJOB -fi -if test "$makebdf" -then - RUN_JOB="$RUN_JOB -bdf $makebdf " -fi -if test $MPITYPE = "myrinet" -a "$host" -a "$MPIVERSION" != "MPICH-GM1.2.1..7" -then - # append $RUN_JOB to all lines of the host file - # and set RUN_JOB - $AWK -v args="$RUN_JOB" '{print $0,args}' $host > $host.$$ - /bin/mv $host.$$ $host - RUN_JOB=$RUN_JOB_TMP -fi -if test $MPITYPE = "intelmpi" -a "$host" -then - # construct config file, append $RUN_JOB to all lines of the config file - # and set RUN_JOB - if test "$INTELMPI_VERSION" = "HYDRA" - then - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf(" -host %s",$1); \ - printf(" -n %s",$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - else - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf("-host %s -n %s",$1,$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - fi - RUN_JOB=$RUN_JOB_TMP -fi -echo " " -echo "Final run stream value" -echo " RUNJOB="$RUN_JOB -if test "$deletelog" = no -then -echo " " >> $jid.log -echo "Final run stream value" >> $jid.log -echo " RUNJOB="$RUN_JOB >> $jid.log -fi - - -############################################################################## -# run marc using valgrind # -############################################################################## -#RUN_JOB="valgrind $RUN_JOB" -#RUN_JOB="valgrind --read-var-info=yes --gen-suppressions=yes $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=all -v $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=yes --error-limit=no $RUN_JOB" -############################################################################## - - -############################################################################## -# run the requested program in a queue # -############################################################################## - -if test "$deletelog" = yes -then - echo - date -else - echo >> $jid.log - date >> $jid.log -fi -if [ $qid = short -o $qid = long -o $qid = verylong -o $qid = at ] -then - -/bin/rm -f $jid.runmarcscript - - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - userobj=$usermoext.o - fi - cat > $jid.runmarcscript << END4 - if test "$user" - then - if test $MACHINENAME = "CRAY" - then - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTRAN $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - $SOLVERLIBS \ - $MARCCUDALIBS \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } -END4 -else - prgsav=yes -fi -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc -# - -cat >> $jid.runmarcscript << END5 - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# first remove all .out files and incremental restart files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - /bin/rm $DIRJOB/$numdom${jid}_i_*.t08 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null - /bin/rm $DIRJOB/${jid}_i_*.t08 2>/dev/null -fi - -if test $nprocdddm -gt 1 -then - $RUN_JOB 2>>$jid.log -else - $RUN_JOB 2>>$jid.log -fi - -if test $dllrun -eq 0; then - if test $prgsav = no - then - /bin/rm -f $bd$program 2>/dev/null - fi -else - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes - then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -fi -END5 - - -# Submit to marc batch queue -# -if [ $qid = at ] -then -QUENAME=at -SUBMCMD= -else -# -# Submit to qsub queue -# -QUENAME=qsub -SUBMCMD="-q $qid -o /dev/null -e $jid.batch_err_log -x -r $jid" -if test "$priority" -then - SUBMCMD=$SUBMCMD" -p $priority" -fi -if test "$att" -then - SUBMCMD=$SUBMCMD" -a $att" -fi -if test "$cpu" -then - SUBMCMD=$SUBMCMD" -lt $cpu" -fi - -fi -echo $QUENAME $SUBMCMD -#cat $jid.runmarcscript -$QUENAME $SUBMCMD < $jid.runmarcscript - -/bin/rm -f $jid.runmarcscript - -############################################################################## -# run the requested program in the background # -############################################################################## - -else -if test $qid = background -then - -# -# first remove all old .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi -# -# compile user subroutine if present -# -( -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - echo " $PRODUCT Exit number 3" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTRAN $user -o $userobj || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - echo " $PRODUCT Exit number 3" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc - -# - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - -$RUN_JOB & - -marcpid=$! -echo $marcpid > $DIRJOB/$jid.pid -wait $marcpid - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - fi - fi - fi -fi - - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi -) 1>>$jid.log 2>&1 & - - -############################################################################## -# run the requested program in the foreground # -############################################################################## - -else - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTRAN $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null -# done if no job id given -if test -z "$jid" -then - echo - echo only compilation requested - echo - exit -fi -# -# run marc -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi -# first remove all .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - $RUN_JOB - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - else - echo " " > /dev/null - fi - else - if test "$host" - then - mpdcleanup -a -f $jid.mfile - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.mfile 2> /dev/null - else - mpdcleanup -a -f $jid.hosts - /bin/rm $jid.hosts 2> /dev/null - fi - fi - fi -fi - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi - - -fi -fi diff --git a/installation/mods_MarcMentat/2016/Marc_tools/run_damask_h b/installation/mods_MarcMentat/2016/Marc_tools/run_damask_h deleted file mode 100644 index 182b5fc25..000000000 --- a/installation/mods_MarcMentat/2016/Marc_tools/run_damask_h +++ /dev/null @@ -1,4112 +0,0 @@ -#!/bin/ksh -############################################################################## -# # -# run_marc - run a marc job # -# ------------------------- # -# # -# usage: run_marc -j jid { options } # -# # -# where standard options are: required: defaults: # -# -------------------------- # -# # -# -j* jid job id number. ** YES ** . # -# -pr* prog program name. . marc # -# -v* y|n do or do not verify inputs. . yes # -# -q* s|l|v|b|f batch queue name or background, . short # -# foreground. # -# -b* as alternative to option -q* # -# # -# ( batch queues only : # -# -pq* intra queue priority. . . # -# -at DATE/TIME delay start of job. . . # -# format : January,1,1990,12:31 # -# or : today,5pm # -# -cpu* secs job CPU limit . . ) # -# # -# -r* rid restart file job id. . . # -# -si* sid substructure file id. . . # -# -pi* post post file job id. . . # -# -de* did defaults file . no # -# -vf vid viewfactor . no # -# # -# -u* user user subroutine. . . # -# -obj obj user objects or libraries. . . # -# -sa* y|n do or do not save load module. . no # -# -autorst auto restart flag for auto forge . no # -# -me manual remeshing control . no # -# -ml memory limit in Mbyte # -# -mo This option is deprecated. As of Marc 2015, only # -# the integer*8 version is available. # -# -mpi selects MPI version # -# each platform has a default MPI version and some # -# have an alternative version. see the include file # -# for the respective platform # -# MPI_DEFAULT defines the default MPI version # -# MPI_OTHER defines versions one can switch to # -# -dcoup for contact decoupling # -# currently not supported # -# -dir directory where the job i/o should take place. # -# defaults to current directory. # -# -sdir directory where scratch files are created # -# defaults to current directory. # -# # -# -alloc only perform memory allocation test, no analysis # -# -list y only list options in the input file, no analysis # -# -fe num set feature number "num" for the run. only one allowed # -# -dytran flag to switch from Dytran to Marc # -# dytran = 0, program will run w/o Marc-Dytran Switch # -# = 1, program will restart Marc after Dytran run # -# >= 2, Not supported yet. # -# currently not supported # -# -ou force analysis to use out-of-core control # -# =0, not used # -# =1, element storage out-of-core # -# -dll run marc using shared library libmarc.so and exe_marc # -# =1, used # -# =2, do not free streaming input memory # -# =3, run with marc input deck # -# -trk run marc for post-tracking # -# -gpuid run marc using GPGPU capability # -# specify gpuid on to be used in the analysis. Multiple # -# IDs may be assigned for DDM runs. # -# Separate a list of IDs with a colon. Each DMP # -# process will be assigned a GPU ID in round robin fastion# -# = 0 # -# = 0:1 etc... # -# # -# where parallel options are: # -# -------------------------- # -# # -# itree, host, and comp options are available for the domain # -# decomposition only. # -# MARC_NUMBER_OF_THREADS, nthread, and dir options always available. # -# # -# # -# -nprocd number of domains. # -# defaults to single domain solution. # -# -nprocds number of domains if single input file. # -# defaults to single domain solution. # -# -nps same as -nprocds. # -# -nsolver number of solver tasks for solver types 12 and 13 # -# these are distributed tasks operating via MPI # -# -nthread_elem number of threads for element assembly and recovery # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by element assembly # -# recovery. # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_elem option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_elem specified. # -# -nthread_solver number of threads for solver types 6, 8, and 11 # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by 6, 8, and 11 # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_solver option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_solver specified. # -# -nthread Same as -nthread_solver. # -# -itree message passing tree type for domain decomposition. # -# for debugging purposes; should not normally be used. # -# -host hostfile name for distributed execution on network. # -# defaults to no hostfile, unless jobid.defhost exists. # -# if jobid.defhost exists, only -np(s) necessary # -# -comp* y|n to be used with user routines on a network of # -# incompatible machines. # -# if set to no, a separate executable will be created # -# for each machine on the network. # -# if set to yes, the executable located on the machine # -# from which marc is started will be used on all machines.# -# defaults to no if O/S versions different on machines. # -# # -# -ci y|n copy input files to remote hosts (default: yes) # -# if "yes", input files are automatically copied to # -# remote hosts for a network run if necessary. # -# -cr y|n copy post files from remote hosts (default: yes) # -# if "yes", post files are automatically copied back from # -# remote hosts for a network run if necessary. # -############################################################################## -# set DIR to the directory in which this script is -REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`" -DIR=`dirname $REALCOM` -# make sure DIR has an absolute path -case $DIR in - \/*) - ;; - *) - DIR=`pwd`/$DIR - ;; -esac -DIRSCRIPT=$DIR -AWK=awk -ARCH=`uname -a | cut -f 1 -d " "` -# Sun has a bad awk, use nawk instead -if test $ARCH = "SunOS" -then - AWK=nawk -fi -BASENAME=basename -# Sun has an incorrect /bin/basename, check if /usr/ucb/basename exists -if test $ARCH = "SunOS" -then - if test -x /usr/ucb/basename - then - BASENAME=/usr/ucb/basename - fi -fi - -# echo command line in the case of ECHO_COMMAND is true -if test "$ECHO_COMMAND" = true ; then - echo command "$0" "$@" -fi - -# -# "mode" selects version, i4 or i8 -# default is i4 -# this can be changed by a file run_marc_defaults -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MODE i8 -# it can also be set by the environmental variable MARC_INTEGER_SIZE -# and by the command line option "-mo" -# -mode= -modeerror= -modeoption= -if test -f $DIRSCRIPT/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $DIRSCRIPT/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $DIRSCRIPT/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $DIRSCRIPT/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -f $HOME/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $HOME/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $HOME/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $HOME/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -n "$MARC_INTEGER_SIZE" ; then - mode=$MARC_INTEGER_SIZE -fi -if test -z "$mode" ; then - mode=i8 -fi -case $mode in - i4) - modeerror="bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - modeoption=error - echo $modeerror - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo "bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - exit - ;; -esac - -setmode=false -for arg in $* ; do - if $setmode ; then - mode=$arg - case $mode in - i4) - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo " " - echo "error, version mode must be i8" - echo " " - echo " use -mo i8 " - echo " " - exit - ;; - esac - setmode=false - fi - if [ ${arg}X = -moX -o ${arg}X = -MOX ] ; then - echo - echo warning: the option -mo is deprecated, as of Marc 2015, only the integer*8 version is available - echo - setmode=true - fi - if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - fi - if [ ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - fi -done - -# set to i4 version for 32 bit Linux -if test "`uname -s`" = "Linux"; then - if test "`uname -m`" = "i686"; then - mode=i4 - MARC_INTEGER_SIZE=i4 - export MARC_INTEGER_SIZE - fi -fi - - -. "$DIR/getarch" - - -# getting user subroutine file name -found=0 -for i in "$@"; do - if test $found = 1; then - DAMASK_USER=$i - found=0 - fi - case $i in - -u* | -U*) - found=1 - ;; - esac -done -# sourcing include_linux64 (needs DAMASK_USER to be set) -. $MARC_INCLUDE - -# - -# -# Dynamically determine the echo syntax -# - -case "`echo '\c'`" in - '\c') - ECHO='echo -n' - ECHOTXT=' ' - ;; - *) - ECHO='echo' - ECHOTXT=' \c' - ;; -esac - -# -# Variables for the MARC environment -# - -PRODUCT="Marc" -EXITMSG=$MARC_TOOLS/MESSAGES -export EXITMSG -FLEXDIR=$DIR/../flexlm/licenses -export FLEXDIR -TIMCHK=3600 -export TIMCHK -BINDIR=$MARC_BIN -export BINDIR -AFMATDAT=$MARC_RUNTIME/AF_flowmat/ -export AFMATDAT -export MESHERDIR -MSC_LICENSE_FINPROC=1 -export MSC_LICENSE_FINPROC -# -# define directory path to global unified material database -# -MATFILE= -export MATFILE - -# -# define memory limit -# first set to MEMLIMIT from include -# -ml option overrules if specified -memlimit=$MEMLIMIT -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -# -if test $MACHINENAME = "HP" -then - SHLIB_PATH=$MARC_LIB:$MARC_LIB_SHARED:$SHLIB_PATH - export SHLIB_PATH -fi -# the one for IBM is defined futher down - -LD_LIBRARY_PATH=$MARC_LIB_SHARED:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MARC_LIB:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MESHERDIR:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$SFMATDIR:$LD_LIBRARY_PATH -LD_LIBRARY64_PATH=$MARC_LIB:$LD_LIBRARY64_PATH -LD_LIBRARYN32_PATH=$MARC_LIB:$LD_LIBRARYN32_PATH -export LD_LIBRARY_PATH -export LD_LIBRARY64_PATH -export LD_LIBRARYN32_PATH - -atexit() { -kill -15 $$ -# -if test $MPITYPE = "myrinet" -then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi -fi -} - -trap "atexit" 2 - -# -# defaults -# - -prog=marc -exefile=marc -jid= -rid= -pid= -sid= -did= -vid= -user= -usernoext= -objs= -qid=background -cpu= -priority= -att= -trk= -verify=yes -prgsav=no -rmdll=no -cpdll=no -progdll= -pathdll= -error= -nprocd=0 -nprocdddm=1 -nprocdddmprint= -icreated=0 -nprocdarg= -nsolver=0 -nsolverarg=-ns -if test $nprocds -then - if test $nprocds -gt 1 - then - nprocdddm=$nprocds - nprocdddmprint=$nprocds - icreated=1 - nprocdarg=-nprocds - fi -fi -ntprint=0 -nt=-1 -nte=-1 -nts=-1 -ntarg=-nt -ntearg=-nte -ntsarg=-nts -nteprint= -ntsprint= -gpuids= -nauto=0 -ndcoup=0 -ndytran=0 -noutcore=0 -dllrun=0 -mesh=0 -itree=0 -iam= -ddm_arc=0 -link= -trkrun=0 -DIRJOB=`pwd` -DIRSCR=$DIRJOB -DIRSCRSET= -autoforge=0 -dotdat=.dat -dotdefhost=.defhost -host= -numhost= -mfile= -userhost= -makebdf= -cpinput=yes -cpresults=yes -marcdll=libmarc.$EXT_DLL -# define hostname and strip off extensions (alpha.aaa.com) -thishost=`hostname` -thishost=${thishost%%.*} -compatible=unknown -numfield=1 -justlist= -feature= -mpioption=false -iprintsimufact= -MDSRCLIB=$MARC_LIB/mdsrc.a -# -# check run_marc_defaults file for default MPI setting -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MPI -# -value= -file= -if test -f $DIRSCRIPT/run_marc_defaults; 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then - gpuoption= -else - gpuoption="-gp $gpuids" -fi - -if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH -else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH -fi -# Linux 64 + HPMPI, Below code is taken from include_linux64 -if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" -then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" -fi - -if test $nprocd -gt 1; then - if test -f $jid$dotdefhost; then - if test "$host" = ""; then - host=$jid$dotdefhost - fi - fi - if test -f hostfile_qa_$nprocd; then - if test "$host" = ""; then - host=hostfile_qa_$nprocd - fi - fi -fi - -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$dllrun" -eq 1 || test "$dllrun" -eq 2; then - dotdat=.inp - fi - - if test "$progdll"; then - /bin/cp ${progdll}_$marcdll $DIRJOB/$marcdll - rmdll=yes - pathdll=yes - progdll=${progdll}_$marcdll - else - progdll=$marcdll - fi - - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - pathdll=yes - fi -fi - -############################################################################## -# check parameter validity # -############################################################################## - -while test forever; do - -# -# check for input file existence -# -if test $nprocdddm -gt 1 -a $icreated -eq 0; then - if test ! -f $DIRJID/1$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/1$jid$dotdat not accessible" - fi - fi -else - if test ! -f $DIRJID/$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/$jid$dotdat not accessible" - fi - fi -fi - if test $nprocd -gt 1; then - if test "$host" ; then - if test ! -f $host; then - error="$error -host name file $host not accessible" - fi - fi - fi - -# -# check if the job is already running in the background -# -if test -f $DIRJOB/$jid.pid; then - error="$error -job is already running (the file $jid.pid exists)" -fi - -# -# if the program name is other than marc, then -# assume that this is a program in the users local directory -# - -bd=$MARC_BIN/ - -case $prog in - marc | MARC | $exefile) - program=$exefile - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 or $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - if test ! -f $user - then - error="$error -user subroutine file $user not accessible" - fi - fi - if test "$objs" - then - missingobjs= - for o in $objs - do - if test ! -f "$o" - then - if test -z "$missingobjs" - then - missingobjs="$o" - else - missingobjs="$missingobjs $o" - fi - fi - done - if test -n "$missingobjs" - then - error="$error -user object/library file(s) $missingobjs not accessible" - fi - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$vid" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRVID/1$vid.vfs - then - error="$error -view factor file $DIRVID/1$vid.vfs not accessible" - fi - else - if test ! -f $DIRVID/$vid.vfs - then - error="$error -view factor file $DIRVID/$vid.vfs not accessible" - fi - fi - fi - if $mpioption - then - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE (valid: $MPI_OTHER)" - fi - fi - ;; - *) - program=$prog.marc - case $prog in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 and $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - error="$error -program option may not be used with user subroutine" - fi - if test "$objs" - then - error="$error -program option may not be used with user objects or libraries" - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$nauto" - then - if test $nauto -gt 2 - then - error="$error -incorrect option for auto restart " - fi - fi - if test "$ndcoup" - then - if test $ndcoup -gt 3 - then - error="$error -incorrect option for contact decoupling " - fi - fi - if test "$ndytran" - then - if test $ndytran -gt 1 - then - error="$error -incorrect option for Marc-Dytran Switch " - fi - fi - if $mpioption - then - if test ! -x $MARC_BIN/$exefile - then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE " - fi - fi - ;; -esac - -############################################################################## -# check argument integrity # -############################################################################## - -if test "$jid" -then - : -else - if test "$user" - then -# allow user sub without giving job id - qid=foreground - verify=no - else - error="$error -job id required" -fi -fi - -if test $nprocd -gt 1 -then - if test $nauto -gt 0 - then - error="$error -cannot run DDM job with auto restart (-au) option " - fi -fi -case $qid in - S* | s*) - qid=short - ;; - L* | l*) - qid=long - ;; - V* | v*) - qid=verylong - ;; - B* | b*) - qid=background - ;; - F* | f*) - qid=foreground - ;; - A* | a*) - qid=at - ;; - *) - error="$error -bad value for queue_id option" - ;; -esac - -case $prgsav in - N* | n*) - prgsav=no - ;; - Y* | y*) - prgsav=yes - ;; - *) - error="$error -bad value for save option" - ;; -esac - -case $verify in - N* | n*) - verify=no - ;; - Y* | y*) - verify=yes - ;; - *) - error="$error -bad value for verify option" - ;; -esac - -case $nprocdddm in - -* ) - error="$error -bad value for nprocd option" - ;; -esac - -case $nt in - -* ) - error="$error -bad value for nt option" - ;; -esac - -case $itree in - -* ) - error="$error -bad value for itree option" - ;; -esac -case $iam in - -* ) - error="$error -bad value for iam option" - ;; -esac -case $compatible in - N* | n*) - compatible=no - ;; - Y* | y*) - compatible=yes - ;; - unknown) - ;; - *) - error="$error -bad value for comp option" - ;; -esac -case $cpinput in - N* | n*) - cpinput=no - ;; - Y* | y*) - cpinput=yes - ;; - *) - error="$error -bad value for copy input option" - ;; -esac -case $cpresults in - N* | n*) - cpresults=no - ;; - Y* | y*) - cpresults=yes - ;; - *) - error="$error -bad value for copy results option" - ;; -esac - -# -# check for external file to run -# -if test -f $MARC_TOOLS/run_marc_check -then - . $MARC_TOOLS/run_marc_check -fi - -############################################################################## -# interact with the user to get the required information to run marc or # -# other marc system program # -############################################################################## - -deletelog=yes -if test $qid = background -a $verify = no -then -echo \ -" -Program name : $prog -Marc shared lib : $progdll -Version type : $mode -Job ID : $DIRJID/$jid -User subroutine name : $user -User objects/libs : $objs -Restart file job ID : $rid -Substructure file ID : $sid -Post file job ID : $pid -Defaults file ID : $did -View Factor file ID : $vid -Save generated module: $prgsav -MPI library : $MPITYPE -DDM processes : $nprocdddmprint -Element loop threads : $nteprint -Solver processes : $nsolverprint -Solver threads : $ntsprint -GPGPU option : $gpuids -Host file name : $host" > $jid.log -if test "$iprintsimufact" = true ; then - echo "DDM with ARC Mapper : $ddm_arc" >> $jid.log -fi -echo \ -"Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto " >> $jid.log -deletelog=no -fi -echo \ -" -Program name : $prog -Marc shared lib : $progdll -Version type : $mode -Job ID : $DIRJID/$jid -User subroutine name : $user -User objects/libs : $objs -Restart file job ID : $rid -Substructure file ID : $sid -Post file job ID : $pid -Defaults file ID : $did -View Factor file ID : $vid -Save generated module: $prgsav -MPI library : $MPITYPE -DDM processes : $nprocdddmprint -Element loop threads : $nteprint -Solver processes : $nsolverprint -Solver threads : $ntsprint" -if test "$iprintsimufact" = true ; then - echo "DDM with ARC Mapper : $ddm_arc" -fi -echo \ -"GPGPU option : $gpuids -Host file name : $host -Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto" - - -case $qid in - s* | S* | l* | L* | v* | V* ) - echo \ -"Queue priority : $priority -Queue CPU limit : $cpu -Queue start time : $att" - ;; -# * ) -# echo \ -#" " -# ;; -esac - -if test "$modeoption" -then - error=$modeerror -fi - -if test "$error" -then - if test $verify = yes - then - $ECHO "$error - -Please correct or quit(correct,quit,): $ECHOTXT" - error= - read answer - case $answer in - q* | Q*) - answer=quit - ;; - *) - answer=correct - ;; - esac - else - $ECHO "$error - $ECHOTXT" - echo " " - if test "$deletelog" = no - then - $ECHO "$error - $ECHOTXT" >> $jid.log - echo " " >> $jid.log - fi - answer=quit - fi -else - if test $verify = yes - then - $ECHO " -Are these parameters correct (yes,no,quit,)? $ECHOTXT" - read answer - case $answer in - q* | Q*) - answer=quit - ;; - y* | Y*) - answer=yes - ;; - *) - answer=no - ;; - esac - else - answer=yes - fi -fi - -case $answer in - no | correct) - -############################################################################## -# prompt for each value # -############################################################################## - - $ECHO " -Program name ($prog)? $ECHOTXT" - read value - if test "$value" - then - prog=$value - fi - $ECHO "Job ID ($jid)? $ECHOTXT" - read value - if test "$value" - then - jid=`$BASENAME $value $dotdat` - DIRJID=`dirname $value` - case $DIRJID in - \/*) - ;; - *) - DIRJID=`pwd`/$DIRJID - ;; - esac - fi - $ECHO "User subroutine name ($user)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - user= - ;; - *) - user=$value - case $user in - \/*) - ;; - *) - user=`pwd`/$user - ;; - esac - usernoext=$user - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - ;; - esac - fi - $ECHO "User objects or libraries ($objs)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - objs= - ;; - *) - objs="$value" - ;; - esac - fi - $ECHO "Restart File Job ID ($rid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - rid= - ;; - *) - rid=`$BASENAME $value .t08` - DIRRID=`dirname $value` - case $DIRRID in - \/*) - ;; - *) - DIRRID=`pwd`/$DIRRID - ;; - esac - ;; - esac - fi - $ECHO "Substructure File ID ($sid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - sid= - ;; - *) - sid=$value - DIRSID=`dirname $value` - case $DIRSID in - \/*) - ;; - *) - DIRSID=`pwd`/$DIRSID - ;; - esac - ;; - esac - fi - $ECHO "Post File Job ID ($pid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - pid= - ;; - *) - pid=$value - DIRPID=`dirname $value` - case $DIRPID in - \/*) - ;; - *) - DIRPID=`pwd`/$DIRPID - ;; - esac - ;; - esac - fi - $ECHO "Defaults File ID ($did)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - did= - ;; - *) - did=`$BASENAME $value $dotdat` - DIRDID=`dirname $value` - case $DIRDID in - \/*) - ;; - *) - DIRDID=`pwd`/$DIRDID - ;; - esac - ;; - esac - fi - $ECHO "View Factor File ID ($vid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - vid= - ;; - *) - vid=`$BASENAME $value .vfs` - DIRVID=`dirname $value` - case $DIRVID in - \/*) - ;; - *) - DIRVID=`pwd`/$DIRVID - ;; - esac - ;; - esac - fi - $ECHO "Save generated module ($prgsav)? $ECHOTXT" - read value - if test "$value" - then - prgsav=$value - fi - $ECHO "Run on tasks ($nprocdddm) tasks? $ECHOTXT" - read value - if test "$value" - then - nprocdddm=$value - nprocdddmprint=$value - fi - $ECHO "Run on ($nte) Element loop threads ? $ECHOTXT" - read value - if test "$value" - then - nte=$value - fi - $ECHO "Run on ($nsolver) solvers ? $ECHOTXT" - read value - if test "$value" - then - nsolver=$value - fi - $ECHO "Run on ($nts) Solver threads ? $ECHOTXT" - read value - if test "$value" - then - nts=$value - fi -# - if test $nprocdddm -gt 0 - then - nprocd=$nprocdddm - fi - if test $nsolver -gt 0 - then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi - fi -# Element loop threads. - if test $nte -eq -1 - then - nte=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nte -lt 0 - then - nte=0 - fi - nteprint=$nte -# Copy from ddm - if test $nprocdddm -gt 1 - then - nteprint=$nprocdddm - fi -# override with -nthread_elem option - if test $nte -ne 0 - then - nteprint=$nte - fi -# check for minimum 1 threads per processes for DDM - if test $nprocdddm -ne 0 - then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi - fi - nte=$nteprint -# Solver threads. - if test $nts -eq -1 - then - nts=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nts -lt 0 - then - nts=0 - fi - ntsprint=$nts -# Copy from ddm - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -# override with -nthread_solver option - if test $nts -ne 0 - then - ntsprint=$nts - fi -# check for minimum 1 threads per solver process. - if test $nsolver -lt $nprocdddm - then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi - else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi - fi - if test $ntsprint -eq 1 - then - set ntsprint=0 - fi - nts=$ntsprint - $ECHO "GPGPU id option ($gpuids)? $ECHOTXT" - read value - if test "$value" - then - gpuids=$value - fi - if test "$gpuids" = "" ; then - gpuoption= - else - gpuoption="-gp $gpuids" - fi - if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH - fi - if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" - then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" - fi -# - if test $nprocd -gt 1 - then - $ECHO "Message passing type ($itree)? $ECHOTXT" - read value - if test "$value" - then - itree=$value - fi - $ECHO "Host file name ($host)? $ECHOTXT" - read value - if test "$value" - then - host=$value - fi - if test $nprocdddm -gt 1 - then - $ECHO "Single input file? $ECHOTXT" - read value - case $value in - y* | Y*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - $ECHO "Compatible machines for DDM ($compatible)? $ECHOTXT" - read value - if test "$value" - then - compatible=$value - fi - $ECHO "Copy input files to remote hosts ($cpinput)? $ECHOTXT" - read value - if test "$value" - then - cpinput=$value - fi - $ECHO "Copy post files from remote hosts ($cpresults)? $ECHOTXT" - read value - if test "$value" - then - cpresults=$value - fi - fi - fi - $ECHO "Run the job in the queue ($qid)? $ECHOTXT" - read value - if test "$value" - then - qid=$value - fi - case $qid in - s* | S* | l* | L* | v* | V* ) - $ECHO "Queue priority ($priority)? $ECHOTXT" - read value - if test "$value" - then - priority=$value - fi - $ECHO "Job starts at ($att)? $ECHOTXT" - read value - if test "$value" - then - att=$value - fi - $ECHO "Queue CPU limit ($cpu)? $ECHOTXT" - read value - if test "$value" - then - cpu=$value - fi - ;; - * ) - ;; - esac - $ECHO "Auto Restart option ($nauto)? $ECHOTXT" - read value - if test "$value" - then - nauto=$value - fi - $ECHO "Run directory ($DIRJOB)? $ECHOTXT" - read value - if test "$value" - then - DIRJOB=$value - DIRSCR=$DIRJOB - fi - $ECHO "Scratch directory ($DIRSCR)? $ECHOTXT" - read value - if test "$value" - then - DIRSCR=$value - fi - ;; - quit) - exit 1 - ;; - *) - break - ;; - -esac - - if test $nt -eq -1 - then - nt=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nt -lt 0 - then - nt=0 - fi - -done -# -if test $nt -eq 0 -then - ntarg= -fi -if test $nt -eq 0 -then - ntprint= -fi -if test $nt -eq 0 -then - nt= -fi - -if test $nte -eq 0 -then - ntearg= -fi -if test $nte -eq 0 -then - nteprint= -fi -if test $nte -eq 0 -then - nte= -fi - -if test $nts -eq 0 -then - ntsarg= -fi -if test $nts -eq 0 -then - ntsprint= -fi -if test $nts -eq 0 -then - nts= -fi -# -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - pathdll=yes - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - fi - - if test "$pathdll"; then -# -# reset share lib path -# - if test $MACHINENAME = "HP" - then - SHLIB_PATH=$DIRJOB:$SHLIB_PATH - export SHLIB_PATH - fi - if test $MACHINENAME = "IBM" - then - LIBPATH=$DIRJOB:$LIBPATH - export LIBPATH - fi -# - LD_LIBRARY_PATH=$DIRJOB:$LD_LIBRARY_PATH - LD_LIBRARY64_PATH=$DIRJOB:$LD_LIBRARY64_PATH - LD_LIBRARYN32_PATH=$DIRJOB:$LD_LIBRARYN32_PATH - export LD_LIBRARY_PATH - export LD_LIBRARY64_PATH - export LD_LIBRARYN32_PATH - fi -fi -# end of dllrun>0 - - -if test $program = $exefile -o $program = $prog.marc -then - -# delete the old .log file unless we run in the background -if test "$deletelog" = yes -then - if test "$jid" - then - /bin/rm $jid.log 2>/dev/null - fi -else - echo - echo running the job in the background, see $jid.log - echo -fi - -# -# check if this is an autoforge or rezoning or radiation job -# -if test $nprocd -eq 1 -a "$jid" - -then - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^autoforge"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^rezoning"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^radiation"` - if test "$line" - then - autoforge=1 - fi -fi -# -# check that jobname for restarted run is not the same -# as restart file basename -# -if test "$rid" -then - if test "$jid" = "$rid" - then - echo " " - echo "ERROR: job name of current run is the same as job name" - echo " of the restarted job" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "ERROR: job name of current run is the same as job name" >> $jid.log - echo " of the restarted job" >> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi -fi - -# -# user objects/libraries used -# - - if test "$objs" - then - program="$DIRJOB/$jid.marc" - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# user subroutine used -# -# add DAMASK options for linking - DAMASK="-lstdc++" - - if test "$user" - then - program=$usernoext.marc - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# Special case for IBM using POE but not an SP machine -# in this case we always need a host file, also for serial jobs. -# -if test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP -then - MP_HOSTFILE=${jid}.host - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $nprocd -gt 1 - then - numdom=$nprocd - while test $numdom -gt 0 - do - hostname -s >> $MP_HOSTFILE - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - else - hostname -s > $MP_HOSTFILE - fi -fi -# -# check ssh for all hosts in host file -# -if test $nprocd -gt 1 -then -if test $MPITYPE = "intelmpi" -a "$INTELMPI_VERSION" = "HYDRA" - then -# get host list - if test "$host" - then - line=`grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' | uniq` -# count failing hosts - counter=0 - for i in $line - do - $RSH -o BatchMode=yes -o ConnectTimeout=10 $i uname -n - status=$? - if [[ $status != 0 ]] ; then - counter=$((counter+1)) - if [ "$counter" = "1" ]; then - echo " " - echo " error - connection test failed... " - echo " " - fi - echo " " - echo " connection test with ssh failed on host $i" - echo " check the following command: ssh $i uname -n " - echo " " - fi - done -# echo error message and quit - if test $counter -ne 0 - then - echo " " - echo " A parallel job using IntelMPI cannot be started. " - echo " The ssh command must be working correctly between " - echo " the computers used in the analysis. Furthermore, " - echo " it must be set up such that it does not prompt the " - echo " user for a password. " - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo " A parallel job using IntelMPI cannot be started. ">> $jid.log - echo " The ssh command must be working correctly between ">> $jid.log - echo " the computers used in the analysis. Furthermore, ">> $jid.log - echo " it must be set up such that it does not prompt the ">> $jid.log - echo " user for a password. ">> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi -fi -fi -# -# check correctness of host file; fix for user sub -# - if test $nprocd -gt 1 - then - -# construct the path name to the executable (execpath) - execpath=$MARC_BIN/$exefile - usersub=0 - if test $program = $prog.marc - then - execpath=$prog.marc - usersub=1 - fi - if test "$objs" - then - execpath="$DIRJOB/$jid.marc" - usersub=1 - fi - if test "$user" - then - execpath=$usernoext.marc - usersub=1 - fi - export execpath - execname=`$BASENAME $execpath` - - if test "$host" - then - userhost=$host - case $userhost in - \/* | \.\/*) - ;; - *) - userhost=`pwd`/$userhost - ;; - esac - -# check that the number of processes specified in the hostfile is -# equal to nprocd specified by -nprocd. - numproc=`grep -v '^#' $host | $AWK -v sum=0 '{sum=sum+$2}; END {print sum}'` - if test $nprocd -ne $numproc - then - echo " " - echo "error, the number of processes specified in the host file" - echo "must be equal to the number of processes given by -nprocd/-nsolver" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, the number of processes specified in the host file" >> $jid.log - echo "must be equal to the number of processes given by -nprocd/-nsolver" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - -# check for Myrinet that the number of processes per host is -# less than number of available user ports, 5 -# .gmpi directory must exist in user's home directory -# and must have write permission from remote hosts - if test $MPITYPE = "myrinet" - then - numproc=`grep -v '^#' $host | $AWK -v sum=1 '{if( $2 > 5) sum=6}; END {print sum}'` - if test $numproc -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes specified " - echo "in the hostfile must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes specified " >> $jid.log - echo "in the hostfile must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - if test ! -d ~/.gmpi - then - echo " " - echo "error, for Myrinet a .gmpi directory must exist " - echo "under the user's home directory" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a .gmpi directory must exist " >> $jid.log - echo "under the user's home directory" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - homedir=`echo ~` - for i in `grep -v '^#' $host | $AWK '{if (NF > 0) print $1}'` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - $RSH $i /bin/touch $homedir/.gmpi/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - echo " " - echo "error, for Myrinet a shared .gmpi directory must exist " - echo "under the user's home directory " - echo "with remote write permission" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a shared .gmpi directory must exist " >> $jid.log - echo "under the user's home directory " >> $jid.log - echo "with remote write permission" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - else - /bin/rm tmp.$$ - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - fi - fi - done - fi - fi - -# construct the host file $jid.host which is used by mpirun -# skip lines starting with # and only consider lines with more than -# one word in them. Note that the hostfile given to this script -# has two columns: the host name and the number of shared processes -# to run on this host. mpirun wants the number of _other_ -# processes to run in addition to the one being run on the machine -# on which the job is started. hence the $2-1 for fnr == 1. - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then -# HPMPI or HP hardware MPI - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ - -v mpihpspecial="$MPIHPSPECIAL" \ -'{if ( NF > 0) {\ - fnr++ ; \ - printf("-h %s -np %s",$1,$2); \ - printf(" %s",mpihpspecial); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF >= 3 ) printf(" -e MPI_WORKDIR=%s", $3);\ - if ( NF >= 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) \ - }\ - }' > $jid.host -# end HPMPI or HP hardware MPI - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then -# IBM using hardware MPI (POE) - MP_HOSTFILE=$jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.host -# end IBM using hardware MPI (POE) -# for Intel MPI, need to create a machinefile for DMP - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then -# Intel MPI - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - /bin/cp $host $jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Intel MPI for DMP -# for Solaris HPC 7.1, need to create a machinefile for DMP - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then -# Solaris HPC 7.1 - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Solaris HPC 7.1 for DMP -# for Myrinet, construct a configuration file in ~/.gmpi -# this must be readable by each process -# format is (hostname) (port number) for each process - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - grep -v '^#' $host | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ -{if ( NF > 0 ) \ - for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc]); \ -}' >> ~/.gmpi/$jid.host - else -# this is for mpich-1.2.5 and later, using the -pg option -# format: host nproc executable user arguments -# the arguments are added later - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub -v user=`whoami` \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s %s\n",path,user);\ - if ( NF == 3 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s %s\n",path,user) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s/bin/%s %s\n",$4,en,user) \ - }\ - }' > $jid.host - fi -# end Myrinet - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then -# Compaq MPI via Memory Channel - grep -v '^#' $host | $AWK '{if (NF > 0) print $1}' > $jid.host -# end Compaq MPI - else -# MPICH - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF == 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s/bin/%s\n",$4,en) \ - }\ - }' > $jid.host - fi -# define the variable host and host_filt -# host_filt is used for loops over hosts -# for Myrinet we need to use a filtered variant of userhost -# for others we can use $host - if test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - host=~/.gmpi/$jid.host - host_filt=$jid.host_tMp - grep -v '^#' $userhost | $AWK '{if (NF > 0) print $1}' > $host_filt - else - host=$jid.host - host_filt=$host - fi - else - host=$jid.host - host_filt=$host - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - host_filt=$jid.mfile - fi - fi -# figure out if the machines in the hostfile are nfs mounted -# or distributed and set the variable "dirstatus" accordingly. -# only perform the check if user subroutine is used -# or a user subroutine executable is used - - numfield=1 - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - numfield=2 - fi - DIR1=$DIRJOB - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - counter=0 - echo " " - echo "checking if local or shared directories for host" - if test "$deletelog" = no - then - echo "checking if local or shared directories for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - dirstatus[$counter]="shared" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - $RSH $i /bin/touch $DIR1/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - dirstatus[$counter]="local" - /bin/rm tmp.$$ - else - if test ! -f $jid.$$ - then - dirstatus[$counter]="local" - $RSH $i /bin/rm $DIR1/$jid.$$ - else - /bin/rm $jid.$$ - fi - fi - if test -f tmp.$$ - then - /bin/rm tmp.$$ - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - echo " ${dirstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${dirstatus[$counter]}" >> $jid.log - fi - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - fi - -# figure out if this is a compatible set of machines -# unless explicitly specified with flag -comp -# only perform the check if user subroutine is used -# or a user subroutine executable is used -# Myrinet does not support heterogeneous - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - if test $compatible = "unknown" - then - thisname=$ARCH - compatible=yes - counter=0 - echo "checking if machines are compatible for host" - if test "$deletelog" = no - then - echo "checking if machines are compatible for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]="yes" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - othername=`$RSH $i uname -a | cut -f 1 -d " "` - if test $thisname != $othername - then - compatible=no - compstatus[$counter]="no" - fi - fi - echo " ${compstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${compstatus[$counter]}" >> $jid.log - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - else - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]=$compatible - fi - done - if test $compatible = "no" - then - echo "all machines assumed incompatible" - if test "$deletelog" = no - then - echo "all machines assumed incompatible" >> $jid.log - fi - else - echo "all machines compatible" - if test "$deletelog" = no - then - echo "all machines compatible" >> $jid.log - fi - fi - fi -# error out if user objects or libraries are used on incompatible machines - if test "$compatible" = "no" -a -n "$objs" - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" - if test "$deletelog" = no - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" >> $jid.log - fi - exit 1 - fi -# modify new host file if NFS mounted heterogeneous machine - doit= - if test $program = $prog.marc - then - doit=yes - fi - if test "$user" - then - doit=yes - fi - if test "$doit" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - $AWK -v hst=$i '{fnr++ ; \ -if ($1 ~ hst) {if ( fnr == 1 ) printf("%s\n",$0); else \ -printf("%s %s %s_%s\n",$1,$2,$3,$1) } else print}' $jid.host > $jid.host{$$} - /bin/mv $jid.host{$$} $jid.host - host=$jid.host - fi - fi - done - fi - fi # if test $program = $prog.marc -o $user -o $obj - - else # if test $host - # assume shared memory machine if no hostfile given and - # MPITYPE is set to mpich or Myrinet - # check for Myrinet that the total number of processes is - # less than number of available user ports, 5 - if test $MPITYPE = "mpich" -o $MPITYPE = "scali" - then - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - host=$jid.host - elif test $MPITYPE = "myrinet" - then - if test $nprocd -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes " - echo "must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes " >> $jid.log - echo "must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - echo `hostname` $nprocd | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ - {for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc])} \ -' >> ~/.gmpi/$jid.host - host=~/.gmpi/$jid.host - else - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - - fi - fi # if test myrinet - - fi # if test $host - - fi # if test $nprocd -gt 1 - -fi # if test $program = $exefile -o $program = $prog.marc - -############################################################################## -# construct run stream (Marc only) # -############################################################################## - -# set maximum message length for ddm to a large number -# for vendor provided mpi -if test $itree -eq 0 -a $MPITYPE = hardware -then - itree=100000000 - if test $MACHINENAME = SGI - then - itree=100000001 - fi -fi -if test $itree -eq 0 -a $MPITYPE = hpmpi -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = myrinet -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = nec -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = scali -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = intelmpi -then - itree=100000000 -fi -if test $nprocdddm -lt 2 -then - nprocdarg= -else - nprocdarg="$nprocdarg $nprocdddm" -fi -if test $nsolver -eq 0 -then - nsolverarg= -else - nsolverarg="$nsolverarg $nsolver" -fi -if test $nprocdddm -lt 2 -a $nsolver -eq 0 -then -nprocd=0 -fi -if test $nprocd -gt 0 -then - if test "$host" - then - if test -z "$RUN_JOB2" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $host -- -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then - RUN_JOB="$RUN_JOB2 $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB_TMP="$RUN_JOB2 $host $bd$program" - RUN_JOB=" -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $nprocd -hf $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - numhost=`uniq $jid.mfile | wc -l` - if test "$INTELMPI_VERSION" = "HYDRA" - then - RUN_JOB_TMP="$RUN_JOB2 -configfile $jid.cfile" - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n $numhost -r $RSH -f $jid.mfile - RUN_JOB_TMP="$RUN_JOB2 $jid.cfile" - fi - -# intelmpi uses configfile. format: -# -host host1 -n n1 executable marcargs -# one such line per host -# collect the marcargs in RUN_JOB and construct the config file later -# collect the run stream in RUN_JOB_TMP - RUN_JOB="-jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - - - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then - RUN_JOB="$RUN_JOB2 $jid.mfile -n $nprocd $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test "$userhost" - then - RUN_JOB="$RUN_JOB -mhost $userhost" - fi - if test $MPITYPE = "scali" - then -# set default working directory to /tmp to allow -# different directory names - SCAMPI_WORKING_DIRECTORY=/tmp - export SCAMPI_WORKING_DIRECTORY - fi - else - if test -z "$RUN_JOB1" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - RUNNPROCD=$nprocd - if test $MACHINENAME = "IBM" -a $MPITYPE = "hardware" - then - RUNNPROCD= - MP_PROCS=$nprocd - export MP_PROCS - fi - if test $MPITYPE = "myrinet" - then - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - echo " " > /dev/null - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n 1 -f $jid.hosts - fi - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - fi -else - if test $nauto -gt 0 -o $ndcoup -gt 0 - then - RUN_JOB="$RUN_JOB0 $BINDIR/exe_auto $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else -# this is for a serial job without auto restart: - RUN_JOB="$RUN_JOB0 $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi -fi -if test "$rid" -then - RUN_JOB="$RUN_JOB -rid $rid -dirrid $DIRRID" -fi -if test "$pid" -then - RUN_JOB="$RUN_JOB -pid $pid -dirpid $DIRPID" -fi -if test "$sid" -then - RUN_JOB="$RUN_JOB -sid $sid -dirsid $DIRSID" -fi -if test "$did" -then - RUN_JOB="$RUN_JOB -def $did -dirdid $DIRDID" -fi -if test "$vid" -then - RUN_JOB="$RUN_JOB -vf $vid -dirvid $DIRVID" -fi -if test $nauto -gt 0 -then - RUN_JOB="$RUN_JOB -autorst $nauto " -fi -if test $ndcoup -gt 0 -then - RUN_JOB="$RUN_JOB -dcoup $ndcoup " -fi -if test $ndytran -gt 0 -then - RUN_JOB="$RUN_JOB -dytran $ndytran " -fi -if test $mesh -gt 0 -then - RUN_JOB="$RUN_JOB -me $mesh " -fi -if test $noutcore -gt 0 -then - RUN_JOB="$RUN_JOB -outcore $noutcore " -fi -if test "$dllrun" -gt 0 -then - RUN_JOB="$RUN_JOB -dll $dllrun " -fi -if test "$trkrun" -gt 0 -then - RUN_JOB="$RUN_JOB -trk $trkrun " -fi -if test "$iam" -then - RUN_JOB="$RUN_JOB -iam $iam " -fi -if test "$justlist" -then - RUN_JOB="$RUN_JOB -list 1 " -fi -if test "$feature" -then - RUN_JOB="$RUN_JOB -feature $feature " -fi -if test "$memlimit" -ne 0 -then - RUN_JOB="$RUN_JOB -ml $memlimit " -fi -if test "$cpinput" -then - RUN_JOB="$RUN_JOB -ci $cpinput " -fi -if test "$cpresults" -then - RUN_JOB="$RUN_JOB -cr $cpresults " -fi -if test "$DIRSCR" != "$DIRJOB" -then - RUN_JOB="$RUN_JOB -dirscr $DIRSCR" -else - DIRSCR=$DIRJOB -fi -if test "$makebdf" -then - RUN_JOB="$RUN_JOB -bdf $makebdf " -fi -if test $MPITYPE = "myrinet" -a "$host" -a "$MPIVERSION" != "MPICH-GM1.2.1..7" -then - # append $RUN_JOB to all lines of the host file - # and set RUN_JOB - $AWK -v args="$RUN_JOB" '{print $0,args}' $host > $host.$$ - /bin/mv $host.$$ $host - RUN_JOB=$RUN_JOB_TMP -fi -if test $MPITYPE = "intelmpi" -a "$host" -then - # construct config file, append $RUN_JOB to all lines of the config file - # and set RUN_JOB - if test "$INTELMPI_VERSION" = "HYDRA" - then - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf(" -host %s",$1); \ - printf(" -n %s",$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - else - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf("-host %s -n %s",$1,$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - fi - RUN_JOB=$RUN_JOB_TMP -fi -echo " " -echo "Final run stream value" -echo " RUNJOB="$RUN_JOB -if test "$deletelog" = no -then -echo " " >> $jid.log -echo "Final run stream value" >> $jid.log -echo " RUNJOB="$RUN_JOB >> $jid.log -fi - - -############################################################################## -# run marc using valgrind # -############################################################################## -#RUN_JOB="valgrind $RUN_JOB" -#RUN_JOB="valgrind --read-var-info=yes --gen-suppressions=yes $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=all -v $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=yes --error-limit=no $RUN_JOB" -############################################################################## - - -############################################################################## -# run the requested program in a queue # -############################################################################## - -if test "$deletelog" = yes -then - echo - date -else - echo >> $jid.log - date >> $jid.log -fi -if [ $qid = short -o $qid = long -o $qid = verylong -o $qid = at ] -then - -/bin/rm -f $jid.runmarcscript - - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - userobj=$usermoext.o - fi - cat > $jid.runmarcscript << END4 - if test "$user" - then - if test $MACHINENAME = "CRAY" - then - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTHIGH $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - $SOLVERLIBS \ - $MARCCUDALIBS \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } -END4 -else - prgsav=yes -fi -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc -# - -cat >> $jid.runmarcscript << END5 - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# first remove all .out files and incremental restart files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - /bin/rm $DIRJOB/$numdom${jid}_i_*.t08 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null - /bin/rm $DIRJOB/${jid}_i_*.t08 2>/dev/null -fi - -if test $nprocdddm -gt 1 -then - $RUN_JOB 2>>$jid.log -else - $RUN_JOB 2>>$jid.log -fi - -if test $dllrun -eq 0; then - if test $prgsav = no - then - /bin/rm -f $bd$program 2>/dev/null - fi -else - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes - then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -fi -END5 - - -# Submit to marc batch queue -# -if [ $qid = at ] -then -QUENAME=at -SUBMCMD= -else -# -# Submit to qsub queue -# -QUENAME=qsub -SUBMCMD="-q $qid -o /dev/null -e $jid.batch_err_log -x -r $jid" -if test "$priority" -then - SUBMCMD=$SUBMCMD" -p $priority" -fi -if test "$att" -then - SUBMCMD=$SUBMCMD" -a $att" -fi -if test "$cpu" -then - SUBMCMD=$SUBMCMD" -lt $cpu" -fi - -fi -echo $QUENAME $SUBMCMD -#cat $jid.runmarcscript -$QUENAME $SUBMCMD < $jid.runmarcscript - -/bin/rm -f $jid.runmarcscript - -############################################################################## -# run the requested program in the background # -############################################################################## - -else -if test $qid = background -then - -# -# first remove all old .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi -# -# compile user subroutine if present -# -( -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_h $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - echo " $PRODUCT Exit number 3" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTHIGH $user -o $userobj || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - echo " $PRODUCT Exit number 3" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc - -# - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - -$RUN_JOB & - -marcpid=$! -echo $marcpid > $DIRJOB/$jid.pid -wait $marcpid - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - fi - fi - fi -fi - - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi -) 1>>$jid.log 2>&1 & - - -############################################################################## -# run the requested program in the foreground # -############################################################################## - -else - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_h $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTHIGH $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null -# done if no job id given -if test -z "$jid" -then - echo - echo only compilation requested - echo - exit -fi -# -# run marc -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi -# first remove all .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - $RUN_JOB - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - else - echo " " > /dev/null - fi - else - if test "$host" - then - mpdcleanup -a -f $jid.mfile - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.mfile 2> /dev/null - else - mpdcleanup -a -f $jid.hosts - /bin/rm $jid.hosts 2> /dev/null - fi - fi - fi -fi - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi - - -fi -fi diff --git a/installation/mods_MarcMentat/2016/Marc_tools/run_damask_l b/installation/mods_MarcMentat/2016/Marc_tools/run_damask_l deleted file mode 100644 index 87cd1e5c6..000000000 --- a/installation/mods_MarcMentat/2016/Marc_tools/run_damask_l +++ /dev/null @@ -1,4112 +0,0 @@ -#!/bin/ksh -############################################################################## -# # -# run_marc - run a marc job # -# ------------------------- # -# # -# usage: run_marc -j jid { options } # -# # -# where standard options are: required: defaults: # -# -------------------------- # -# # -# -j* jid job id number. ** YES ** . # -# -pr* prog program name. . marc # -# -v* y|n do or do not verify inputs. . yes # -# -q* s|l|v|b|f batch queue name or background, . short # -# foreground. # -# -b* as alternative to option -q* # -# # -# ( batch queues only : # -# -pq* intra queue priority. . . # -# -at DATE/TIME delay start of job. . . # -# format : January,1,1990,12:31 # -# or : today,5pm # -# -cpu* secs job CPU limit . . ) # -# # -# -r* rid restart file job id. . . # -# -si* sid substructure file id. . . # -# -pi* post post file job id. . . # -# -de* did defaults file . no # -# -vf vid viewfactor . no # -# # -# -u* user user subroutine. . . # -# -obj obj user objects or libraries. . . # -# -sa* y|n do or do not save load module. . no # -# -autorst auto restart flag for auto forge . no # -# -me manual remeshing control . no # -# -ml memory limit in Mbyte # -# -mo This option is deprecated. As of Marc 2015, only # -# the integer*8 version is available. # -# -mpi selects MPI version # -# each platform has a default MPI version and some # -# have an alternative version. see the include file # -# for the respective platform # -# MPI_DEFAULT defines the default MPI version # -# MPI_OTHER defines versions one can switch to # -# -dcoup for contact decoupling # -# currently not supported # -# -dir directory where the job i/o should take place. # -# defaults to current directory. # -# -sdir directory where scratch files are created # -# defaults to current directory. # -# # -# -alloc only perform memory allocation test, no analysis # -# -list y only list options in the input file, no analysis # -# -fe num set feature number "num" for the run. only one allowed # -# -dytran flag to switch from Dytran to Marc # -# dytran = 0, program will run w/o Marc-Dytran Switch # -# = 1, program will restart Marc after Dytran run # -# >= 2, Not supported yet. # -# currently not supported # -# -ou force analysis to use out-of-core control # -# =0, not used # -# =1, element storage out-of-core # -# -dll run marc using shared library libmarc.so and exe_marc # -# =1, used # -# =2, do not free streaming input memory # -# =3, run with marc input deck # -# -trk run marc for post-tracking # -# -gpuid run marc using GPGPU capability # -# specify gpuid on to be used in the analysis. Multiple # -# IDs may be assigned for DDM runs. # -# Separate a list of IDs with a colon. Each DMP # -# process will be assigned a GPU ID in round robin fastion# -# = 0 # -# = 0:1 etc... # -# # -# where parallel options are: # -# -------------------------- # -# # -# itree, host, and comp options are available for the domain # -# decomposition only. # -# MARC_NUMBER_OF_THREADS, nthread, and dir options always available. # -# # -# # -# -nprocd number of domains. # -# defaults to single domain solution. # -# -nprocds number of domains if single input file. # -# defaults to single domain solution. # -# -nps same as -nprocds. # -# -nsolver number of solver tasks for solver types 12 and 13 # -# these are distributed tasks operating via MPI # -# -nthread_elem number of threads for element assembly and recovery # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by element assembly # -# recovery. # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_elem option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_elem specified. # -# -nthread_solver number of threads for solver types 6, 8, and 11 # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by 6, 8, and 11 # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_solver option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_solver specified. # -# -nthread Same as -nthread_solver. # -# -itree message passing tree type for domain decomposition. # -# for debugging purposes; should not normally be used. # -# -host hostfile name for distributed execution on network. # -# defaults to no hostfile, unless jobid.defhost exists. # -# if jobid.defhost exists, only -np(s) necessary # -# -comp* y|n to be used with user routines on a network of # -# incompatible machines. # -# if set to no, a separate executable will be created # -# for each machine on the network. # -# if set to yes, the executable located on the machine # -# from which marc is started will be used on all machines.# -# defaults to no if O/S versions different on machines. # -# # -# -ci y|n copy input files to remote hosts (default: yes) # -# if "yes", input files are automatically copied to # -# remote hosts for a network run if necessary. # -# -cr y|n copy post files from remote hosts (default: yes) # -# if "yes", post files are automatically copied back from # -# remote hosts for a network run if necessary. # -############################################################################## -# set DIR to the directory in which this script is -REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`" -DIR=`dirname $REALCOM` -# make sure DIR has an absolute path -case $DIR in - \/*) - ;; - *) - DIR=`pwd`/$DIR - ;; -esac -DIRSCRIPT=$DIR -AWK=awk -ARCH=`uname -a | cut -f 1 -d " "` -# Sun has a bad awk, use nawk instead -if test $ARCH = "SunOS" -then - AWK=nawk -fi -BASENAME=basename -# Sun has an incorrect /bin/basename, check if /usr/ucb/basename exists -if test $ARCH = "SunOS" -then - if test -x /usr/ucb/basename - then - BASENAME=/usr/ucb/basename - fi -fi - -# echo command line in the case of ECHO_COMMAND is true -if test "$ECHO_COMMAND" = true ; then - echo command "$0" "$@" -fi - -# -# "mode" selects version, i4 or i8 -# default is i4 -# this can be changed by a file run_marc_defaults -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MODE i8 -# it can also be set by the environmental variable MARC_INTEGER_SIZE -# and by the command line option "-mo" -# -mode= -modeerror= -modeoption= -if test -f $DIRSCRIPT/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $DIRSCRIPT/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $DIRSCRIPT/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $DIRSCRIPT/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -f $HOME/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $HOME/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $HOME/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $HOME/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -n "$MARC_INTEGER_SIZE" ; then - mode=$MARC_INTEGER_SIZE -fi -if test -z "$mode" ; then - mode=i8 -fi -case $mode in - i4) - modeerror="bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - modeoption=error - echo $modeerror - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo "bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - exit - ;; -esac - -setmode=false -for arg in $* ; do - if $setmode ; then - mode=$arg - case $mode in - i4) - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo " " - echo "error, version mode must be i8" - echo " " - echo " use -mo i8 " - echo " " - exit - ;; - esac - setmode=false - fi - if [ ${arg}X = -moX -o ${arg}X = -MOX ] ; then - echo - echo warning: the option -mo is deprecated, as of Marc 2015, only the integer*8 version is available - echo - setmode=true - fi - if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - fi - if [ ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - fi -done - -# set to i4 version for 32 bit Linux -if test "`uname -s`" = "Linux"; then - if test "`uname -m`" = "i686"; then - mode=i4 - MARC_INTEGER_SIZE=i4 - export MARC_INTEGER_SIZE - fi -fi - - -. "$DIR/getarch" - - -# getting user subroutine file name -found=0 -for i in "$@"; do - if test $found = 1; then - DAMASK_USER=$i - found=0 - fi - case $i in - -u* | -U*) - found=1 - ;; - esac -done -# sourcing include_linux64 (needs DAMASK_USER to be set) -. $MARC_INCLUDE - -# - -# -# Dynamically determine the echo syntax -# - -case "`echo '\c'`" in - '\c') - ECHO='echo -n' - ECHOTXT=' ' - ;; - *) - ECHO='echo' - ECHOTXT=' \c' - ;; -esac - -# -# Variables for the MARC environment -# - -PRODUCT="Marc" -EXITMSG=$MARC_TOOLS/MESSAGES -export EXITMSG -FLEXDIR=$DIR/../flexlm/licenses -export FLEXDIR -TIMCHK=3600 -export TIMCHK -BINDIR=$MARC_BIN -export BINDIR -AFMATDAT=$MARC_RUNTIME/AF_flowmat/ -export AFMATDAT -export MESHERDIR -MSC_LICENSE_FINPROC=1 -export MSC_LICENSE_FINPROC -# -# define directory path to global unified material database -# -MATFILE= -export MATFILE - -# -# define memory limit -# first set to MEMLIMIT from include -# -ml option overrules if specified -memlimit=$MEMLIMIT -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -# -if test $MACHINENAME = "HP" -then - SHLIB_PATH=$MARC_LIB:$MARC_LIB_SHARED:$SHLIB_PATH - export SHLIB_PATH -fi -# the one for IBM is defined futher down - -LD_LIBRARY_PATH=$MARC_LIB_SHARED:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MARC_LIB:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MESHERDIR:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$SFMATDIR:$LD_LIBRARY_PATH -LD_LIBRARY64_PATH=$MARC_LIB:$LD_LIBRARY64_PATH -LD_LIBRARYN32_PATH=$MARC_LIB:$LD_LIBRARYN32_PATH -export LD_LIBRARY_PATH -export LD_LIBRARY64_PATH -export LD_LIBRARYN32_PATH - -atexit() { -kill -15 $$ -# -if test $MPITYPE = "myrinet" -then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi -fi -} - -trap "atexit" 2 - -# -# defaults -# - -prog=marc -exefile=marc -jid= -rid= -pid= -sid= -did= -vid= -user= -usernoext= -objs= -qid=background -cpu= -priority= -att= -trk= -verify=yes -prgsav=no -rmdll=no -cpdll=no -progdll= -pathdll= -error= -nprocd=0 -nprocdddm=1 -nprocdddmprint= -icreated=0 -nprocdarg= -nsolver=0 -nsolverarg=-ns -if test $nprocds -then - if test $nprocds -gt 1 - then - nprocdddm=$nprocds - nprocdddmprint=$nprocds - icreated=1 - nprocdarg=-nprocds - fi -fi -ntprint=0 -nt=-1 -nte=-1 -nts=-1 -ntarg=-nt -ntearg=-nte -ntsarg=-nts -nteprint= -ntsprint= -gpuids= -nauto=0 -ndcoup=0 -ndytran=0 -noutcore=0 -dllrun=0 -mesh=0 -itree=0 -iam= -ddm_arc=0 -link= -trkrun=0 -DIRJOB=`pwd` -DIRSCR=$DIRJOB -DIRSCRSET= -autoforge=0 -dotdat=.dat -dotdefhost=.defhost -host= -numhost= -mfile= -userhost= -makebdf= -cpinput=yes -cpresults=yes -marcdll=libmarc.$EXT_DLL -# define hostname and strip off extensions (alpha.aaa.com) -thishost=`hostname` -thishost=${thishost%%.*} -compatible=unknown -numfield=1 -justlist= -feature= -mpioption=false -iprintsimufact= -MDSRCLIB=$MARC_LIB/mdsrc.a -# -# check run_marc_defaults file for default MPI setting -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MPI -# -value= -file= -if test -f $DIRSCRIPT/run_marc_defaults; then - value=`$AWK '{if ($1 == "MARC_MPI") {print $2}}' $DIRSCRIPT/run_marc_defaults` - value=`echo $value | $AWK '{print $NF}'` - if test -n "$value"; then - file=$DIRSCRIPT/run_marc_defaults - fi -fi -if test -f $HOME/run_marc_defaults; then - value=`$AWK '{if ($1 == "MARC_MPI") {print $2}}' $HOME/run_marc_defaults` - value=`echo $value | $AWK '{print $NF}'` - if test -n "$value"; then - file=$HOME/run_marc_defaults - fi -fi -if test -n "$value"; then - MARC_MPITYPE=$value - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - echo " " - echo " error, incorrect option for MARC_MPI" - echo " defined in $file: $MARC_MPITYPE" - echo " valid options: $MPI_DEFAULT $MPI_OTHER" - echo " " - exit - fi - if test "$value" != "$MPI_DEFAULT"; then - exefile=marc_$value - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a_$value - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a_$value" - fi - fi -fi -# -# -# allow scratch directory to be specified with environmental variable -# MARCSCRATCH -if test $MARCSCRATCH -then - if test -d $MARCSCRATCH - then - DIRSCR=$MARCSCRATCH - else - echo "error, scratch directory '$MARCSCRATCH'" - echo " specified via environmental variable MARCSCRATCH does not exist" - exit - fi -fi -# -############################################################################## -# parse input - arguments always come in pairs # -############################################################################## - -arg=$1 -if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - shift - arg=$1 -fi -while [ -n "$arg" ] -do - shift - value=$1 - case $arg in - -al* | -AL*) - LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - export LD_LIBRARY_PATH - $MARC_BIN/marc -alloc 1 - exit - ;; - -li* | -LI*) - justlist=yes - ;; - -fe* | -FE*) - feature=$value - - ;; - -pr* | -PR*) - if test `dirname $value` = '.' - then - prog=`$BASENAME $value .marc` - progdll=`$BASENAME $value` - else - prog=`dirname $value`/`$BASENAME $value .marc` - progdll=`dirname $value`/`$BASENAME $value` - fi - prdir=`dirname $value` - case $prdir in - \/*) - ;; - *) - prog=`pwd`/$prdir/$prog - ;; - esac - ;; - -j* | -J*) - jid=`$BASENAME $value $dotdat` - DIRJID=`dirname $value` - case $DIRJID in - \/*) - ;; - *) - DIRJID=`pwd`/$DIRJID - ;; - esac - ;; - -r* | -R*) - rid=`$BASENAME $value .t08` - DIRRID=`dirname $value` - case $DIRRID in - \/*) - ;; - *) - DIRRID=`pwd`/$DIRRID - ;; - esac - ;; - -si* | -SI*) - sid=$value - DIRSID=`dirname $value` - case $DIRSID in - \/*) - ;; - *) - DIRSID=`pwd`/$DIRSID - ;; - esac - ;; - -pi* | -PI*) - if test -f $value.t19 - then - pid=`$BASENAME $value .t19` - else - pid=`$BASENAME $value .t16` - fi - DIRPID=`dirname $value` - case $DIRPID in - \/*) - ;; - *) - DIRPID=`pwd`/$DIRPID - ;; - esac - ;; - -bdf | -BDF) - makebdf=1 - ;; - -de* | -DE*) - did=`$BASENAME $value $dotdat` - DIRDID=`dirname $value` - case $DIRDID in - \/*) - ;; - *) - DIRDID=`pwd`/$DIRDID - ;; - esac - ;; - -vf | -VF) - vid=`$BASENAME $value .vfs` - DIRVID=`dirname $value` - case $DIRVID in - \/*) - ;; - *) - DIRVID=`pwd`/$DIRVID - ;; - esac - ;; - -u* | -U*) - user=$value - case $user in - \/*) - ;; - *) - user=`pwd`/$user - ;; - esac - usernoext=$user - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - ;; - -obj | -OBJ) - objs="$value" - ;; - -q* | -Q*) - qid=$value - ;; - -b* | -B*) - case $value in - y* | Y*) - qid=background - ;; - n* | N*) - qid=foreground - ;; - *) - ;; - esac - ;; - -at | -AT) - att=$value - ;; - -cpu* | -CPU*) - cpu=$value - ;; - -pq | -PQ*) - priority=$value - ;; - -v* | -V*) - verify=$value - ;; - -sa* | -SA*) - prgsav=$value - ;; - -np* | -NP*) - nprocdddm=$value - nprocdddmprint=$value - case $arg in - -nps* | -NPS* | -nprocds* | -NPROCDS*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - case $arg in - -np | -NP | -nprocd | -NPROCD) - icreated=0 - nprocdarg=-nprocd - ;; - esac - ;; - -ns* | -NS*) - nsolver=$value - ;; - -nt* | -NT*) - case $arg in - -nte | -NTE | -nthread_e* | -NTHREAD_E*) - nte=$value - ;; - esac - case $arg in - -nts | -NTS | -nthread_s* | -NTHREAD_S*) - nts=$value - ;; - esac - case $arg in - -nt | -NT | -nth* | -NTH* | -nthread* | -NTHREAD*) - nt=$value - ;; - esac - ;; - -gp* | -GP*) - gpuids=$value - ;; - -it* | -IT*) - itree=$value - ;; - -iam | -IAM) - iam=$value - case $value in - sfg | sfm | sim) - iprintsimufact=true - ;; - esac - ;; - -au* | -AU*) - nauto=$value - ;; - -dc* | -DC*) - ndcoup=$value - ;; - -dy* | -DY*) - ndytran=$value - ;; - -ou* | -OU*) - noutcore=$value - ;; - -dll | -DLL) - dllrun=$value - ;; - -trk | -TRK) - trkrun=$value - ;; - -ddm | -DDM) - ddm_arc=$value - ;; - -me | -ME ) - mesh=$value - ;; - -ml | -ML ) - memlimit=$value - ;; - -mo | -MO ) - ;; - -mpi | -MPI ) - mpioption=true - MARC_MPITYPE=$value - if test "$value" != "$MPI_DEFAULT"; then - exefile=marc_$value - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a_$value - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a_$value" - fi - else - exefile=marc - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a" - fi - fi - ;; - -dir* | -DIR*) - DIRJOB=$value - case $DIRJOB in - \/*) - ;; - *) - DIRJOB=`pwd`/$DIRJOB - ;; - esac - if test -z "$DIRSCRSET" - then - DIRSCR=$DIRJOB - fi - ;; - -sd* | -SD*) - DIRSCR=$value - DIRSCRSET=yes - case $DIRSCR in - \/*) - ;; - *) - DIRSCR=`pwd`/$DIRSCR - ;; - esac - ;; - -ho* | -HO*) - host=$value - ;; - -co* | -CO*) - compatible=$value - ;; - -ci* | -CI*) - cpinput=$value - ;; - -cr* | -CR*) - cpresults=$value - ;; - *) - error="$error -$arg: invalid option" - break - ;; - esac - case $value in - -*) - error="$error -$arg: invalid name $value" - break - ;; - esac - shift - arg=$1 - if [ ${arg}X = -i8X -o ${arg}X = -I8X -o ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - shift - arg=$1 - fi -done -argc=`expr $# % 2` -if test $argc -eq 1 -then -# -# odd number of arguments -# - error="$error -argument list incomplete" -fi - -if test $nprocdddm -gt 0 -then -nprocd=$nprocdddm -fi - -if test $nsolver -gt 0 -then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi -fi -# Set defaults -if test $nt -eq -1 -then -nt=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nt -lt 0 -then -nt=0 -fi -if test $nte -eq -1 -then -nte=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nte -lt 0 -then -nte=0 -fi -if test $nts -eq -1 -then -nts=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nts -lt 0 -then -nts=0 -fi -# -# set number of element loop threads -# -ntprint=$nt -nteprint=$nte -# copy from -nprocd[s] -if test $nprocdddm -gt 1 -then - nteprint=$nprocdddm -fi -# override with -nthread_elem option -if test $nte -ne 0 -then -nteprint=$nte -fi -# check for minimum 1 threads per processes for DDM -if test $nprocdddm -gt 1 -then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi -fi -nte=$nteprint -# -# set number of Solver threads -# -ntsprint=$nts -# copy from -nthread or -nprocd[s] -if test $ntprint -ne 0 -then - ntsprint=$ntprint -else - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -fi -# override with -nthread_solver option -if test $nts -ne 0 -then - ntsprint=$nts -fi -# check for minimum 1 threads per solver process. -if test $nsolver -lt $nprocdddm -then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi -else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi -fi -if test $ntsprint -eq 1 -then - set ntsprint=0 -fi -nts=$ntsprint - -# set stack size for multi-threading. -export KMP_MONITOR_STACKSIZE=7M -export OMP_STACKSIZE=7M - -# -# deprecate -nthread option at arugment of marc -nt=0 -# Reset nprocdddmm, nsolver and threads if not given. -if test $nprocdddm -eq 0 -then - nprocdarg= -fi -if test $nprocdddm -eq 0 -then - nprocdddmprint= -fi -if test $nprocdddm -eq 0 -then - nprocdddm= -fi - -if test $nsolver -eq 0 -then - nsolverprint= -fi -# end of threads setting. -gpuoption= -if test "$gpuids" = "" ; then - gpuoption= -else - gpuoption="-gp $gpuids" -fi - -if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH -else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH -fi -# Linux 64 + HPMPI, Below code is taken from include_linux64 -if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" -then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" -fi - -if test $nprocd -gt 1; then - if test -f $jid$dotdefhost; then - if test "$host" = ""; then - host=$jid$dotdefhost - fi - fi - if test -f hostfile_qa_$nprocd; then - if test "$host" = ""; then - host=hostfile_qa_$nprocd - fi - fi -fi - -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$dllrun" -eq 1 || test "$dllrun" -eq 2; then - dotdat=.inp - fi - - if test "$progdll"; then - /bin/cp ${progdll}_$marcdll $DIRJOB/$marcdll - rmdll=yes - pathdll=yes - progdll=${progdll}_$marcdll - else - progdll=$marcdll - fi - - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - pathdll=yes - fi -fi - -############################################################################## -# check parameter validity # -############################################################################## - -while test forever; do - -# -# check for input file existence -# -if test $nprocdddm -gt 1 -a $icreated -eq 0; then - if test ! -f $DIRJID/1$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/1$jid$dotdat not accessible" - fi - fi -else - if test ! -f $DIRJID/$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/$jid$dotdat not accessible" - fi - fi -fi - if test $nprocd -gt 1; then - if test "$host" ; then - if test ! -f $host; then - error="$error -host name file $host not accessible" - fi - fi - fi - -# -# check if the job is already running in the background -# -if test -f $DIRJOB/$jid.pid; then - error="$error -job is already running (the file $jid.pid exists)" -fi - -# -# if the program name is other than marc, then -# assume that this is a program in the users local directory -# - -bd=$MARC_BIN/ - -case $prog in - marc | MARC | $exefile) - program=$exefile - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 or $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - if test ! -f $user - then - error="$error -user subroutine file $user not accessible" - fi - fi - if test "$objs" - then - missingobjs= - for o in $objs - do - if test ! -f "$o" - then - if test -z "$missingobjs" - then - missingobjs="$o" - else - missingobjs="$missingobjs $o" - fi - fi - done - if test -n "$missingobjs" - then - error="$error -user object/library file(s) $missingobjs not accessible" - fi - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$vid" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRVID/1$vid.vfs - then - error="$error -view factor file $DIRVID/1$vid.vfs not accessible" - fi - else - if test ! -f $DIRVID/$vid.vfs - then - error="$error -view factor file $DIRVID/$vid.vfs not accessible" - fi - fi - fi - if $mpioption - then - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE (valid: $MPI_OTHER)" - fi - fi - ;; - *) - program=$prog.marc - case $prog in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 and $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - error="$error -program option may not be used with user subroutine" - fi - if test "$objs" - then - error="$error -program option may not be used with user objects or libraries" - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$nauto" - then - if test $nauto -gt 2 - then - error="$error -incorrect option for auto restart " - fi - fi - if test "$ndcoup" - then - if test $ndcoup -gt 3 - then - error="$error -incorrect option for contact decoupling " - fi - fi - if test "$ndytran" - then - if test $ndytran -gt 1 - then - error="$error -incorrect option for Marc-Dytran Switch " - fi - fi - if $mpioption - then - if test ! -x $MARC_BIN/$exefile - then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE " - fi - fi - ;; -esac - -############################################################################## -# check argument integrity # -############################################################################## - -if test "$jid" -then - : -else - if test "$user" - then -# allow user sub without giving job id - qid=foreground - verify=no - else - error="$error -job id required" -fi -fi - -if test $nprocd -gt 1 -then - if test $nauto -gt 0 - then - error="$error -cannot run DDM job with auto restart (-au) option " - fi -fi -case $qid in - S* | s*) - qid=short - ;; - L* | l*) - qid=long - ;; - V* | v*) - qid=verylong - ;; - B* | b*) - qid=background - ;; - F* | f*) - qid=foreground - ;; - A* | a*) - qid=at - ;; - *) - error="$error -bad value for queue_id option" - ;; -esac - -case $prgsav in - N* | n*) - prgsav=no - ;; - Y* | y*) - prgsav=yes - ;; - *) - error="$error -bad value for save option" - ;; -esac - -case $verify in - N* | n*) - verify=no - ;; - Y* | y*) - verify=yes - ;; - *) - error="$error -bad value for verify option" - ;; 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- *) - sid=$value - DIRSID=`dirname $value` - case $DIRSID in - \/*) - ;; - *) - DIRSID=`pwd`/$DIRSID - ;; - esac - ;; - esac - fi - $ECHO "Post File Job ID ($pid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - pid= - ;; - *) - pid=$value - DIRPID=`dirname $value` - case $DIRPID in - \/*) - ;; - *) - DIRPID=`pwd`/$DIRPID - ;; - esac - ;; - esac - fi - $ECHO "Defaults File ID ($did)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - did= - ;; - *) - did=`$BASENAME $value $dotdat` - DIRDID=`dirname $value` - case $DIRDID in - \/*) - ;; - *) - DIRDID=`pwd`/$DIRDID - ;; - esac - ;; - esac - fi - $ECHO "View Factor File ID ($vid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - vid= - ;; - *) - vid=`$BASENAME $value .vfs` - DIRVID=`dirname $value` - case $DIRVID in - \/*) - ;; - *) - DIRVID=`pwd`/$DIRVID - ;; - esac - ;; - esac - fi - $ECHO "Save generated module ($prgsav)? $ECHOTXT" - read value - if test "$value" - then - prgsav=$value - fi - $ECHO "Run on tasks ($nprocdddm) tasks? $ECHOTXT" - read value - if test "$value" - then - nprocdddm=$value - nprocdddmprint=$value - fi - $ECHO "Run on ($nte) Element loop threads ? $ECHOTXT" - read value - if test "$value" - then - nte=$value - fi - $ECHO "Run on ($nsolver) solvers ? $ECHOTXT" - read value - if test "$value" - then - nsolver=$value - fi - $ECHO "Run on ($nts) Solver threads ? $ECHOTXT" - read value - if test "$value" - then - nts=$value - fi -# - if test $nprocdddm -gt 0 - then - nprocd=$nprocdddm - fi - if test $nsolver -gt 0 - then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi - fi -# Element loop threads. - if test $nte -eq -1 - then - nte=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nte -lt 0 - then - nte=0 - fi - nteprint=$nte -# Copy from ddm - if test $nprocdddm -gt 1 - then - nteprint=$nprocdddm - fi -# override with -nthread_elem option - if test $nte -ne 0 - then - nteprint=$nte - fi -# check for minimum 1 threads per processes for DDM - if test $nprocdddm -ne 0 - then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi - fi - nte=$nteprint -# Solver threads. - if test $nts -eq -1 - then - nts=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nts -lt 0 - then - nts=0 - fi - ntsprint=$nts -# Copy from ddm - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -# override with -nthread_solver option - if test $nts -ne 0 - then - ntsprint=$nts - fi -# check for minimum 1 threads per solver process. - if test $nsolver -lt $nprocdddm - then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi - else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi - fi - if test $ntsprint -eq 1 - then - set ntsprint=0 - fi - nts=$ntsprint - $ECHO "GPGPU id option ($gpuids)? $ECHOTXT" - read value - if test "$value" - then - gpuids=$value - fi - if test "$gpuids" = "" ; then - gpuoption= - else - gpuoption="-gp $gpuids" - fi - if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH - fi - if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" - then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" - fi -# - if test $nprocd -gt 1 - then - $ECHO "Message passing type ($itree)? $ECHOTXT" - read value - if test "$value" - then - itree=$value - fi - $ECHO "Host file name ($host)? $ECHOTXT" - read value - if test "$value" - then - host=$value - fi - if test $nprocdddm -gt 1 - then - $ECHO "Single input file? $ECHOTXT" - read value - case $value in - y* | Y*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - $ECHO "Compatible machines for DDM ($compatible)? $ECHOTXT" - read value - if test "$value" - then - compatible=$value - fi - $ECHO "Copy input files to remote hosts ($cpinput)? $ECHOTXT" - read value - if test "$value" - then - cpinput=$value - fi - $ECHO "Copy post files from remote hosts ($cpresults)? $ECHOTXT" - read value - if test "$value" - then - cpresults=$value - fi - fi - fi - $ECHO "Run the job in the queue ($qid)? $ECHOTXT" - read value - if test "$value" - then - qid=$value - fi - case $qid in - s* | S* | l* | L* | v* | V* ) - $ECHO "Queue priority ($priority)? $ECHOTXT" - read value - if test "$value" - then - priority=$value - fi - $ECHO "Job starts at ($att)? $ECHOTXT" - read value - if test "$value" - then - att=$value - fi - $ECHO "Queue CPU limit ($cpu)? $ECHOTXT" - read value - if test "$value" - then - cpu=$value - fi - ;; - * ) - ;; - esac - $ECHO "Auto Restart option ($nauto)? $ECHOTXT" - read value - if test "$value" - then - nauto=$value - fi - $ECHO "Run directory ($DIRJOB)? $ECHOTXT" - read value - if test "$value" - then - DIRJOB=$value - DIRSCR=$DIRJOB - fi - $ECHO "Scratch directory ($DIRSCR)? $ECHOTXT" - read value - if test "$value" - then - DIRSCR=$value - fi - ;; - quit) - exit 1 - ;; - *) - break - ;; - -esac - - if test $nt -eq -1 - then - nt=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nt -lt 0 - then - nt=0 - fi - -done -# -if test $nt -eq 0 -then - ntarg= -fi -if test $nt -eq 0 -then - ntprint= -fi -if test $nt -eq 0 -then - nt= -fi - -if test $nte -eq 0 -then - ntearg= -fi -if test $nte -eq 0 -then - nteprint= -fi -if test $nte -eq 0 -then - nte= -fi - -if test $nts -eq 0 -then - ntsarg= -fi -if test $nts -eq 0 -then - ntsprint= -fi -if test $nts -eq 0 -then - nts= -fi -# -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - pathdll=yes - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - fi - - if test "$pathdll"; then -# -# reset share lib path -# - if test $MACHINENAME = "HP" - then - SHLIB_PATH=$DIRJOB:$SHLIB_PATH - export SHLIB_PATH - fi - if test $MACHINENAME = "IBM" - then - LIBPATH=$DIRJOB:$LIBPATH - export LIBPATH - fi -# - LD_LIBRARY_PATH=$DIRJOB:$LD_LIBRARY_PATH - LD_LIBRARY64_PATH=$DIRJOB:$LD_LIBRARY64_PATH - LD_LIBRARYN32_PATH=$DIRJOB:$LD_LIBRARYN32_PATH - export LD_LIBRARY_PATH - export LD_LIBRARY64_PATH - export LD_LIBRARYN32_PATH - fi -fi -# end of dllrun>0 - - -if test $program = $exefile -o $program = $prog.marc -then - -# delete the old .log file unless we run in the background -if test "$deletelog" = yes -then - if test "$jid" - then - /bin/rm $jid.log 2>/dev/null - fi -else - echo - echo running the job in the background, see $jid.log - echo -fi - -# -# check if this is an autoforge or rezoning or radiation job -# -if test $nprocd -eq 1 -a "$jid" - -then - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^autoforge"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^rezoning"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^radiation"` - if test "$line" - then - autoforge=1 - fi -fi -# -# check that jobname for restarted run is not the same -# as restart file basename -# -if test "$rid" -then - if test "$jid" = "$rid" - then - echo " " - echo "ERROR: job name of current run is the same as job name" - echo " of the restarted job" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "ERROR: job name of current run is the same as job name" >> $jid.log - echo " of the restarted job" >> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi -fi - -# -# user objects/libraries used -# - - if test "$objs" - then - program="$DIRJOB/$jid.marc" - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# user subroutine used -# -# add DAMASK options for linking - DAMASK="-lstdc++" - - if test "$user" - then - program=$usernoext.marc - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# Special case for IBM using POE but not an SP machine -# in this case we always need a host file, also for serial jobs. -# -if test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP -then - MP_HOSTFILE=${jid}.host - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $nprocd -gt 1 - then - numdom=$nprocd - while test $numdom -gt 0 - do - hostname -s >> $MP_HOSTFILE - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - else - hostname -s > $MP_HOSTFILE - fi -fi -# -# check ssh for all hosts in host file -# -if test $nprocd -gt 1 -then -if test $MPITYPE = "intelmpi" -a "$INTELMPI_VERSION" = "HYDRA" - then -# get host list - if test "$host" - then - line=`grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' | uniq` -# count failing hosts - counter=0 - for i in $line - do - $RSH -o BatchMode=yes -o ConnectTimeout=10 $i uname -n - status=$? - if [[ $status != 0 ]] ; then - counter=$((counter+1)) - if [ "$counter" = "1" ]; then - echo " " - echo " error - connection test failed... " - echo " " - fi - echo " " - echo " connection test with ssh failed on host $i" - echo " check the following command: ssh $i uname -n " - echo " " - fi - done -# echo error message and quit - if test $counter -ne 0 - then - echo " " - echo " A parallel job using IntelMPI cannot be started. " - echo " The ssh command must be working correctly between " - echo " the computers used in the analysis. Furthermore, " - echo " it must be set up such that it does not prompt the " - echo " user for a password. " - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo " A parallel job using IntelMPI cannot be started. ">> $jid.log - echo " The ssh command must be working correctly between ">> $jid.log - echo " the computers used in the analysis. Furthermore, ">> $jid.log - echo " it must be set up such that it does not prompt the ">> $jid.log - echo " user for a password. ">> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi -fi -fi -# -# check correctness of host file; fix for user sub -# - if test $nprocd -gt 1 - then - -# construct the path name to the executable (execpath) - execpath=$MARC_BIN/$exefile - usersub=0 - if test $program = $prog.marc - then - execpath=$prog.marc - usersub=1 - fi - if test "$objs" - then - execpath="$DIRJOB/$jid.marc" - usersub=1 - fi - if test "$user" - then - execpath=$usernoext.marc - usersub=1 - fi - export execpath - execname=`$BASENAME $execpath` - - if test "$host" - then - userhost=$host - case $userhost in - \/* | \.\/*) - ;; - *) - userhost=`pwd`/$userhost - ;; - esac - -# check that the number of processes specified in the hostfile is -# equal to nprocd specified by -nprocd. - numproc=`grep -v '^#' $host | $AWK -v sum=0 '{sum=sum+$2}; END {print sum}'` - if test $nprocd -ne $numproc - then - echo " " - echo "error, the number of processes specified in the host file" - echo "must be equal to the number of processes given by -nprocd/-nsolver" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, the number of processes specified in the host file" >> $jid.log - echo "must be equal to the number of processes given by -nprocd/-nsolver" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - -# check for Myrinet that the number of processes per host is -# less than number of available user ports, 5 -# .gmpi directory must exist in user's home directory -# and must have write permission from remote hosts - if test $MPITYPE = "myrinet" - then - numproc=`grep -v '^#' $host | $AWK -v sum=1 '{if( $2 > 5) sum=6}; END {print sum}'` - if test $numproc -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes specified " - echo "in the hostfile must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes specified " >> $jid.log - echo "in the hostfile must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - if test ! -d ~/.gmpi - then - echo " " - echo "error, for Myrinet a .gmpi directory must exist " - echo "under the user's home directory" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a .gmpi directory must exist " >> $jid.log - echo "under the user's home directory" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - homedir=`echo ~` - for i in `grep -v '^#' $host | $AWK '{if (NF > 0) print $1}'` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - $RSH $i /bin/touch $homedir/.gmpi/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - echo " " - echo "error, for Myrinet a shared .gmpi directory must exist " - echo "under the user's home directory " - echo "with remote write permission" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a shared .gmpi directory must exist " >> $jid.log - echo "under the user's home directory " >> $jid.log - echo "with remote write permission" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - else - /bin/rm tmp.$$ - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - fi - fi - done - fi - fi - -# construct the host file $jid.host which is used by mpirun -# skip lines starting with # and only consider lines with more than -# one word in them. Note that the hostfile given to this script -# has two columns: the host name and the number of shared processes -# to run on this host. mpirun wants the number of _other_ -# processes to run in addition to the one being run on the machine -# on which the job is started. hence the $2-1 for fnr == 1. - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then -# HPMPI or HP hardware MPI - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ - -v mpihpspecial="$MPIHPSPECIAL" \ -'{if ( NF > 0) {\ - fnr++ ; \ - printf("-h %s -np %s",$1,$2); \ - printf(" %s",mpihpspecial); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF >= 3 ) printf(" -e MPI_WORKDIR=%s", $3);\ - if ( NF >= 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) \ - }\ - }' > $jid.host -# end HPMPI or HP hardware MPI - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then -# IBM using hardware MPI (POE) - MP_HOSTFILE=$jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.host -# end IBM using hardware MPI (POE) -# for Intel MPI, need to create a machinefile for DMP - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then -# Intel MPI - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - /bin/cp $host $jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Intel MPI for DMP -# for Solaris HPC 7.1, need to create a machinefile for DMP - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then -# Solaris HPC 7.1 - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Solaris HPC 7.1 for DMP -# for Myrinet, construct a configuration file in ~/.gmpi -# this must be readable by each process -# format is (hostname) (port number) for each process - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - grep -v '^#' $host | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ -{if ( NF > 0 ) \ - for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc]); \ -}' >> ~/.gmpi/$jid.host - else -# this is for mpich-1.2.5 and later, using the -pg option -# format: host nproc executable user arguments -# the arguments are added later - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub -v user=`whoami` \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s %s\n",path,user);\ - if ( NF == 3 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s %s\n",path,user) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s/bin/%s %s\n",$4,en,user) \ - }\ - }' > $jid.host - fi -# end Myrinet - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then -# Compaq MPI via Memory Channel - grep -v '^#' $host | $AWK '{if (NF > 0) print $1}' > $jid.host -# end Compaq MPI - else -# MPICH - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF == 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s/bin/%s\n",$4,en) \ - }\ - }' > $jid.host - fi -# define the variable host and host_filt -# host_filt is used for loops over hosts -# for Myrinet we need to use a filtered variant of userhost -# for others we can use $host - if test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - host=~/.gmpi/$jid.host - host_filt=$jid.host_tMp - grep -v '^#' $userhost | $AWK '{if (NF > 0) print $1}' > $host_filt - else - host=$jid.host - host_filt=$host - fi - else - host=$jid.host - host_filt=$host - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - host_filt=$jid.mfile - fi - fi -# figure out if the machines in the hostfile are nfs mounted -# or distributed and set the variable "dirstatus" accordingly. -# only perform the check if user subroutine is used -# or a user subroutine executable is used - - numfield=1 - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - numfield=2 - fi - DIR1=$DIRJOB - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - counter=0 - echo " " - echo "checking if local or shared directories for host" - if test "$deletelog" = no - then - echo "checking if local or shared directories for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - dirstatus[$counter]="shared" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - $RSH $i /bin/touch $DIR1/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - dirstatus[$counter]="local" - /bin/rm tmp.$$ - else - if test ! -f $jid.$$ - then - dirstatus[$counter]="local" - $RSH $i /bin/rm $DIR1/$jid.$$ - else - /bin/rm $jid.$$ - fi - fi - if test -f tmp.$$ - then - /bin/rm tmp.$$ - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - echo " ${dirstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${dirstatus[$counter]}" >> $jid.log - fi - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - fi - -# figure out if this is a compatible set of machines -# unless explicitly specified with flag -comp -# only perform the check if user subroutine is used -# or a user subroutine executable is used -# Myrinet does not support heterogeneous - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - if test $compatible = "unknown" - then - thisname=$ARCH - compatible=yes - counter=0 - echo "checking if machines are compatible for host" - if test "$deletelog" = no - then - echo "checking if machines are compatible for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]="yes" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - othername=`$RSH $i uname -a | cut -f 1 -d " "` - if test $thisname != $othername - then - compatible=no - compstatus[$counter]="no" - fi - fi - echo " ${compstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${compstatus[$counter]}" >> $jid.log - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - else - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]=$compatible - fi - done - if test $compatible = "no" - then - echo "all machines assumed incompatible" - if test "$deletelog" = no - then - echo "all machines assumed incompatible" >> $jid.log - fi - else - echo "all machines compatible" - if test "$deletelog" = no - then - echo "all machines compatible" >> $jid.log - fi - fi - fi -# error out if user objects or libraries are used on incompatible machines - if test "$compatible" = "no" -a -n "$objs" - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" - if test "$deletelog" = no - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" >> $jid.log - fi - exit 1 - fi -# modify new host file if NFS mounted heterogeneous machine - doit= - if test $program = $prog.marc - then - doit=yes - fi - if test "$user" - then - doit=yes - fi - if test "$doit" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - $AWK -v hst=$i '{fnr++ ; \ -if ($1 ~ hst) {if ( fnr == 1 ) printf("%s\n",$0); else \ -printf("%s %s %s_%s\n",$1,$2,$3,$1) } else print}' $jid.host > $jid.host{$$} - /bin/mv $jid.host{$$} $jid.host - host=$jid.host - fi - fi - done - fi - fi # if test $program = $prog.marc -o $user -o $obj - - else # if test $host - # assume shared memory machine if no hostfile given and - # MPITYPE is set to mpich or Myrinet - # check for Myrinet that the total number of processes is - # less than number of available user ports, 5 - if test $MPITYPE = "mpich" -o $MPITYPE = "scali" - then - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - host=$jid.host - elif test $MPITYPE = "myrinet" - then - if test $nprocd -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes " - echo "must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes " >> $jid.log - echo "must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - echo `hostname` $nprocd | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ - {for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc])} \ -' >> ~/.gmpi/$jid.host - host=~/.gmpi/$jid.host - else - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - - fi - fi # if test myrinet - - fi # if test $host - - fi # if test $nprocd -gt 1 - -fi # if test $program = $exefile -o $program = $prog.marc - -############################################################################## -# construct run stream (Marc only) # -############################################################################## - -# set maximum message length for ddm to a large number -# for vendor provided mpi -if test $itree -eq 0 -a $MPITYPE = hardware -then - itree=100000000 - if test $MACHINENAME = SGI - then - itree=100000001 - fi -fi -if test $itree -eq 0 -a $MPITYPE = hpmpi -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = myrinet -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = nec -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = scali -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = intelmpi -then - itree=100000000 -fi -if test $nprocdddm -lt 2 -then - nprocdarg= -else - nprocdarg="$nprocdarg $nprocdddm" -fi -if test $nsolver -eq 0 -then - nsolverarg= -else - nsolverarg="$nsolverarg $nsolver" -fi -if test $nprocdddm -lt 2 -a $nsolver -eq 0 -then -nprocd=0 -fi -if test $nprocd -gt 0 -then - if test "$host" - then - if test -z "$RUN_JOB2" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $host -- -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then - RUN_JOB="$RUN_JOB2 $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB_TMP="$RUN_JOB2 $host $bd$program" - RUN_JOB=" -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $nprocd -hf $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - numhost=`uniq $jid.mfile | wc -l` - if test "$INTELMPI_VERSION" = "HYDRA" - then - RUN_JOB_TMP="$RUN_JOB2 -configfile $jid.cfile" - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n $numhost -r $RSH -f $jid.mfile - RUN_JOB_TMP="$RUN_JOB2 $jid.cfile" - fi - -# intelmpi uses configfile. format: -# -host host1 -n n1 executable marcargs -# one such line per host -# collect the marcargs in RUN_JOB and construct the config file later -# collect the run stream in RUN_JOB_TMP - RUN_JOB="-jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - - - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then - RUN_JOB="$RUN_JOB2 $jid.mfile -n $nprocd $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test "$userhost" - then - RUN_JOB="$RUN_JOB -mhost $userhost" - fi - if test $MPITYPE = "scali" - then -# set default working directory to /tmp to allow -# different directory names - SCAMPI_WORKING_DIRECTORY=/tmp - export SCAMPI_WORKING_DIRECTORY - fi - else - if test -z "$RUN_JOB1" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - RUNNPROCD=$nprocd - if test $MACHINENAME = "IBM" -a $MPITYPE = "hardware" - then - RUNNPROCD= - MP_PROCS=$nprocd - export MP_PROCS - fi - if test $MPITYPE = "myrinet" - then - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - echo " " > /dev/null - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n 1 -f $jid.hosts - fi - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - fi -else - if test $nauto -gt 0 -o $ndcoup -gt 0 - then - RUN_JOB="$RUN_JOB0 $BINDIR/exe_auto $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else -# this is for a serial job without auto restart: - RUN_JOB="$RUN_JOB0 $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi -fi -if test "$rid" -then - RUN_JOB="$RUN_JOB -rid $rid -dirrid $DIRRID" -fi -if test "$pid" -then - RUN_JOB="$RUN_JOB -pid $pid -dirpid $DIRPID" -fi -if test "$sid" -then - RUN_JOB="$RUN_JOB -sid $sid -dirsid $DIRSID" -fi -if test "$did" -then - RUN_JOB="$RUN_JOB -def $did -dirdid $DIRDID" -fi -if test "$vid" -then - RUN_JOB="$RUN_JOB -vf $vid -dirvid $DIRVID" -fi -if test $nauto -gt 0 -then - RUN_JOB="$RUN_JOB -autorst $nauto " -fi -if test $ndcoup -gt 0 -then - RUN_JOB="$RUN_JOB -dcoup $ndcoup " -fi -if test $ndytran -gt 0 -then - RUN_JOB="$RUN_JOB -dytran $ndytran " -fi -if test $mesh -gt 0 -then - RUN_JOB="$RUN_JOB -me $mesh " -fi -if test $noutcore -gt 0 -then - RUN_JOB="$RUN_JOB -outcore $noutcore " -fi -if test "$dllrun" -gt 0 -then - RUN_JOB="$RUN_JOB -dll $dllrun " -fi -if test "$trkrun" -gt 0 -then - RUN_JOB="$RUN_JOB -trk $trkrun " -fi -if test "$iam" -then - RUN_JOB="$RUN_JOB -iam $iam " -fi -if test "$justlist" -then - RUN_JOB="$RUN_JOB -list 1 " -fi -if test "$feature" -then - RUN_JOB="$RUN_JOB -feature $feature " -fi -if test "$memlimit" -ne 0 -then - RUN_JOB="$RUN_JOB -ml $memlimit " -fi -if test "$cpinput" -then - RUN_JOB="$RUN_JOB -ci $cpinput " -fi -if test "$cpresults" -then - RUN_JOB="$RUN_JOB -cr $cpresults " -fi -if test "$DIRSCR" != "$DIRJOB" -then - RUN_JOB="$RUN_JOB -dirscr $DIRSCR" -else - DIRSCR=$DIRJOB -fi -if test "$makebdf" -then - RUN_JOB="$RUN_JOB -bdf $makebdf " -fi -if test $MPITYPE = "myrinet" -a "$host" -a "$MPIVERSION" != "MPICH-GM1.2.1..7" -then - # append $RUN_JOB to all lines of the host file - # and set RUN_JOB - $AWK -v args="$RUN_JOB" '{print $0,args}' $host > $host.$$ - /bin/mv $host.$$ $host - RUN_JOB=$RUN_JOB_TMP -fi -if test $MPITYPE = "intelmpi" -a "$host" -then - # construct config file, append $RUN_JOB to all lines of the config file - # and set RUN_JOB - if test "$INTELMPI_VERSION" = "HYDRA" - then - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf(" -host %s",$1); \ - printf(" -n %s",$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - else - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf("-host %s -n %s",$1,$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - fi - RUN_JOB=$RUN_JOB_TMP -fi -echo " " -echo "Final run stream value" -echo " RUNJOB="$RUN_JOB -if test "$deletelog" = no -then -echo " " >> $jid.log -echo "Final run stream value" >> $jid.log -echo " RUNJOB="$RUN_JOB >> $jid.log -fi - - -############################################################################## -# run marc using valgrind # -############################################################################## -#RUN_JOB="valgrind $RUN_JOB" -#RUN_JOB="valgrind --read-var-info=yes --gen-suppressions=yes $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=all -v $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=yes --error-limit=no $RUN_JOB" -############################################################################## - - -############################################################################## -# run the requested program in a queue # -############################################################################## - -if test "$deletelog" = yes -then - echo - date -else - echo >> $jid.log - date >> $jid.log -fi -if [ $qid = short -o $qid = long -o $qid = verylong -o $qid = at ] -then - -/bin/rm -f $jid.runmarcscript - - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - userobj=$usermoext.o - fi - cat > $jid.runmarcscript << END4 - if test "$user" - then - if test $MACHINENAME = "CRAY" - then - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTLOW $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - $SOLVERLIBS \ - $MARCCUDALIBS \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } -END4 -else - prgsav=yes -fi -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc -# - -cat >> $jid.runmarcscript << END5 - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# first remove all .out files and incremental restart files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - /bin/rm $DIRJOB/$numdom${jid}_i_*.t08 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null - /bin/rm $DIRJOB/${jid}_i_*.t08 2>/dev/null -fi - -if test $nprocdddm -gt 1 -then - $RUN_JOB 2>>$jid.log -else - $RUN_JOB 2>>$jid.log -fi - -if test $dllrun -eq 0; then - if test $prgsav = no - then - /bin/rm -f $bd$program 2>/dev/null - fi -else - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes - then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -fi -END5 - - -# Submit to marc batch queue -# -if [ $qid = at ] -then -QUENAME=at -SUBMCMD= -else -# -# Submit to qsub queue -# -QUENAME=qsub -SUBMCMD="-q $qid -o /dev/null -e $jid.batch_err_log -x -r $jid" -if test "$priority" -then - SUBMCMD=$SUBMCMD" -p $priority" -fi -if test "$att" -then - SUBMCMD=$SUBMCMD" -a $att" -fi -if test "$cpu" -then - SUBMCMD=$SUBMCMD" -lt $cpu" -fi - -fi -echo $QUENAME $SUBMCMD -#cat $jid.runmarcscript -$QUENAME $SUBMCMD < $jid.runmarcscript - -/bin/rm -f $jid.runmarcscript - -############################################################################## -# run the requested program in the background # -############################################################################## - -else -if test $qid = background -then - -# -# first remove all old .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi -# -# compile user subroutine if present -# -( -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_l $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - echo " $PRODUCT Exit number 3" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTLOW $user -o $userobj || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - echo " $PRODUCT Exit number 3" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc - -# - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - -$RUN_JOB & - -marcpid=$! -echo $marcpid > $DIRJOB/$jid.pid -wait $marcpid - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - fi - fi - fi -fi - - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi -) 1>>$jid.log 2>&1 & - - -############################################################################## -# run the requested program in the foreground # -############################################################################## - -else - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_l $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTLOW $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null -# done if no job id given -if test -z "$jid" -then - echo - echo only compilation requested - echo - exit -fi -# -# run marc -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi -# first remove all .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - $RUN_JOB - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - else - echo " " > /dev/null - fi - else - if test "$host" - then - mpdcleanup -a -f $jid.mfile - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.mfile 2> /dev/null - else - mpdcleanup -a -f $jid.hosts - /bin/rm $jid.hosts 2> /dev/null - fi - fi - fi -fi - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi - - -fi -fi diff --git a/installation/mods_MarcMentat/2016/Mentat_bin/kill7 b/installation/mods_MarcMentat/2016/Mentat_bin/kill7 deleted file mode 100644 index 6d1ff84bf..000000000 --- a/installation/mods_MarcMentat/2016/Mentat_bin/kill7 +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/sh - -if [ "$1" = "" ]; then - echo "usage: $0 job_name" - exit 1 -fi - -echo STOP > $1.cnt diff --git a/installation/mods_MarcMentat/2016/Mentat_bin/kill8 b/installation/mods_MarcMentat/2016/Mentat_bin/kill8 deleted file mode 100644 index 6d1ff84bf..000000000 --- a/installation/mods_MarcMentat/2016/Mentat_bin/kill8 +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/sh - -if [ "$1" = "" ]; then - echo "usage: $0 job_name" - exit 1 -fi - -echo STOP > $1.cnt diff --git a/installation/mods_MarcMentat/2016/Mentat_bin/kill9 b/installation/mods_MarcMentat/2016/Mentat_bin/kill9 deleted file mode 100644 index 6d1ff84bf..000000000 --- a/installation/mods_MarcMentat/2016/Mentat_bin/kill9 +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/sh - -if [ "$1" = "" ]; then - echo "usage: $0 job_name" - exit 1 -fi - -echo STOP > $1.cnt diff --git a/installation/mods_MarcMentat/2016/Mentat_bin/submit7 b/installation/mods_MarcMentat/2016/Mentat_bin/submit7 deleted file mode 100644 index d0e3be475..000000000 --- a/installation/mods_MarcMentat/2016/Mentat_bin/submit7 +++ /dev/null @@ -1,187 +0,0 @@ -#!/bin/sh -# -# The exit status of this script is read by Mentat. -# Normal exit status is 0. -# - -DIR=%INSTALLDIR%/marc%VERSION% -if test $MARCDIR1 -then - DIR=$MARCDIR1 -fi - -if test -z "$DIR"; then - REALCOM="`ls -l $0 |awk '{ print $NF; }'`" - DIRSCRIPT=`dirname $REALCOM` - case $DIRSCRIPT in - \/*) - ;; - *) - DIRSCRIPT=`pwd`/$DIRSCRIPT - ;; - esac - . $DIRSCRIPT/getarch - - DIR="$MENTAT_MARCDIR" -fi - -SRCEXT=.f -SRCEXTC=.F -RSTEXT=.t08 -PSTEXT=.t19 -PSTEXTB=.t16 -VWFCEXT=.vfs - -slv=$1 -version=$2 -ndom_fea_solver=$3 -ndom_preprocessor=$4 -hostfile=$5 -compat=$6 -job=$7 -srcfile=$8 -srcmeth=$9 -shift 9 # cannot use $10, $11, ... -restart=$1 -postfile=$2 -viewfactorsfile=$3 -autorst=$4 -copy_datfile="-ci $5" -copy_postfile="-cr $6" -scr_dir=$7 -dcoup=$8 -assem_recov_nthread=$9 -shift 9 # cannot use $10, $11, ... -nthread=$1 -nsolver=$2 -mode=$3 -gpu=$4 - -if [ "$slv" != "" -a "$slv" != "marc" ]; then - slv="-iam sfm" -else - slv="" -fi - -if [ "$ndom_fea_solver" != "" -a "$ndom_fea_solver" != "1" ]; then - nprocds="-nprocds $ndom_fea_solver" -else - nprocd="" - if [ "$ndom_preprocessor" != "" -a "$ndom_preprocessor" != "1" ]; then - nprocd="-nprocd $ndom_preprocessor" - else - nprocd="" - fi -fi - -if [ "$srcfile" != "" -a "$srcfile" != "-" ]; then - srcfile=`echo $srcfile | sed "s/$SRCEXT$//" | sed "s/$SRCEXTC$//"` - case "$srcmeth" in - -) - srcfile="-u $srcfile" - ;; - compsave) - srcfile="-u $srcfile -save y" - ;; - runsaved) - srcfile=${srcfile%.*}".marc" - srcfile="-prog $srcfile" - ;; - esac -else - srcfile="" -fi - -if [ "$restart" != "" -a "$restart" != "-" ]; then - restart=`echo $restart | sed "s/$RSTEXT$//"` - restart="-r $restart" -else - restart="" -fi - -if [ "$postfile" != "" -a "$postfile" != "-" ]; then - postfile=`echo $postfile | sed "s/$PSTEXT$//"` - postfile=`echo $postfile | sed "s/$PSTEXTB$//"` - postfile="-pid $postfile" -else - postfile="" -fi - -if [ "$viewfactorsfile" != "" -a "$viewfactorsfile" != "-" ]; then - viewfactorsfile=`echo $viewfactorsfile | sed "s/$VWFCEXT$//"` - viewfactorsfile="-vf $viewfactorsfile" -else - viewfactorsfile="" -fi - -if [ "$hostfile" != "" -a "$hostfile" != "-" ]; then - hostfile="-ho $hostfile" -else - hostfile="" -fi - -if [ "$compat" != "" -a "$compat" != "-" ]; then - compat="-co $compat" -else - compat="" -fi - -if [ "$scr_dir" != "" -a "$scr_dir" != "-" ]; then - scr_dir="-sd $scr_dir" -else - scr_dir="" -fi - -if [ "$dcoup" != "" -a "$dcoup" != "0" ]; then - dcoup="-dcoup $dcoup" -else - dcoup="" -fi - -if [ "$assem_recov_nthread" != "" -a "$assem_recov_nthread" != "1" ]; then - assem_recov_nthread="-nthread_elem $assem_recov_nthread" -else - assem_recov_nthread="" -fi - -if [ "$nthread" != "" -a "$nthread" != "0" -a "$nthread" != "1" ]; then - nthread="-nthread $nthread" -else - nthread="" -fi - -if [ "$nsolver" != "" -a "$nsolver" != "0" ]; then - nsolver="-nsolver $nsolver" -else - nsolver="" -fi - -case "$mode" in - 4) mode="-mo i4" ;; - 8) mode="-mo i8" ;; - *) mode= ;; -esac - -if [ "$gpu" != "" -a "$gpu" != "-" ]; then - gpu="-gpu $gpu" -else - gpu="" -fi - -rm -f $job.cnt -rm -f $job.sts -rm -f $job.out -rm -f $job.log - -# To prevent a mismatch with the python version used by the solver -# do *not* prepend $MENTAT_INSTALL_DIR/python/bin to environment variable PATH -# unset environment variables PYTHONHOME and PYTHONPATH -unset PYTHONHOME -unset PYTHONPATH - -"${DIR}/tools/run_damask_h" $slv -j $job -v n -b y $nprocds $nprocd -autorst $autorst \ - $srcfile $restart $postfile $viewfactorsfile $hostfile \ - $compat $copy_datfile $copy_postfile $scr_dir $dcoup \ - $assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1 -sleep 1 -exit 0 diff --git a/installation/mods_MarcMentat/2016/Mentat_bin/submit8 b/installation/mods_MarcMentat/2016/Mentat_bin/submit8 deleted file mode 100644 index d466fc6ab..000000000 --- a/installation/mods_MarcMentat/2016/Mentat_bin/submit8 +++ /dev/null @@ -1,187 +0,0 @@ -#!/bin/sh -# -# The exit status of this script is read by Mentat. -# Normal exit status is 0. -# - -DIR=%INSTALLDIR%/marc%VERSION% -if test $MARCDIR1 -then - DIR=$MARCDIR1 -fi - -if test -z "$DIR"; then - REALCOM="`ls -l $0 |awk '{ print $NF; }'`" - DIRSCRIPT=`dirname $REALCOM` - case $DIRSCRIPT in - \/*) - ;; - *) - DIRSCRIPT=`pwd`/$DIRSCRIPT - ;; - esac - . $DIRSCRIPT/getarch - - DIR="$MENTAT_MARCDIR" -fi - -SRCEXT=.f -SRCEXTC=.F -RSTEXT=.t08 -PSTEXT=.t19 -PSTEXTB=.t16 -VWFCEXT=.vfs - -slv=$1 -version=$2 -ndom_fea_solver=$3 -ndom_preprocessor=$4 -hostfile=$5 -compat=$6 -job=$7 -srcfile=$8 -srcmeth=$9 -shift 9 # cannot use $10, $11, ... -restart=$1 -postfile=$2 -viewfactorsfile=$3 -autorst=$4 -copy_datfile="-ci $5" -copy_postfile="-cr $6" -scr_dir=$7 -dcoup=$8 -assem_recov_nthread=$9 -shift 9 # cannot use $10, $11, ... -nthread=$1 -nsolver=$2 -mode=$3 -gpu=$4 - -if [ "$slv" != "" -a "$slv" != "marc" ]; then - slv="-iam sfm" -else - slv="" -fi - -if [ "$ndom_fea_solver" != "" -a "$ndom_fea_solver" != "1" ]; then - nprocds="-nprocds $ndom_fea_solver" -else - nprocd="" - if [ "$ndom_preprocessor" != "" -a "$ndom_preprocessor" != "1" ]; then - nprocd="-nprocd $ndom_preprocessor" - else - nprocd="" - fi -fi - -if [ "$srcfile" != "" -a "$srcfile" != "-" ]; then - srcfile=`echo $srcfile | sed "s/$SRCEXT$//" | sed "s/$SRCEXTC$//"` - case "$srcmeth" in - -) - srcfile="-u $srcfile" - ;; - compsave) - srcfile="-u $srcfile -save y" - ;; - runsaved) - srcfile=${srcfile%.*}".marc" - srcfile="-prog $srcfile" - ;; - esac -else - srcfile="" -fi - -if [ "$restart" != "" -a "$restart" != "-" ]; then - restart=`echo $restart | sed "s/$RSTEXT$//"` - restart="-r $restart" -else - restart="" -fi - -if [ "$postfile" != "" -a "$postfile" != "-" ]; then - postfile=`echo $postfile | sed "s/$PSTEXT$//"` - postfile=`echo $postfile | sed "s/$PSTEXTB$//"` - postfile="-pid $postfile" -else - postfile="" -fi - -if [ "$viewfactorsfile" != "" -a "$viewfactorsfile" != "-" ]; then - viewfactorsfile=`echo $viewfactorsfile | sed "s/$VWFCEXT$//"` - viewfactorsfile="-vf $viewfactorsfile" -else - viewfactorsfile="" -fi - -if [ "$hostfile" != "" -a "$hostfile" != "-" ]; then - hostfile="-ho $hostfile" -else - hostfile="" -fi - -if [ "$compat" != "" -a "$compat" != "-" ]; then - compat="-co $compat" -else - compat="" -fi - -if [ "$scr_dir" != "" -a "$scr_dir" != "-" ]; then - scr_dir="-sd $scr_dir" -else - scr_dir="" -fi - -if [ "$dcoup" != "" -a "$dcoup" != "0" ]; then - dcoup="-dcoup $dcoup" -else - dcoup="" -fi - -if [ "$assem_recov_nthread" != "" -a "$assem_recov_nthread" != "1" ]; then - assem_recov_nthread="-nthread_elem $assem_recov_nthread" -else - assem_recov_nthread="" -fi - -if [ "$nthread" != "" -a "$nthread" != "0" -a "$nthread" != "1" ]; then - nthread="-nthread $nthread" -else - nthread="" -fi - -if [ "$nsolver" != "" -a "$nsolver" != "0" ]; then - nsolver="-nsolver $nsolver" -else - nsolver="" -fi - -case "$mode" in - 4) mode="-mo i4" ;; - 8) mode="-mo i8" ;; - *) mode= ;; -esac - -if [ "$gpu" != "" -a "$gpu" != "-" ]; then - gpu="-gpu $gpu" -else - gpu="" -fi - -rm -f $job.cnt -rm -f $job.sts -rm -f $job.out -rm -f $job.log - -# To prevent a mismatch with the python version used by the solver -# do *not* prepend $MENTAT_INSTALL_DIR/python/bin to environment variable PATH -# unset environment variables PYTHONHOME and PYTHONPATH -unset PYTHONHOME -unset PYTHONPATH - -"${DIR}/tools/run_damask" $slv -j $job -v n -b y $nprocds $nprocd -autorst $autorst \ - $srcfile $restart $postfile $viewfactorsfile $hostfile \ - $compat $copy_datfile $copy_postfile $scr_dir $dcoup \ - $assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1 -sleep 1 -exit 0 diff --git a/installation/mods_MarcMentat/2016/Mentat_bin/submit9 b/installation/mods_MarcMentat/2016/Mentat_bin/submit9 deleted file mode 100644 index 207a61803..000000000 --- a/installation/mods_MarcMentat/2016/Mentat_bin/submit9 +++ /dev/null @@ -1,187 +0,0 @@ -#!/bin/sh -# -# The exit status of this script is read by Mentat. -# Normal exit status is 0. -# - -DIR=%INSTALLDIR%/marc%VERSION% -if test $MARCDIR1 -then - DIR=$MARCDIR1 -fi - -if test -z "$DIR"; then - REALCOM="`ls -l $0 |awk '{ print $NF; }'`" - DIRSCRIPT=`dirname $REALCOM` - case $DIRSCRIPT in - \/*) - ;; - *) - DIRSCRIPT=`pwd`/$DIRSCRIPT - ;; - esac - . $DIRSCRIPT/getarch - - DIR="$MENTAT_MARCDIR" -fi - -SRCEXT=.f -SRCEXTC=.F -RSTEXT=.t08 -PSTEXT=.t19 -PSTEXTB=.t16 -VWFCEXT=.vfs - -slv=$1 -version=$2 -ndom_fea_solver=$3 -ndom_preprocessor=$4 -hostfile=$5 -compat=$6 -job=$7 -srcfile=$8 -srcmeth=$9 -shift 9 # cannot use $10, $11, ... -restart=$1 -postfile=$2 -viewfactorsfile=$3 -autorst=$4 -copy_datfile="-ci $5" -copy_postfile="-cr $6" -scr_dir=$7 -dcoup=$8 -assem_recov_nthread=$9 -shift 9 # cannot use $10, $11, ... -nthread=$1 -nsolver=$2 -mode=$3 -gpu=$4 - -if [ "$slv" != "" -a "$slv" != "marc" ]; then - slv="-iam sfm" -else - slv="" -fi - -if [ "$ndom_fea_solver" != "" -a "$ndom_fea_solver" != "1" ]; then - nprocds="-nprocds $ndom_fea_solver" -else - nprocd="" - if [ "$ndom_preprocessor" != "" -a "$ndom_preprocessor" != "1" ]; then - nprocd="-nprocd $ndom_preprocessor" - else - nprocd="" - fi -fi - -if [ "$srcfile" != "" -a "$srcfile" != "-" ]; then - srcfile=`echo $srcfile | sed "s/$SRCEXT$//" | sed "s/$SRCEXTC$//"` - case "$srcmeth" in - -) - srcfile="-u $srcfile" - ;; - compsave) - srcfile="-u $srcfile -save y" - ;; - runsaved) - srcfile=${srcfile%.*}".marc" - srcfile="-prog $srcfile" - ;; - esac -else - srcfile="" -fi - -if [ "$restart" != "" -a "$restart" != "-" ]; then - restart=`echo $restart | sed "s/$RSTEXT$//"` - restart="-r $restart" -else - restart="" -fi - -if [ "$postfile" != "" -a "$postfile" != "-" ]; then - postfile=`echo $postfile | sed "s/$PSTEXT$//"` - postfile=`echo $postfile | sed "s/$PSTEXTB$//"` - postfile="-pid $postfile" -else - postfile="" -fi - -if [ "$viewfactorsfile" != "" -a "$viewfactorsfile" != "-" ]; then - viewfactorsfile=`echo $viewfactorsfile | sed "s/$VWFCEXT$//"` - viewfactorsfile="-vf $viewfactorsfile" -else - viewfactorsfile="" -fi - -if [ "$hostfile" != "" -a "$hostfile" != "-" ]; then - hostfile="-ho $hostfile" -else - hostfile="" -fi - -if [ "$compat" != "" -a "$compat" != "-" ]; then - compat="-co $compat" -else - compat="" -fi - -if [ "$scr_dir" != "" -a "$scr_dir" != "-" ]; then - scr_dir="-sd $scr_dir" -else - scr_dir="" -fi - -if [ "$dcoup" != "" -a "$dcoup" != "0" ]; then - dcoup="-dcoup $dcoup" -else - dcoup="" -fi - -if [ "$assem_recov_nthread" != "" -a "$assem_recov_nthread" != "1" ]; then - assem_recov_nthread="-nthread_elem $assem_recov_nthread" -else - assem_recov_nthread="" -fi - -if [ "$nthread" != "" -a "$nthread" != "0" -a "$nthread" != "1" ]; then - nthread="-nthread $nthread" -else - nthread="" -fi - -if [ "$nsolver" != "" -a "$nsolver" != "0" ]; then - nsolver="-nsolver $nsolver" -else - nsolver="" -fi - -case "$mode" in - 4) mode="-mo i4" ;; - 8) mode="-mo i8" ;; - *) mode= ;; -esac - -if [ "$gpu" != "" -a "$gpu" != "-" ]; then - gpu="-gpu $gpu" -else - gpu="" -fi - -rm -f $job.cnt -rm -f $job.sts -rm -f $job.out -rm -f $job.log - -# To prevent a mismatch with the python version used by the solver -# do *not* prepend $MENTAT_INSTALL_DIR/python/bin to environment variable PATH -# unset environment variables PYTHONHOME and PYTHONPATH -unset PYTHONHOME -unset PYTHONPATH - -"${DIR}/tools/run_damask_l" $slv -j $job -v n -b y $nprocds $nprocd -autorst $autorst \ - $srcfile $restart $postfile $viewfactorsfile $hostfile \ - $compat $copy_datfile $copy_postfile $scr_dir $dcoup \ - $assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1 -sleep 1 -exit 0 diff --git a/installation/mods_MarcMentat/2017/Marc_tools/comp_damask b/installation/mods_MarcMentat/2017/Marc_tools/comp_damask deleted file mode 100644 index 2d144b8a4..000000000 --- a/installation/mods_MarcMentat/2017/Marc_tools/comp_damask +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/ksh -# 1st arg: $DIR -# 2nd arg: $DIRJOB -# 3rd arg: $user -# 4th arg: $program -DIR=$1 -user=$3 -program=$4 -usernoext=$user -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - -# add BLAS options for linking - BLAS="%BLAS%" - -. $DIR/tools/include -DIRJOB=$2 -cd $DIRJOB -echo "Compiling and linking user subroutine $user on host `hostname`" -echo "program: $program" - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - userobj=$usernoext.o - - - $LOAD ${program} $DIR/lib/main.o\ - $DIR/lib/blkdta.o $DIR/lib/comm?.o \ - ${userobj-} \ - $DIR/lib/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ../lib/mdsrc.a \ - ../lib/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $BLAS \ - $SYSLIBS || \ - { - echo "$0: link failed for $usernoext.o on host `hostname`" - exit 1 - } - /bin/rm $userobj - /bin/rm $DIRJOB/*.mod diff --git a/installation/mods_MarcMentat/2017/Marc_tools/comp_damask_h b/installation/mods_MarcMentat/2017/Marc_tools/comp_damask_h deleted file mode 100644 index 01464f095..000000000 --- a/installation/mods_MarcMentat/2017/Marc_tools/comp_damask_h +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/ksh -# 1st arg: $DIR -# 2nd arg: $DIRJOB -# 3rd arg: $user -# 4th arg: $program -DIR=$1 -user=$3 -program=$4 -usernoext=$user -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - -# add BLAS options for linking - BLAS="%BLAS%" - -. $DIR/tools/include -DIRJOB=$2 -cd $DIRJOB -echo "Compiling and linking user subroutine $user on host `hostname`" -echo "program: $program" - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - userobj=$usernoext.o - - - $LOAD ${program} $DIR/lib/main.o\ - $DIR/lib/blkdta.o $DIR/lib/comm?.o \ - ${userobj-} \ - $DIR/lib/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ../lib/mdsrc.a \ - ../lib/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $BLAS \ - $SYSLIBS || \ - { - echo "$0: link failed for $usernoext.o on host `hostname`" - exit 1 - } - /bin/rm $userobj - /bin/rm $DIRJOB/*.mod diff --git a/installation/mods_MarcMentat/2017/Marc_tools/comp_damask_l b/installation/mods_MarcMentat/2017/Marc_tools/comp_damask_l deleted file mode 100644 index 31b5cd175..000000000 --- a/installation/mods_MarcMentat/2017/Marc_tools/comp_damask_l +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/ksh -# 1st arg: $DIR -# 2nd arg: $DIRJOB -# 3rd arg: $user -# 4th arg: $program -DIR=$1 -user=$3 -program=$4 -usernoext=$user -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` -usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - -# add BLAS options for linking - BLAS="%BLAS%" - -. $DIR/tools/include -DIRJOB=$2 -cd $DIRJOB -echo "Compiling and linking user subroutine $user on host `hostname`" -echo "program: $program" - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - userobj=$usernoext.o - - - $LOAD ${program} $DIR/lib/main.o\ - $DIR/lib/blkdta.o $DIR/lib/comm?.o \ - ${userobj-} \ - $DIR/lib/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ../lib/mdsrc.a \ - ../lib/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $BLAS \ - $SYSLIBS || \ - { - echo "$0: link failed for $usernoext.o on host `hostname`" - exit 1 - } - /bin/rm $userobj - /bin/rm $DIRJOB/*.mod diff --git a/installation/mods_MarcMentat/2017/Marc_tools/run_damask b/installation/mods_MarcMentat/2017/Marc_tools/run_damask deleted file mode 100644 index 77977db78..000000000 --- a/installation/mods_MarcMentat/2017/Marc_tools/run_damask +++ /dev/null @@ -1,4122 +0,0 @@ -#!/bin/ksh -############################################################################## -# # -# run_marc - run a marc job # -# ------------------------- # -# # -# usage: run_marc -j jid { options } # -# # -# where standard options are: required: defaults: # -# -------------------------- # -# # -# -j* jid job id number. ** YES ** . # -# -pr* prog program name. . marc # -# -v* y|n do or do not verify inputs. . yes # -# -q* s|l|v|b|f batch queue name or background, . short # -# foreground. # -# -b* as alternative to option -q* # -# # -# ( batch queues only : # -# -pq* intra queue priority. . . # -# -at DATE/TIME delay start of job. . . # -# format : January,1,1990,12:31 # -# or : today,5pm # -# -cpu* secs job CPU limit . . ) # -# # -# -r* rid restart file job id. . . # -# -si* sid substructure file id. . . # -# -pi* post post file job id. . . # -# -de* did defaults file . no # -# -vf vid viewfactor . no # -# # -# -u* user user subroutine. . . # -# -obj obj user objects or libraries. . . # -# -sa* y|n do or do not save load module. . no # -# -autorst auto restart flag for auto forge . no # -# -me manual remeshing control . no # -# -ml memory limit in Mbyte # -# -mo This option is deprecated. As of Marc 2015, only # -# the integer*8 version is available. # -# -mpi selects MPI version # -# each platform has a default MPI version and some # -# have an alternative version. see the include file # -# for the respective platform # -# MPI_DEFAULT defines the default MPI version # -# MPI_OTHER defines versions one can switch to # -# -dcoup for contact decoupling # -# currently not supported # -# -dir directory where the job i/o should take place. # -# defaults to current directory. # -# -sdir directory where scratch files are created # -# defaults to current directory. # -# # -# -alloc only perform memory allocation test, no analysis # -# -list y only list options in the input file, no analysis # -# -fe num set feature number "num" for the run. only one allowed # -# -dytran flag to switch from Dytran to Marc # -# dytran = 0, program will run w/o Marc-Dytran Switch # -# = 1, program will restart Marc after Dytran run # -# >= 2, Not supported yet. # -# currently not supported # -# -ou force analysis to use out-of-core control # -# =0, not used # -# =1, element storage out-of-core # -# -dll run marc using shared library libmarc.so and exe_marc # -# =1, used # -# =2, do not free streaming input memory # -# =3, run with marc input deck # -# -trk run marc for post-tracking # -# -gpuid run marc using GPGPU capability # -# specify gpuid on to be used in the analysis. Multiple # -# IDs may be assigned for DDM runs. # -# Separate a list of IDs with a colon. Each DMP # -# process will be assigned a GPU ID in round robin fastion# -# = 0 # -# = 0:1 etc... # -# # -# where parallel options are: # -# -------------------------- # -# # -# itree, host, and comp options are available for the domain # -# decomposition only. # -# MARC_NUMBER_OF_THREADS, nthread, and dir options always available. # -# # -# # -# -nprocd number of domains. # -# defaults to single domain solution. # -# -nprocds number of domains if single input file. # -# defaults to single domain solution. # -# -nps same as -nprocds. # -# -nsolver number of solver tasks for solver types 12 and 13 # -# these are distributed tasks operating via MPI # -# -nthread_elem number of threads for element assembly and recovery # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by element assembly # -# recovery. # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_elem option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_elem specified. # -# -nthread_solver number of threads for solver types 6, 8, and 11 # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by 6, 8, and 11 # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_solver option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_solver specified. # -# -nthread Same as -nthread_solver. # -# -itree message passing tree type for domain decomposition. # -# for debugging purposes; should not normally be used. # -# -host hostfile name for distributed execution on network. # -# defaults to no hostfile, unless jobid.defhost exists. # -# if jobid.defhost exists, only -np(s) necessary # -# -comp* y|n to be used with user routines on a network of # -# incompatible machines. # -# if set to no, a separate executable will be created # -# for each machine on the network. # -# if set to yes, the executable located on the machine # -# from which marc is started will be used on all machines.# -# defaults to no if O/S versions different on machines. # -# # -# -ci y|n copy input files to remote hosts (default: yes) # -# if "yes", input files are automatically copied to # -# remote hosts for a network run if necessary. # -# -cr y|n copy post files from remote hosts (default: yes) # -# if "yes", post files are automatically copied back from # -# remote hosts for a network run if necessary. # -############################################################################## -# set DIR to the directory in which this script is -REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`" -DIR=`dirname $REALCOM` -# make sure DIR has an absolute path -case $DIR in - \/*) - ;; - *) - DIR=`pwd`/$DIR - ;; -esac -DIRSCRIPT=$DIR -AWK=awk -ARCH=`uname -a | cut -f 1 -d " "` -# Sun has a bad awk, use nawk instead -if test $ARCH = "SunOS" -then - AWK=nawk -fi -BASENAME=basename -# Sun has an incorrect /bin/basename, check if /usr/ucb/basename exists -if test $ARCH = "SunOS" -then - if test -x /usr/ucb/basename - then - BASENAME=/usr/ucb/basename - fi -fi - -# echo command line in the case of ECHO_COMMAND is true -if test "$ECHO_COMMAND" = true ; then - echo command "$0" "$@" -fi - -# -# "mode" selects version, i4 or i8 -# default is i4 -# this can be changed by a file run_marc_defaults -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MODE i8 -# it can also be set by the environmental variable MARC_INTEGER_SIZE -# and by the command line option "-mo" -# -mode= -modeerror= -modeoption= -if test -f $DIRSCRIPT/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $DIRSCRIPT/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $DIRSCRIPT/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $DIRSCRIPT/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -f $HOME/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $HOME/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $HOME/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $HOME/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -n "$MARC_INTEGER_SIZE" ; then - mode=$MARC_INTEGER_SIZE -fi -if test -z "$mode" ; then - mode=i8 -fi -case $mode in - i4) - modeerror="bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - modeoption=error - echo $modeerror - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo "bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - exit - ;; -esac - -setmode=false -for arg in $* ; do - if $setmode ; then - mode=$arg - case $mode in - i4) - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo " " - echo "error, version mode must be i8" - echo " " - echo " use -mo i8 " - echo " " - exit - ;; - esac - setmode=false - fi - if [ ${arg}X = -moX -o ${arg}X = -MOX ] ; then - echo - echo warning: the option -mo is deprecated, as of Marc 2015, only the integer*8 version is available - echo - setmode=true - fi - if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - fi - if [ ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - fi -done - -# set to i4 version for 32 bit Linux -if test "`uname -s`" = "Linux"; then - if test "`uname -m`" = "i686"; then - mode=i4 - MARC_INTEGER_SIZE=i4 - export MARC_INTEGER_SIZE - fi -fi - - -. "$DIR/getarch" - - -# getting user subroutine file name -found=0 -for i in "$@"; do - if test $found = 1; then - DAMASK_USER=$i - found=0 - fi - case $i in - -u* | -U*) - found=1 - ;; - esac -done -# sourcing include_linux64 (needs DAMASK_USER to be set) -. $MARC_INCLUDE - -# - -# -# Dynamically determine the echo syntax -# - -case "`echo '\c'`" in - '\c') - ECHO='echo -n' - ECHOTXT=' ' - ;; - *) - ECHO='echo' - ECHOTXT=' \c' - ;; -esac - -# -# Variables for the MARC environment -# - -PRODUCT="Marc" -EXITMSG=$MARC_TOOLS/MESSAGES -export EXITMSG -FLEXDIR=$DIR/../flexlm/licenses -export FLEXDIR -TIMCHK=3600 -export TIMCHK -BINDIR=$MARC_BIN -export BINDIR -AFMATDAT=$MARC_RUNTIME/AF_flowmat/ -export AFMATDAT -export MESHERDIR -MSC_LICENSE_FINPROC=0 -export MSC_LICENSE_FINPROC -# -# define directory path to global unified material database -# -MATFILE= -export MATFILE - -# -# define memory limit -# first set to MEMLIMIT from include -# -ml option overrules if specified -memlimit=$MEMLIMIT -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -# -if test $MACHINENAME = "HP" -then - SHLIB_PATH=$MARC_LIB:$MARC_LIB_SHARED:$SHLIB_PATH - export SHLIB_PATH -fi -# the one for IBM is defined futher down - -LD_LIBRARY_PATH=$MARC_LIB_SHARED:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MARC_LIB:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MESHERDIR:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$SFMATDIR:$LD_LIBRARY_PATH -LD_LIBRARY64_PATH=$MARC_LIB:$LD_LIBRARY64_PATH -LD_LIBRARYN32_PATH=$MARC_LIB:$LD_LIBRARYN32_PATH -export LD_LIBRARY_PATH -export LD_LIBRARY64_PATH -export LD_LIBRARYN32_PATH - -atexit() { -kill -15 $$ -# -if test $MPITYPE = "myrinet" -then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi -fi -} - -trap "atexit" 2 - -# -# defaults -# - -prog=marc -exefile=marc -jid= -rid= -pid= -sid= -did= -vid= -user= -usernoext= -objs= -qid=background -cpu= -priority= -att= -trk= -verify=yes -prgsav=no -rmdll=no -cpdll=no -progdll= -pathdll= -error= -nprocd=0 -nprocdddm=1 -nprocdddmprint= -icreated=0 -nprocdarg= -nsolver=0 -nsolverarg=-ns -if test $nprocds -then - if test $nprocds -gt 1 - then - nprocdddm=$nprocds - nprocdddmprint=$nprocds - icreated=1 - nprocdarg=-nprocds - fi -fi -ntprint=0 -nt=-1 -nte=-1 -nts=-1 -ntarg=-nt -ntearg=-nte -ntsarg=-nts -nteprint= -ntsprint= -gpuids= -nauto=0 -ndcoup=0 -ndytran=0 -noutcore=0 -dllrun=0 -mesh=0 -itree=0 -iam= -ddm_arc=0 -link= -trkrun=0 -DIRJOB=`pwd` -DIRSCR=$DIRJOB -DIRSCRSET= -autoforge=0 -dotdat=.dat -dotdefhost=.defhost -host= -numhost= -mfile= -userhost= -makebdf= -cpinput=yes -cpresults=yes -marcdll=libmarc.$EXT_DLL -# define hostname and strip off extensions (alpha.aaa.com) -thishost=`hostname` -thishost=${thishost%%.*} -compatible=unknown -numfield=1 -justlist= -feature= -mpioption=false -iprintsimufact= -MDSRCLIB=$MARC_LIB/mdsrc.a -# -# check run_marc_defaults file for default MPI setting -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MPI -# -value= -file= -if test -f $DIRSCRIPT/run_marc_defaults; then - value=`$AWK '{if ($1 == "MARC_MPI") {print $2}}' $DIRSCRIPT/run_marc_defaults` - value=`echo $value | $AWK '{print $NF}'` - if test -n "$value"; then - file=$DIRSCRIPT/run_marc_defaults - fi -fi -if test -f $HOME/run_marc_defaults; then - value=`$AWK '{if ($1 == "MARC_MPI") {print $2}}' $HOME/run_marc_defaults` - value=`echo $value | $AWK '{print $NF}'` - if test -n "$value"; then - file=$HOME/run_marc_defaults - fi -fi -if test -n "$value"; then - MARC_MPITYPE=$value - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - echo " " - echo " error, incorrect option for MARC_MPI" - echo " defined in $file: $MARC_MPITYPE" - echo " valid options: $MPI_DEFAULT $MPI_OTHER" - echo " " - exit - fi - if test "$value" != "$MPI_DEFAULT"; then - exefile=marc_$value - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a_$value - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a_$value" - fi - fi -fi -# -# -# allow scratch directory to be specified with environmental variable -# MARCSCRATCH -if test $MARCSCRATCH -then - if test -d $MARCSCRATCH - then - DIRSCR=$MARCSCRATCH - else - echo "error, scratch directory '$MARCSCRATCH'" - echo " specified via environmental variable MARCSCRATCH does not exist" - exit - fi -fi -# -############################################################################## -# parse input - arguments always come in pairs # -############################################################################## - -arg=$1 -if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - shift - arg=$1 -fi -while [ -n "$arg" ] -do - shift - value=$1 - case $arg in - -al* | -AL*) - LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - export LD_LIBRARY_PATH - $MARC_BIN/marc -alloc 1 - exit - ;; - -li* | -LI*) - justlist=yes - ;; - -fe* | -FE*) - feature=$value - - ;; - -pr* | -PR*) - if test `dirname $value` = '.' - then - prog=`$BASENAME $value .marc` - progdll=`$BASENAME $value` - else - prog=`dirname $value`/`$BASENAME $value .marc` - progdll=`dirname $value`/`$BASENAME $value` - fi - prdir=`dirname $value` - case $prdir in - \/*) - ;; - *) - prog=`pwd`/$prdir/$prog - ;; - esac - ;; - -j* | -J*) - jid=`$BASENAME $value $dotdat` - DIRJID=`dirname $value` - case $DIRJID in - \/*) - ;; - *) - DIRJID=`pwd`/$DIRJID - ;; - esac - ;; - -r* | -R*) - rid=`$BASENAME $value .t08` - DIRRID=`dirname $value` - case $DIRRID in - \/*) - ;; - *) - DIRRID=`pwd`/$DIRRID - ;; - esac - ;; - -si* | -SI*) - sid=$value - DIRSID=`dirname $value` - case $DIRSID in - \/*) - ;; - *) - DIRSID=`pwd`/$DIRSID - ;; - esac - ;; - -pi* | -PI*) - if test -f $value.t19 - then - pid=`$BASENAME $value .t19` - else - pid=`$BASENAME $value .t16` - fi - DIRPID=`dirname $value` - case $DIRPID in - \/*) - ;; - *) - DIRPID=`pwd`/$DIRPID - ;; - esac - ;; - -bdf | -BDF) - makebdf=1 - ;; - -de* | -DE*) - did=`$BASENAME $value $dotdat` - DIRDID=`dirname $value` - case $DIRDID in - \/*) - ;; - *) - DIRDID=`pwd`/$DIRDID - ;; - esac - ;; - -vf | -VF) - vid=`$BASENAME $value .vfs` - DIRVID=`dirname $value` - case $DIRVID in - \/*) - ;; - *) - DIRVID=`pwd`/$DIRVID - ;; - esac - ;; - -u* | -U*) - user=$value - case $user in - \/*) - ;; - *) - user=`pwd`/$user - ;; - esac - usernoext=$user - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - ;; - -obj | -OBJ) - objs="$value" - ;; - -q* | -Q*) - qid=$value - ;; - -b* | -B*) - case $value in - y* | Y*) - qid=background - ;; 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- -dc* | -DC*) - ndcoup=$value - ;; - -dy* | -DY*) - ndytran=$value - ;; - -ou* | -OU*) - noutcore=$value - ;; - -dll | -DLL) - dllrun=$value - ;; - -trk | -TRK) - trkrun=$value - ;; - -ddm | -DDM) - ddm_arc=$value - ;; - -me | -ME ) - mesh=$value - ;; - -ml | -ML ) - memlimit=$value - ;; - -mo | -MO ) - ;; - -mpi | -MPI ) - mpioption=true - MARC_MPITYPE=$value - if test "$value" != "$MPI_DEFAULT"; then - exefile=marc_$value - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a_$value - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a_$value" - fi - else - exefile=marc - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a" - fi - fi - ;; - -dir* | -DIR*) - DIRJOB=$value - case $DIRJOB in - \/*) - ;; - *) - DIRJOB=`pwd`/$DIRJOB - ;; - esac - if test -z "$DIRSCRSET" - then - DIRSCR=$DIRJOB - fi - ;; - -sd* | -SD*) - DIRSCR=$value - DIRSCRSET=yes - case $DIRSCR in - \/*) - ;; - *) - DIRSCR=`pwd`/$DIRSCR - ;; - esac - ;; - -ho* | -HO*) - host=$value - ;; - -co* | -CO*) - compatible=$value - ;; - -ci* | -CI*) - cpinput=$value - ;; - -cr* | -CR*) - cpresults=$value - ;; - *) - error="$error -$arg: invalid option" - break - ;; - esac - case $value in - -*) - error="$error -$arg: invalid name $value" - break - ;; - esac - shift - arg=$1 - if [ ${arg}X = -i8X -o ${arg}X = -I8X -o ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - shift - arg=$1 - fi -done -argc=`expr $# % 2` -if test $argc -eq 1 -then -# -# odd number of arguments -# - error="$error -argument list incomplete" -fi - -if test $nprocdddm -gt 0 -then -nprocd=$nprocdddm -fi - -if test $nsolver -gt 0 -then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi -fi -# Set defaults -if test $nt -eq -1 -then -nt=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nt -lt 0 -then -nt=0 -fi -if test $nte -eq -1 -then -nte=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nte -lt 0 -then -nte=0 -fi -if test $nts -eq -1 -then -nts=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nts -lt 0 -then -nts=0 -fi -# -# set number of element loop threads -# -ntprint=$nt -nteprint=$nte -# copy from -nprocd[s] -if test $nprocdddm -gt 1 -then - nteprint=$nprocdddm -fi -# override with -nthread_elem option -if test $nte -ne 0 -then -nteprint=$nte -fi -# check for minimum 1 threads per processes for DDM -if test $nprocdddm -gt 1 -then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi -fi -nte=$nteprint -# -# set number of Solver threads -# -ntsprint=$nts -# copy from -nthread or -nprocd[s] -if test $ntprint -ne 0 -then - ntsprint=$ntprint -else - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -fi -# override with -nthread_solver option -if test $nts -ne 0 -then - ntsprint=$nts -fi -# check for minimum 1 threads per solver process. -if test $nsolver -lt $nprocdddm -then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi -else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi -fi -if test $ntsprint -eq 1 -then - set ntsprint=0 -fi -nts=$ntsprint - -# set stack size for multi-threading. -export KMP_MONITOR_STACKSIZE=7M -export OMP_STACKSIZE=7M - -# -# deprecate -nthread option at arugment of marc -nt=0 -# Reset nprocdddmm, nsolver and threads if not given. -if test $nprocdddm -eq 0 -then - nprocdarg= -fi -if test $nprocdddm -eq 0 -then - nprocdddmprint= -fi -if test $nprocdddm -eq 0 -then - nprocdddm= -fi - -nsolverprint=$nsolver -if test $nsolver -eq 0 -then - nsolverprint= -fi -# end of threads setting. -gpuoption= -if test "$gpuids" = "" ; then - gpuoption= -else - gpuoption="-gp $gpuids" -fi - -if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH -else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH -fi -# Linux 64 + HPMPI, Below code is taken from include_linux64 -if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" -then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" -fi - -if test $nprocd -gt 1; then - if test -f $jid$dotdefhost; then - if test "$host" = ""; then - host=$jid$dotdefhost - fi - fi - if test -f hostfile_qa_$nprocd; then - if test "$host" = ""; then - host=hostfile_qa_$nprocd - fi - fi -fi - -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$dllrun" -eq 1 || test "$dllrun" -eq 2; then - dotdat=.inp - fi - - if test "$progdll"; then - /bin/cp ${progdll}_$marcdll $DIRJOB/$marcdll - rmdll=yes - pathdll=yes - progdll=${progdll}_$marcdll - else - progdll=$marcdll - fi - - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - pathdll=yes - fi -fi - -############################################################################## -# check parameter validity # -############################################################################## - -while test forever; do - -# -# check for input file existence -# -if test $nprocdddm -gt 1 -a $icreated -eq 0; then - if test ! -f $DIRJID/1$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/1$jid$dotdat not accessible" - fi - fi -else - if test ! -f $DIRJID/$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/$jid$dotdat not accessible" - fi - fi -fi - if test $nprocd -gt 1; then - if test "$host" ; then - if test ! -f $host; then - error="$error -host name file $host not accessible" - fi - fi - fi - -# -# check if the job is already running in the background -# -if test -f $DIRJOB/$jid.pid; then - error="$error -job is already running (the file $jid.pid exists)" -fi - -# -# if the program name is other than marc, then -# assume that this is a program in the users local directory -# - -bd=$MARC_BIN/ - -case $prog in - marc | MARC | $exefile) - program=$exefile - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 or $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - if test ! -f $user - then - error="$error -user subroutine file $user not accessible" - fi - fi - if test "$objs" - then - missingobjs= - for o in $objs - do - if test ! -f "$o" - then - if test -z "$missingobjs" - then - missingobjs="$o" - else - missingobjs="$missingobjs $o" - fi - fi - done - if test -n "$missingobjs" - then - error="$error -user object/library file(s) $missingobjs not accessible" - fi - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$vid" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRVID/1$vid.vfs - then - error="$error -view factor file $DIRVID/1$vid.vfs not accessible" - fi - else - if test ! -f $DIRVID/$vid.vfs - then - error="$error -view factor file $DIRVID/$vid.vfs not accessible" - fi - fi - fi - if $mpioption - then - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE (valid: $MPI_OTHER)" - fi - fi - ;; - *) - program=$prog.marc - case $prog in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 and $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - error="$error -program option may not be used with user subroutine" - fi - if test "$objs" - then - error="$error -program option may not be used with user objects or libraries" - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$nauto" - then - if test $nauto -gt 2 - then - error="$error -incorrect option for auto restart " - fi - fi - if test "$ndcoup" - then - if test $ndcoup -gt 3 - then - error="$error -incorrect option for contact decoupling " - fi - fi - if test "$ndytran" - then - if test $ndytran -gt 1 - then - error="$error -incorrect option for Marc-Dytran Switch " - fi - fi - if $mpioption - then - if test ! -x $MARC_BIN/$exefile - then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE " - fi - fi - ;; -esac - -############################################################################## -# check argument integrity # -############################################################################## - -if test "$jid" -then - : -else - if test "$user" - then -# allow user sub without giving job id - qid=foreground - verify=no - else - error="$error -job id required" -fi -fi - -if test $nprocd -gt 1 -then - if test $nauto -gt 0 - then - error="$error -cannot run DDM job with auto restart (-au) option " - fi -fi -case $qid in - S* | s*) - qid=short - ;; - L* | l*) - qid=long - ;; - V* | v*) - qid=verylong - ;; - B* | b*) - qid=background - ;; - F* | f*) - qid=foreground - ;; - A* | a*) - qid=at - ;; - *) - error="$error -bad value for queue_id option" - ;; -esac - -case $prgsav in - N* | n*) - prgsav=no - ;; - Y* | y*) - prgsav=yes - ;; - *) - error="$error -bad value for save option" - ;; -esac - -case $verify in - N* | n*) - verify=no - ;; - Y* | y*) - verify=yes - ;; - *) - error="$error -bad value for verify option" - ;; 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then - echo "DDM with ARC Mapper : $ddm_arc" >> $jid.log -fi -echo \ -"Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto " >> $jid.log -deletelog=no -fi -echo \ -" -Program name : $prog -Marc shared lib : $progdll -Version type : $mode -Job ID : $DIRJID/$jid -User subroutine name : $user -User objects/libs : $objs -Restart file job ID : $rid -Substructure file ID : $sid -Post file job ID : $pid -Defaults file ID : $did -View Factor file ID : $vid -Save generated module: $prgsav -MPI library : $MPITYPE -DDM processes : $nprocdddmprint -Element loop threads : $nteprint -Solver processes : $nsolverprint -Solver threads : $ntsprint" -if test "$iprintsimufact" = true ; then - echo "DDM with ARC Mapper : $ddm_arc" -fi -echo \ -"GPGPU option : $gpuids -Host file name : $host -Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto" - - -case $qid in - s* | S* | l* | L* | v* | V* ) - echo \ -"Queue priority : $priority -Queue CPU limit : $cpu -Queue start time : $att" - ;; -# * ) -# echo \ -#" " -# ;; -esac - -if test "$modeoption" -then - error=$modeerror -fi - -if test "$error" -then - if test $verify = yes - then - $ECHO "$error - -Please correct or quit(correct,quit,): $ECHOTXT" - error= - read answer - case $answer in - q* | Q*) - answer=quit - ;; - *) - answer=correct - ;; - esac - else - $ECHO "$error - $ECHOTXT" - echo " " - if test "$deletelog" = no - then - $ECHO "$error - $ECHOTXT" >> $jid.log - echo " " >> $jid.log - fi - answer=quit - fi -else - if test $verify = yes - then - $ECHO " -Are these parameters correct (yes,no,quit,)? $ECHOTXT" - read answer - case $answer in - q* | Q*) - answer=quit - ;; - y* | Y*) - answer=yes - ;; - *) - answer=no - ;; - esac - else - answer=yes - fi -fi - -case $answer in - no | correct) - -############################################################################## -# prompt for each value # -############################################################################## - - $ECHO " -Program name ($prog)? $ECHOTXT" - read value - if test "$value" - then - prog=$value - fi - $ECHO "Job ID ($jid)? $ECHOTXT" - read value - if test "$value" - then - jid=`$BASENAME $value $dotdat` - DIRJID=`dirname $value` - case $DIRJID in - \/*) - ;; 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then - gpuoption= - else - gpuoption="-gp $gpuids" - fi - if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH - fi - if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" - then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" - fi -# - if test $nprocd -gt 1 - then - $ECHO "Message passing type ($itree)? $ECHOTXT" - read value - if test "$value" - then - itree=$value - fi - $ECHO "Host file name ($host)? $ECHOTXT" - read value - if test "$value" - then - host=$value - fi - if test $nprocdddm -gt 1 - then - $ECHO "Single input file? $ECHOTXT" - read value - case $value in - y* | Y*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - $ECHO "Compatible machines for DDM ($compatible)? $ECHOTXT" - read value - if test "$value" - then - compatible=$value - fi - $ECHO "Copy input files to remote hosts ($cpinput)? $ECHOTXT" - read value - if test "$value" - then - cpinput=$value - fi - $ECHO "Copy post files from remote hosts ($cpresults)? $ECHOTXT" - read value - if test "$value" - then - cpresults=$value - fi - fi - fi - $ECHO "Run the job in the queue ($qid)? $ECHOTXT" - read value - if test "$value" - then - qid=$value - fi - case $qid in - s* | S* | l* | L* | v* | V* ) - $ECHO "Queue priority ($priority)? $ECHOTXT" - read value - if test "$value" - then - priority=$value - fi - $ECHO "Job starts at ($att)? $ECHOTXT" - read value - if test "$value" - then - att=$value - fi - $ECHO "Queue CPU limit ($cpu)? $ECHOTXT" - read value - if test "$value" - then - cpu=$value - fi - ;; - * ) - ;; - esac - $ECHO "Auto Restart option ($nauto)? $ECHOTXT" - read value - if test "$value" - then - nauto=$value - fi - $ECHO "Run directory ($DIRJOB)? $ECHOTXT" - read value - if test "$value" - then - DIRJOB=$value - DIRSCR=$DIRJOB - fi - $ECHO "Scratch directory ($DIRSCR)? $ECHOTXT" - read value - if test "$value" - then - DIRSCR=$value - fi - ;; - quit) - exit 1 - ;; - *) - break - ;; - -esac - - if test $nt -eq -1 - then - nt=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nt -lt 0 - then - nt=0 - fi - -done -# -if test $nt -eq 0 -then - ntarg= -fi -if test $nt -eq 0 -then - ntprint= -fi -if test $nt -eq 0 -then - nt= -fi - -if test $nte -eq 0 -then - ntearg= -fi -if test $nte -eq 0 -then - nteprint= -fi -if test $nte -eq 0 -then - nte= -fi - -if test $nts -eq 0 -then - ntsarg= -fi -if test $nts -eq 0 -then - ntsprint= -fi -if test $nts -eq 0 -then - nts= -fi -# -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - pathdll=yes - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - fi - - if test "$pathdll"; then -# -# reset share lib path -# - if test $MACHINENAME = "HP" - then - SHLIB_PATH=$DIRJOB:$SHLIB_PATH - export SHLIB_PATH - fi - if test $MACHINENAME = "IBM" - then - LIBPATH=$DIRJOB:$LIBPATH - export LIBPATH - fi -# - LD_LIBRARY_PATH=$DIRJOB:$LD_LIBRARY_PATH - LD_LIBRARY64_PATH=$DIRJOB:$LD_LIBRARY64_PATH - LD_LIBRARYN32_PATH=$DIRJOB:$LD_LIBRARYN32_PATH - export LD_LIBRARY_PATH - export LD_LIBRARY64_PATH - export LD_LIBRARYN32_PATH - fi -fi -# end of dllrun>0 - - -if test $program = $exefile -o $program = $prog.marc -then - -# delete the old .log file unless we run in the background -if test "$deletelog" = yes -then - if test "$jid" - then - /bin/rm $jid.log 2>/dev/null - fi -else - echo - echo running the job in the background, see $jid.log - echo -fi - -# -# check if this is an autoforge or rezoning or radiation job -# -if test $nprocd -eq 1 -a "$jid" - -then - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^autoforge"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^rezoning"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^radiation"` - if test "$line" - then - autoforge=1 - fi -fi -# -# check that jobname for restarted run is not the same -# as restart file basename -# -if test "$rid" -then - if test "$jid" = "$rid" - then - echo " " - echo "ERROR: job name of current run is the same as job name" - echo " of the restarted job" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "ERROR: job name of current run is the same as job name" >> $jid.log - echo " of the restarted job" >> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi -fi - -# -# user objects/libraries used -# - - if test "$objs" - then - program="$DIRJOB/$jid.marc" - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# user subroutine used -# -# add DAMASK options for linking - DAMASK="-lstdc++" - - if test "$user" - then - program=$usernoext.marc - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# Special case for IBM using POE but not an SP machine -# in this case we always need a host file, also for serial jobs. -# -if test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP -then - MP_HOSTFILE=${jid}.host - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $nprocd -gt 1 - then - numdom=$nprocd - while test $numdom -gt 0 - do - hostname -s >> $MP_HOSTFILE - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - else - hostname -s > $MP_HOSTFILE - fi -fi -# -# check ssh for all hosts in host file -# -if test $nprocd -gt 1 -then -if test $MPITYPE = "intelmpi" -a "$INTELMPI_VERSION" = "HYDRA" - then -# get host list - if test "$host" - then - line=`grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' | uniq` -# count failing hosts - counter=0 - for i in $line - do - $RSH -o BatchMode=yes -o ConnectTimeout=10 $i uname -n - status=$? - if [[ $status != 0 ]] ; then - counter=$((counter+1)) - if [ "$counter" = "1" ]; then - echo " " - echo " error - connection test failed... " - echo " " - fi - echo " " - echo " connection test with ssh failed on host $i" - echo " check the following command: ssh $i uname -n " - echo " " - fi - done -# echo error message and quit - if test $counter -ne 0 - then - echo " " - echo " A parallel job using IntelMPI cannot be started. " - echo " The ssh command must be working correctly between " - echo " the computers used in the analysis. Furthermore, " - echo " it must be set up such that it does not prompt the " - echo " user for a password. " - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo " A parallel job using IntelMPI cannot be started. ">> $jid.log - echo " The ssh command must be working correctly between ">> $jid.log - echo " the computers used in the analysis. Furthermore, ">> $jid.log - echo " it must be set up such that it does not prompt the ">> $jid.log - echo " user for a password. ">> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi -fi -fi -# -# check correctness of host file; fix for user sub -# - if test $nprocd -gt 1 - then - -# construct the path name to the executable (execpath) - execpath=$MARC_BIN/$exefile - usersub=0 - if test $program = $prog.marc - then - execpath=$prog.marc - usersub=1 - fi - if test "$objs" - then - execpath="$DIRJOB/$jid.marc" - usersub=1 - fi - if test "$user" - then - execpath=$usernoext.marc - usersub=1 - fi - export execpath - execname=`$BASENAME $execpath` - - if test "$host" - then - userhost=$host - case $userhost in - \/* | \.\/*) - ;; - *) - userhost=`pwd`/$userhost - ;; - esac - -# check that the number of processes specified in the hostfile is -# equal to nprocd specified by -nprocd. - numproc=`grep -v '^#' $host | $AWK -v sum=0 '{sum=sum+$2}; END {print sum}'` - if test $nprocd -ne $numproc - then - echo " " - echo "error, the number of processes specified in the host file" - echo "must be equal to the number of processes given by -nprocd/-nsolver" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, the number of processes specified in the host file" >> $jid.log - echo "must be equal to the number of processes given by -nprocd/-nsolver" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - -# check for Myrinet that the number of processes per host is -# less than number of available user ports, 5 -# .gmpi directory must exist in user's home directory -# and must have write permission from remote hosts - if test $MPITYPE = "myrinet" - then - numproc=`grep -v '^#' $host | $AWK -v sum=1 '{if( $2 > 5) sum=6}; END {print sum}'` - if test $numproc -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes specified " - echo "in the hostfile must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes specified " >> $jid.log - echo "in the hostfile must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - if test ! -d ~/.gmpi - then - echo " " - echo "error, for Myrinet a .gmpi directory must exist " - echo "under the user's home directory" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a .gmpi directory must exist " >> $jid.log - echo "under the user's home directory" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - homedir=`echo ~` - for i in `grep -v '^#' $host | $AWK '{if (NF > 0) print $1}'` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - $RSH $i /bin/touch $homedir/.gmpi/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - echo " " - echo "error, for Myrinet a shared .gmpi directory must exist " - echo "under the user's home directory " - echo "with remote write permission" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a shared .gmpi directory must exist " >> $jid.log - echo "under the user's home directory " >> $jid.log - echo "with remote write permission" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - else - /bin/rm tmp.$$ - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - fi - fi - done - fi - fi - -# construct the host file $jid.host which is used by mpirun -# skip lines starting with # and only consider lines with more than -# one word in them. Note that the hostfile given to this script -# has two columns: the host name and the number of shared processes -# to run on this host. mpirun wants the number of _other_ -# processes to run in addition to the one being run on the machine -# on which the job is started. hence the $2-1 for fnr == 1. - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then -# HPMPI or HP hardware MPI - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ - -v mpihpspecial="$MPIHPSPECIAL" \ -'{if ( NF > 0) {\ - fnr++ ; \ - printf("-h %s -np %s",$1,$2); \ - printf(" %s",mpihpspecial); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF >= 3 ) printf(" -e MPI_WORKDIR=%s", $3);\ - if ( NF >= 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) \ - }\ - }' > $jid.host -# end HPMPI or HP hardware MPI - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then -# IBM using hardware MPI (POE) - MP_HOSTFILE=$jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.host -# end IBM using hardware MPI (POE) -# for Intel MPI, need to create a machinefile for DMP - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then -# Intel MPI - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - /bin/cp $host $jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Intel MPI for DMP -# for Solaris HPC 7.1, need to create a machinefile for DMP - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then -# Solaris HPC 7.1 - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Solaris HPC 7.1 for DMP -# for Myrinet, construct a configuration file in ~/.gmpi -# this must be readable by each process -# format is (hostname) (port number) for each process - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - grep -v '^#' $host | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ -{if ( NF > 0 ) \ - for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc]); \ -}' >> ~/.gmpi/$jid.host - else -# this is for mpich-1.2.5 and later, using the -pg option -# format: host nproc executable user arguments -# the arguments are added later - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub -v user=`whoami` \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s %s\n",path,user);\ - if ( NF == 3 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s %s\n",path,user) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s/bin/%s %s\n",$4,en,user) \ - }\ - }' > $jid.host - fi -# end Myrinet - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then -# Compaq MPI via Memory Channel - grep -v '^#' $host | $AWK '{if (NF > 0) print $1}' > $jid.host -# end Compaq MPI - else -# MPICH - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF == 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s/bin/%s\n",$4,en) \ - }\ - }' > $jid.host - fi -# define the variable host and host_filt -# host_filt is used for loops over hosts -# for Myrinet we need to use a filtered variant of userhost -# for others we can use $host - if test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - host=~/.gmpi/$jid.host - host_filt=$jid.host_tMp - grep -v '^#' $userhost | $AWK '{if (NF > 0) print $1}' > $host_filt - else - host=$jid.host - host_filt=$host - fi - else - host=$jid.host - host_filt=$host - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - host_filt=$jid.mfile - fi - fi -# figure out if the machines in the hostfile are nfs mounted -# or distributed and set the variable "dirstatus" accordingly. -# only perform the check if user subroutine is used -# or a user subroutine executable is used - - numfield=1 - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - numfield=2 - fi - DIR1=$DIRJOB - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - counter=0 - echo " " - echo "checking if local or shared directories for host" - if test "$deletelog" = no - then - echo "checking if local or shared directories for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - dirstatus[$counter]="shared" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - $RSH $i /bin/touch $DIR1/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - dirstatus[$counter]="local" - /bin/rm tmp.$$ - else - if test ! -f $jid.$$ - then - dirstatus[$counter]="local" - $RSH $i /bin/rm $DIR1/$jid.$$ - else - /bin/rm $jid.$$ - fi - fi - if test -f tmp.$$ - then - /bin/rm tmp.$$ - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - echo " ${dirstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${dirstatus[$counter]}" >> $jid.log - fi - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - fi - -# figure out if this is a compatible set of machines -# unless explicitly specified with flag -comp -# only perform the check if user subroutine is used -# or a user subroutine executable is used -# Myrinet does not support heterogeneous - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - if test $compatible = "unknown" - then - thisname=$ARCH - compatible=yes - counter=0 - echo "checking if machines are compatible for host" - if test "$deletelog" = no - then - echo "checking if machines are compatible for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]="yes" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - othername=`$RSH $i uname -a | cut -f 1 -d " "` - if test $thisname != $othername - then - compatible=no - compstatus[$counter]="no" - fi - fi - echo " ${compstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${compstatus[$counter]}" >> $jid.log - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - else - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]=$compatible - fi - done - if test $compatible = "no" - then - echo "all machines assumed incompatible" - if test "$deletelog" = no - then - echo "all machines assumed incompatible" >> $jid.log - fi - else - echo "all machines compatible" - if test "$deletelog" = no - then - echo "all machines compatible" >> $jid.log - fi - fi - fi -# error out if user objects or libraries are used on incompatible machines - if test "$compatible" = "no" -a -n "$objs" - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" - if test "$deletelog" = no - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" >> $jid.log - fi - exit 1 - fi -# modify new host file if NFS mounted heterogeneous machine - doit= - if test $program = $prog.marc - then - doit=yes - fi - if test "$user" - then - doit=yes - fi - if test "$doit" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - $AWK -v hst=$i '{fnr++ ; \ -if ($1 ~ hst) {if ( fnr == 1 ) printf("%s\n",$0); else \ -printf("%s %s %s_%s\n",$1,$2,$3,$1) } else print}' $jid.host > $jid.host{$$} - /bin/mv $jid.host{$$} $jid.host - host=$jid.host - fi - fi - done - fi - fi # if test $program = $prog.marc -o $user -o $obj - - else # if test $host - # assume shared memory machine if no hostfile given and - # MPITYPE is set to mpich or Myrinet - # check for Myrinet that the total number of processes is - # less than number of available user ports, 5 - if test $MPITYPE = "mpich" -o $MPITYPE = "scali" - then - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - host=$jid.host - elif test $MPITYPE = "myrinet" - then - if test $nprocd -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes " - echo "must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes " >> $jid.log - echo "must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - echo `hostname` $nprocd | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ - {for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc])} \ -' >> ~/.gmpi/$jid.host - host=~/.gmpi/$jid.host - else - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - - fi - fi # if test myrinet - - fi # if test $host - - fi # if test $nprocd -gt 1 - -fi # if test $program = $exefile -o $program = $prog.marc - -############################################################################## -# construct run stream (Marc only) # -############################################################################## - -# set maximum message length for ddm to a large number -# for vendor provided mpi -if test $itree -eq 0 -a $MPITYPE = hardware -then - itree=100000000 - if test $MACHINENAME = SGI - then - itree=100000001 - fi -fi -if test $itree -eq 0 -a $MPITYPE = hpmpi -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = myrinet -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = nec -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = scali -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = intelmpi -then - itree=100000000 -fi -if test $nprocdddm -lt 2 -then - nprocdarg= -else - nprocdarg="$nprocdarg $nprocdddm" -fi -if test $nsolver -eq 0 -then - nsolverarg= -else - nsolverarg="$nsolverarg $nsolver" -fi -if test $nprocdddm -lt 2 -a $nsolver -eq 0 -then -nprocd=0 -fi -if test $nprocd -gt 0 -then - if test "$host" - then - if test -z "$RUN_JOB2" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $host -- -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then - RUN_JOB="$RUN_JOB2 $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB_TMP="$RUN_JOB2 $host $bd$program" - RUN_JOB=" -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $nprocd -hf $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - numhost=`uniq $jid.mfile | wc -l` - if test "$INTELMPI_VERSION" = "HYDRA" - then - RUN_JOB_TMP="$RUN_JOB2 -configfile $jid.cfile" - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n $numhost -r $RSH -f $jid.mfile - RUN_JOB_TMP="$RUN_JOB2 $jid.cfile" - fi - -# intelmpi uses configfile. format: -# -host host1 -n n1 executable marcargs -# one such line per host -# collect the marcargs in RUN_JOB and construct the config file later -# collect the run stream in RUN_JOB_TMP - RUN_JOB="-jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - - - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then - RUN_JOB="$RUN_JOB2 $jid.mfile -n $nprocd $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test "$userhost" - then - RUN_JOB="$RUN_JOB -mhost $userhost" - fi - if test $MPITYPE = "scali" - then -# set default working directory to /tmp to allow -# different directory names - SCAMPI_WORKING_DIRECTORY=/tmp - export SCAMPI_WORKING_DIRECTORY - fi - else - if test -z "$RUN_JOB1" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - RUNNPROCD=$nprocd - if test $MACHINENAME = "IBM" -a $MPITYPE = "hardware" - then - RUNNPROCD= - MP_PROCS=$nprocd - export MP_PROCS - fi - if test $MPITYPE = "myrinet" - then - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - echo " " > /dev/null - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n 1 -f $jid.hosts - fi - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - fi -else - if test $nauto -gt 0 -o $ndcoup -gt 0 - then - RUN_JOB="$RUN_JOB0 $BINDIR/exe_auto $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else -# this is for a serial job without auto restart: - RUN_JOB="$RUN_JOB0 $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi -fi -if test "$rid" -then - RUN_JOB="$RUN_JOB -rid $rid -dirrid $DIRRID" -fi -if test "$pid" -then - RUN_JOB="$RUN_JOB -pid $pid -dirpid $DIRPID" -fi -if test "$sid" -then - RUN_JOB="$RUN_JOB -sid $sid -dirsid $DIRSID" -fi -if test "$did" -then - RUN_JOB="$RUN_JOB -def $did -dirdid $DIRDID" -fi -if test "$vid" -then - RUN_JOB="$RUN_JOB -vf $vid -dirvid $DIRVID" -fi -if test $nauto -gt 0 -then - RUN_JOB="$RUN_JOB -autorst $nauto " -fi -if test $ndcoup -gt 0 -then - RUN_JOB="$RUN_JOB -dcoup $ndcoup " -fi -if test $ndytran -gt 0 -then - RUN_JOB="$RUN_JOB -dytran $ndytran " -fi -if test $mesh -gt 0 -then - RUN_JOB="$RUN_JOB -me $mesh " -fi -if test $noutcore -gt 0 -then - RUN_JOB="$RUN_JOB -outcore $noutcore " -fi -if test "$dllrun" -gt 0 -then - RUN_JOB="$RUN_JOB -dll $dllrun " -fi -if test "$trkrun" -gt 0 -then - RUN_JOB="$RUN_JOB -trk $trkrun " -fi -if test "$iam" -then - RUN_JOB="$RUN_JOB -iam $iam " -fi -if test "$justlist" -then - RUN_JOB="$RUN_JOB -list 1 " -fi -if test "$feature" -then - RUN_JOB="$RUN_JOB -feature $feature " -fi -if test "$memlimit" -ne 0 -then - RUN_JOB="$RUN_JOB -ml $memlimit " -fi -if test "$cpinput" -then - RUN_JOB="$RUN_JOB -ci $cpinput " -fi -if test "$cpresults" -then - RUN_JOB="$RUN_JOB -cr $cpresults " -fi -if test "$DIRSCR" != "$DIRJOB" -then - RUN_JOB="$RUN_JOB -dirscr $DIRSCR" -else - DIRSCR=$DIRJOB -fi -if test "$makebdf" -then - RUN_JOB="$RUN_JOB -bdf $makebdf " -fi -if test $MPITYPE = "myrinet" -a "$host" -a "$MPIVERSION" != "MPICH-GM1.2.1..7" -then - # append $RUN_JOB to all lines of the host file - # and set RUN_JOB - $AWK -v args="$RUN_JOB" '{print $0,args}' $host > $host.$$ - /bin/mv $host.$$ $host - RUN_JOB=$RUN_JOB_TMP -fi -if test $MPITYPE = "intelmpi" -a "$host" -then - # construct config file, append $RUN_JOB to all lines of the config file - # and set RUN_JOB - if test "$INTELMPI_VERSION" = "HYDRA" - then - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf(" -host %s",$1); \ - printf(" -n %s",$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - else - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf("-host %s -n %s",$1,$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - fi - RUN_JOB=$RUN_JOB_TMP -fi -echo " " -echo "Final run stream value" -echo " RUNJOB="$RUN_JOB -if test "$deletelog" = no -then -echo " " >> $jid.log -echo "Final run stream value" >> $jid.log -echo " RUNJOB="$RUN_JOB >> $jid.log -fi - - -############################################################################## -# run marc using valgrind # -############################################################################## -#RUN_JOB="valgrind $RUN_JOB" -#RUN_JOB="valgrind --read-var-info=yes --gen-suppressions=yes $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=all -v $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=yes --error-limit=no $RUN_JOB" -############################################################################## - - -############################################################################## -# run the requested program in a queue # -############################################################################## - -if test "$deletelog" = yes -then - echo - date -else - echo >> $jid.log - date >> $jid.log -fi -if [ $qid = short -o $qid = long -o $qid = verylong -o $qid = at ] -then - -/bin/rm -f $jid.runmarcscript - - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - userobj=$usermoext.o - fi - cat > $jid.runmarcscript << END4 - if test "$user" - then - if test $MACHINENAME = "CRAY" - then - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTRAN $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - $SOLVERLIBS \ - $MARCCUDALIBS \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } -END4 -else - prgsav=yes -fi -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc -# - -cat >> $jid.runmarcscript << END5 - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# first remove all .out files and incremental restart files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - /bin/rm $DIRJOB/$numdom${jid}_i_*.t08 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null - /bin/rm $DIRJOB/${jid}_i_*.t08 2>/dev/null -fi - -if test $nprocdddm -gt 1 -then - $RUN_JOB 2>>$jid.log -else - $RUN_JOB 2>>$jid.log -fi - -if test $dllrun -eq 0; then - if test $prgsav = no - then - /bin/rm -f $bd$program 2>/dev/null - fi -else - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes - then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -fi -END5 - - -# Submit to marc batch queue -# -if [ $qid = at ] -then -QUENAME=at -SUBMCMD= -else -# -# Submit to qsub queue -# -QUENAME=qsub -SUBMCMD="-q $qid -o /dev/null -e $jid.batch_err_log -x -r $jid" -if test "$priority" -then - SUBMCMD=$SUBMCMD" -p $priority" -fi -if test "$att" -then - SUBMCMD=$SUBMCMD" -a $att" -fi -if test "$cpu" -then - SUBMCMD=$SUBMCMD" -lt $cpu" -fi - -fi -echo $QUENAME $SUBMCMD -#cat $jid.runmarcscript -$QUENAME $SUBMCMD < $jid.runmarcscript - -/bin/rm -f $jid.runmarcscript - -############################################################################## -# run the requested program in the background # -############################################################################## - -else -if test $qid = background -then - -# -# first remove all old .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi -# -# compile user subroutine if present -# -( -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - echo " $PRODUCT Exit number 3" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTRAN $user -o $userobj || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - echo " $PRODUCT Exit number 3" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc - -# - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - -$RUN_JOB & - -marcpid=$! -echo $marcpid > $DIRJOB/$jid.pid -wait $marcpid - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - fi - fi - fi -fi - - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi -) 1>>$jid.log 2>&1 & - - -############################################################################## -# run the requested program in the foreground # -############################################################################## - -else - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTRAN $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTRAN $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null -# done if no job id given -if test -z "$jid" -then - echo - echo only compilation requested - echo - exit -fi -# -# run marc -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi -# first remove all .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - $RUN_JOB - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - else - echo " " > /dev/null - fi - else - if test "$host" - then - mpdcleanup -a -f $jid.mfile - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.mfile 2> /dev/null - else - mpdcleanup -a -f $jid.hosts - /bin/rm $jid.hosts 2> /dev/null - fi - fi - fi -fi - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi - - -fi -fi diff --git a/installation/mods_MarcMentat/2017/Marc_tools/run_damask_h b/installation/mods_MarcMentat/2017/Marc_tools/run_damask_h deleted file mode 100644 index 6247486b9..000000000 --- a/installation/mods_MarcMentat/2017/Marc_tools/run_damask_h +++ /dev/null @@ -1,4122 +0,0 @@ -#!/bin/ksh -############################################################################## -# # -# run_marc - run a marc job # -# ------------------------- # -# # -# usage: run_marc -j jid { options } # -# # -# where standard options are: required: defaults: # -# -------------------------- # -# # -# -j* jid job id number. ** YES ** . # -# -pr* prog program name. . marc # -# -v* y|n do or do not verify inputs. . yes # -# -q* s|l|v|b|f batch queue name or background, . short # -# foreground. # -# -b* as alternative to option -q* # -# # -# ( batch queues only : # -# -pq* intra queue priority. . . # -# -at DATE/TIME delay start of job. . . # -# format : January,1,1990,12:31 # -# or : today,5pm # -# -cpu* secs job CPU limit . . ) # -# # -# -r* rid restart file job id. . . # -# -si* sid substructure file id. . . # -# -pi* post post file job id. . . # -# -de* did defaults file . no # -# -vf vid viewfactor . no # -# # -# -u* user user subroutine. . . # -# -obj obj user objects or libraries. . . # -# -sa* y|n do or do not save load module. . no # -# -autorst auto restart flag for auto forge . no # -# -me manual remeshing control . no # -# -ml memory limit in Mbyte # -# -mo This option is deprecated. As of Marc 2015, only # -# the integer*8 version is available. # -# -mpi selects MPI version # -# each platform has a default MPI version and some # -# have an alternative version. see the include file # -# for the respective platform # -# MPI_DEFAULT defines the default MPI version # -# MPI_OTHER defines versions one can switch to # -# -dcoup for contact decoupling # -# currently not supported # -# -dir directory where the job i/o should take place. # -# defaults to current directory. # -# -sdir directory where scratch files are created # -# defaults to current directory. # -# # -# -alloc only perform memory allocation test, no analysis # -# -list y only list options in the input file, no analysis # -# -fe num set feature number "num" for the run. only one allowed # -# -dytran flag to switch from Dytran to Marc # -# dytran = 0, program will run w/o Marc-Dytran Switch # -# = 1, program will restart Marc after Dytran run # -# >= 2, Not supported yet. # -# currently not supported # -# -ou force analysis to use out-of-core control # -# =0, not used # -# =1, element storage out-of-core # -# -dll run marc using shared library libmarc.so and exe_marc # -# =1, used # -# =2, do not free streaming input memory # -# =3, run with marc input deck # -# -trk run marc for post-tracking # -# -gpuid run marc using GPGPU capability # -# specify gpuid on to be used in the analysis. Multiple # -# IDs may be assigned for DDM runs. # -# Separate a list of IDs with a colon. Each DMP # -# process will be assigned a GPU ID in round robin fastion# -# = 0 # -# = 0:1 etc... # -# # -# where parallel options are: # -# -------------------------- # -# # -# itree, host, and comp options are available for the domain # -# decomposition only. # -# MARC_NUMBER_OF_THREADS, nthread, and dir options always available. # -# # -# # -# -nprocd number of domains. # -# defaults to single domain solution. # -# -nprocds number of domains if single input file. # -# defaults to single domain solution. # -# -nps same as -nprocds. # -# -nsolver number of solver tasks for solver types 12 and 13 # -# these are distributed tasks operating via MPI # -# -nthread_elem number of threads for element assembly and recovery # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by element assembly # -# recovery. # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_elem option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_elem specified. # -# -nthread_solver number of threads for solver types 6, 8, and 11 # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by 6, 8, and 11 # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_solver option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_solver specified. # -# -nthread Same as -nthread_solver. # -# -itree message passing tree type for domain decomposition. # -# for debugging purposes; should not normally be used. # -# -host hostfile name for distributed execution on network. # -# defaults to no hostfile, unless jobid.defhost exists. # -# if jobid.defhost exists, only -np(s) necessary # -# -comp* y|n to be used with user routines on a network of # -# incompatible machines. # -# if set to no, a separate executable will be created # -# for each machine on the network. # -# if set to yes, the executable located on the machine # -# from which marc is started will be used on all machines.# -# defaults to no if O/S versions different on machines. # -# # -# -ci y|n copy input files to remote hosts (default: yes) # -# if "yes", input files are automatically copied to # -# remote hosts for a network run if necessary. # -# -cr y|n copy post files from remote hosts (default: yes) # -# if "yes", post files are automatically copied back from # -# remote hosts for a network run if necessary. # -############################################################################## -# set DIR to the directory in which this script is -REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`" -DIR=`dirname $REALCOM` -# make sure DIR has an absolute path -case $DIR in - \/*) - ;; - *) - DIR=`pwd`/$DIR - ;; -esac -DIRSCRIPT=$DIR -AWK=awk -ARCH=`uname -a | cut -f 1 -d " "` -# Sun has a bad awk, use nawk instead -if test $ARCH = "SunOS" -then - AWK=nawk -fi -BASENAME=basename -# Sun has an incorrect /bin/basename, check if /usr/ucb/basename exists -if test $ARCH = "SunOS" -then - if test -x /usr/ucb/basename - then - BASENAME=/usr/ucb/basename - fi -fi - -# echo command line in the case of ECHO_COMMAND is true -if test "$ECHO_COMMAND" = true ; then - echo command "$0" "$@" -fi - -# -# "mode" selects version, i4 or i8 -# default is i4 -# this can be changed by a file run_marc_defaults -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MODE i8 -# it can also be set by the environmental variable MARC_INTEGER_SIZE -# and by the command line option "-mo" -# -mode= -modeerror= -modeoption= -if test -f $DIRSCRIPT/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $DIRSCRIPT/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $DIRSCRIPT/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $DIRSCRIPT/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -f $HOME/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $HOME/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $HOME/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $HOME/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -n "$MARC_INTEGER_SIZE" ; then - mode=$MARC_INTEGER_SIZE -fi -if test -z "$mode" ; then - mode=i8 -fi -case $mode in - i4) - modeerror="bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - modeoption=error - echo $modeerror - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo "bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - exit - ;; -esac - -setmode=false -for arg in $* ; do - if $setmode ; then - mode=$arg - case $mode in - i4) - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo " " - echo "error, version mode must be i8" - echo " " - echo " use -mo i8 " - echo " " - exit - ;; - esac - setmode=false - fi - if [ ${arg}X = -moX -o ${arg}X = -MOX ] ; then - echo - echo warning: the option -mo is deprecated, as of Marc 2015, only the integer*8 version is available - echo - setmode=true - fi - if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - fi - if [ ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - fi -done - -# set to i4 version for 32 bit Linux -if test "`uname -s`" = "Linux"; then - if test "`uname -m`" = "i686"; then - mode=i4 - MARC_INTEGER_SIZE=i4 - export MARC_INTEGER_SIZE - fi -fi - - -. "$DIR/getarch" - - -# getting user subroutine file name -found=0 -for i in "$@"; do - if test $found = 1; then - DAMASK_USER=$i - found=0 - fi - case $i in - -u* | -U*) - found=1 - ;; - esac -done -# sourcing include_linux64 (needs DAMASK_USER to be set) -. $MARC_INCLUDE - -# - -# -# Dynamically determine the echo syntax -# - -case "`echo '\c'`" in - '\c') - ECHO='echo -n' - ECHOTXT=' ' - ;; - *) - ECHO='echo' - ECHOTXT=' \c' - ;; -esac - -# -# Variables for the MARC environment -# - -PRODUCT="Marc" -EXITMSG=$MARC_TOOLS/MESSAGES -export EXITMSG -FLEXDIR=$DIR/../flexlm/licenses -export FLEXDIR -TIMCHK=3600 -export TIMCHK -BINDIR=$MARC_BIN -export BINDIR -AFMATDAT=$MARC_RUNTIME/AF_flowmat/ -export AFMATDAT -export MESHERDIR -MSC_LICENSE_FINPROC=0 -export MSC_LICENSE_FINPROC -# -# define directory path to global unified material database -# -MATFILE= -export MATFILE - -# -# define memory limit -# first set to MEMLIMIT from include -# -ml option overrules if specified -memlimit=$MEMLIMIT -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -# -if test $MACHINENAME = "HP" -then - SHLIB_PATH=$MARC_LIB:$MARC_LIB_SHARED:$SHLIB_PATH - export SHLIB_PATH -fi -# the one for IBM is defined futher down - -LD_LIBRARY_PATH=$MARC_LIB_SHARED:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MARC_LIB:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MESHERDIR:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$SFMATDIR:$LD_LIBRARY_PATH -LD_LIBRARY64_PATH=$MARC_LIB:$LD_LIBRARY64_PATH -LD_LIBRARYN32_PATH=$MARC_LIB:$LD_LIBRARYN32_PATH -export LD_LIBRARY_PATH -export LD_LIBRARY64_PATH -export LD_LIBRARYN32_PATH - -atexit() { -kill -15 $$ -# -if test $MPITYPE = "myrinet" -then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi -fi -} - -trap "atexit" 2 - -# -# defaults -# - -prog=marc -exefile=marc -jid= -rid= -pid= -sid= -did= -vid= -user= -usernoext= -objs= -qid=background -cpu= -priority= -att= -trk= -verify=yes -prgsav=no -rmdll=no -cpdll=no -progdll= -pathdll= -error= -nprocd=0 -nprocdddm=1 -nprocdddmprint= -icreated=0 -nprocdarg= -nsolver=0 -nsolverarg=-ns -if test $nprocds -then - if test $nprocds -gt 1 - then - nprocdddm=$nprocds - nprocdddmprint=$nprocds - icreated=1 - nprocdarg=-nprocds - fi -fi -ntprint=0 -nt=-1 -nte=-1 -nts=-1 -ntarg=-nt -ntearg=-nte -ntsarg=-nts -nteprint= -ntsprint= -gpuids= -nauto=0 -ndcoup=0 -ndytran=0 -noutcore=0 -dllrun=0 -mesh=0 -itree=0 -iam= -ddm_arc=0 -link= -trkrun=0 -DIRJOB=`pwd` -DIRSCR=$DIRJOB -DIRSCRSET= -autoforge=0 -dotdat=.dat -dotdefhost=.defhost -host= -numhost= -mfile= -userhost= -makebdf= -cpinput=yes -cpresults=yes -marcdll=libmarc.$EXT_DLL -# define hostname and strip off extensions (alpha.aaa.com) -thishost=`hostname` -thishost=${thishost%%.*} -compatible=unknown -numfield=1 -justlist= -feature= -mpioption=false -iprintsimufact= -MDSRCLIB=$MARC_LIB/mdsrc.a -# -# check run_marc_defaults file for default MPI setting -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MPI -# -value= -file= -if test -f $DIRSCRIPT/run_marc_defaults; 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- esac - ;; - -ho* | -HO*) - host=$value - ;; - -co* | -CO*) - compatible=$value - ;; - -ci* | -CI*) - cpinput=$value - ;; - -cr* | -CR*) - cpresults=$value - ;; - *) - error="$error -$arg: invalid option" - break - ;; - esac - case $value in - -*) - error="$error -$arg: invalid name $value" - break - ;; - esac - shift - arg=$1 - if [ ${arg}X = -i8X -o ${arg}X = -I8X -o ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - shift - arg=$1 - fi -done -argc=`expr $# % 2` -if test $argc -eq 1 -then -# -# odd number of arguments -# - error="$error -argument list incomplete" -fi - -if test $nprocdddm -gt 0 -then -nprocd=$nprocdddm -fi - -if test $nsolver -gt 0 -then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi -fi -# Set defaults -if test $nt -eq -1 -then -nt=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nt -lt 0 -then -nt=0 -fi -if test $nte -eq -1 -then -nte=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nte -lt 0 -then -nte=0 -fi -if test $nts -eq -1 -then -nts=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nts -lt 0 -then -nts=0 -fi -# -# set number of element loop threads -# -ntprint=$nt -nteprint=$nte -# copy from -nprocd[s] -if test $nprocdddm -gt 1 -then - nteprint=$nprocdddm -fi -# override with -nthread_elem option -if test $nte -ne 0 -then -nteprint=$nte -fi -# check for minimum 1 threads per processes for DDM -if test $nprocdddm -gt 1 -then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi -fi -nte=$nteprint -# -# set number of Solver threads -# -ntsprint=$nts -# copy from -nthread or -nprocd[s] -if test $ntprint -ne 0 -then - ntsprint=$ntprint -else - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -fi -# override with -nthread_solver option -if test $nts -ne 0 -then - ntsprint=$nts -fi -# check for minimum 1 threads per solver process. -if test $nsolver -lt $nprocdddm -then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi -else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi -fi -if test $ntsprint -eq 1 -then - set ntsprint=0 -fi -nts=$ntsprint - -# set stack size for multi-threading. -export KMP_MONITOR_STACKSIZE=7M -export OMP_STACKSIZE=7M - -# -# deprecate -nthread option at arugment of marc -nt=0 -# Reset nprocdddmm, nsolver and threads if not given. -if test $nprocdddm -eq 0 -then - nprocdarg= -fi -if test $nprocdddm -eq 0 -then - nprocdddmprint= -fi -if test $nprocdddm -eq 0 -then - nprocdddm= -fi - -nsolverprint=$nsolver -if test $nsolver -eq 0 -then - nsolverprint= -fi -# end of threads setting. -gpuoption= -if test "$gpuids" = "" ; then - gpuoption= -else - gpuoption="-gp $gpuids" -fi - -if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH -else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH -fi -# Linux 64 + HPMPI, Below code is taken from include_linux64 -if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" -then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" -fi - -if test $nprocd -gt 1; then - if test -f $jid$dotdefhost; then - if test "$host" = ""; then - host=$jid$dotdefhost - fi - fi - if test -f hostfile_qa_$nprocd; then - if test "$host" = ""; then - host=hostfile_qa_$nprocd - fi - fi -fi - -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$dllrun" -eq 1 || test "$dllrun" -eq 2; then - dotdat=.inp - fi - - if test "$progdll"; then - /bin/cp ${progdll}_$marcdll $DIRJOB/$marcdll - rmdll=yes - pathdll=yes - progdll=${progdll}_$marcdll - else - progdll=$marcdll - fi - - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - pathdll=yes - fi -fi - -############################################################################## -# check parameter validity # -############################################################################## - -while test forever; do - -# -# check for input file existence -# -if test $nprocdddm -gt 1 -a $icreated -eq 0; then - if test ! -f $DIRJID/1$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/1$jid$dotdat not accessible" - fi - fi -else - if test ! -f $DIRJID/$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/$jid$dotdat not accessible" - fi - fi -fi - if test $nprocd -gt 1; then - if test "$host" ; then - if test ! -f $host; then - error="$error -host name file $host not accessible" - fi - fi - fi - -# -# check if the job is already running in the background -# -if test -f $DIRJOB/$jid.pid; then - error="$error -job is already running (the file $jid.pid exists)" -fi - -# -# if the program name is other than marc, then -# assume that this is a program in the users local directory -# - -bd=$MARC_BIN/ - -case $prog in - marc | MARC | $exefile) - program=$exefile - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 or $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - if test ! -f $user - then - error="$error -user subroutine file $user not accessible" - fi - fi - if test "$objs" - then - missingobjs= - for o in $objs - do - if test ! -f "$o" - then - if test -z "$missingobjs" - then - missingobjs="$o" - else - missingobjs="$missingobjs $o" - fi - fi - done - if test -n "$missingobjs" - then - error="$error -user object/library file(s) $missingobjs not accessible" - fi - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$vid" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRVID/1$vid.vfs - then - error="$error -view factor file $DIRVID/1$vid.vfs not accessible" - fi - else - if test ! -f $DIRVID/$vid.vfs - then - error="$error -view factor file $DIRVID/$vid.vfs not accessible" - fi - fi - fi - if $mpioption - then - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE (valid: $MPI_OTHER)" - fi - fi - ;; - *) - program=$prog.marc - case $prog in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 and $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - error="$error -program option may not be used with user subroutine" - fi - if test "$objs" - then - error="$error -program option may not be used with user objects or libraries" - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$nauto" - then - if test $nauto -gt 2 - then - error="$error -incorrect option for auto restart " - fi - fi - if test "$ndcoup" - then - if test $ndcoup -gt 3 - then - error="$error -incorrect option for contact decoupling " - fi - fi - if test "$ndytran" - then - if test $ndytran -gt 1 - then - error="$error -incorrect option for Marc-Dytran Switch " - fi - fi - if $mpioption - then - if test ! -x $MARC_BIN/$exefile - then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE " - fi - fi - ;; -esac - -############################################################################## -# check argument integrity # -############################################################################## - -if test "$jid" -then - : -else - if test "$user" - then -# allow user sub without giving job id - qid=foreground - verify=no - else - error="$error -job id required" -fi -fi - -if test $nprocd -gt 1 -then - if test $nauto -gt 0 - then - error="$error -cannot run DDM job with auto restart (-au) option " - fi -fi -case $qid in - S* | s*) - qid=short - ;; - L* | l*) - qid=long - ;; - V* | v*) - qid=verylong - ;; - B* | b*) - qid=background - ;; - F* | f*) - qid=foreground - ;; - A* | a*) - qid=at - ;; - *) - error="$error -bad value for queue_id option" - ;; -esac - -case $prgsav in - N* | n*) - prgsav=no - ;; - Y* | y*) - prgsav=yes - ;; - *) - error="$error -bad value for save option" - ;; -esac - -case $verify in - N* | n*) - verify=no - ;; - Y* | y*) - verify=yes - ;; - *) - error="$error -bad value for verify option" - ;; -esac - -case $nprocdddm in - -* ) - error="$error -bad value for nprocd option" - ;; -esac - -case $nt in - -* ) - error="$error -bad value for nt option" - ;; -esac - -case $itree in - -* ) - error="$error -bad value for itree option" - ;; -esac -case $iam in - -* ) - error="$error -bad value for iam option" - ;; -esac -case $compatible in - N* | n*) - compatible=no - ;; - Y* | y*) - compatible=yes - ;; - unknown) - ;; - *) - error="$error -bad value for comp option" - ;; -esac -case $cpinput in - N* | n*) - cpinput=no - ;; - Y* | y*) - cpinput=yes - ;; - *) - error="$error -bad value for copy input option" - ;; -esac -case $cpresults in - N* | n*) - cpresults=no - ;; - Y* | y*) - cpresults=yes - ;; - *) - error="$error -bad value for copy results option" - ;; -esac - -# -# check for external file to run -# -if test -f $MARC_TOOLS/run_marc_check -then - . $MARC_TOOLS/run_marc_check -fi - -############################################################################## -# interact with the user to get the required information to run marc or # -# other marc system program # -############################################################################## - -deletelog=yes -if test $qid = background -a $verify = no -then -echo \ -" -Program name : $prog -Marc shared lib : $progdll -Version type : $mode -Job ID : $DIRJID/$jid -User subroutine name : $user -User objects/libs : $objs -Restart file job ID : $rid -Substructure file ID : $sid -Post file job ID : $pid -Defaults file ID : $did -View Factor file ID : $vid -Save generated module: $prgsav -MPI library : $MPITYPE -DDM processes : $nprocdddmprint -Element loop threads : $nteprint -Solver processes : $nsolverprint -Solver threads : $ntsprint -GPGPU option : $gpuids -Host file name : $host" > $jid.log -if test "$iprintsimufact" = true ; then - echo "DDM with ARC Mapper : $ddm_arc" >> $jid.log -fi -echo \ -"Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto " >> $jid.log -deletelog=no -fi -echo \ -" -Program name : $prog -Marc shared lib : $progdll -Version type : $mode -Job ID : $DIRJID/$jid -User subroutine name : $user -User objects/libs : $objs -Restart file job ID : $rid -Substructure file ID : $sid -Post file job ID : $pid -Defaults file ID : $did -View Factor file ID : $vid -Save generated module: $prgsav -MPI library : $MPITYPE -DDM processes : $nprocdddmprint -Element loop threads : $nteprint -Solver processes : $nsolverprint -Solver threads : $ntsprint" -if test "$iprintsimufact" = true ; then - echo "DDM with ARC Mapper : $ddm_arc" -fi -echo \ -"GPGPU option : $gpuids -Host file name : $host -Message passing type : $itree -Run job in queue : $qid -Run directory : $DIRJOB -Scratch directory : $DIRSCR -Memory limit in Mbyte: $memlimit -Auto Restart : $nauto" - - -case $qid in - s* | S* | l* | L* | v* | V* ) - echo \ -"Queue priority : $priority -Queue CPU limit : $cpu -Queue start time : $att" - ;; -# * ) -# echo \ -#" " -# ;; -esac - -if test "$modeoption" -then - error=$modeerror -fi - -if test "$error" -then - if test $verify = yes - then - $ECHO "$error - -Please correct or quit(correct,quit,): $ECHOTXT" - error= - read answer - case $answer in - q* | Q*) - answer=quit - ;; - *) - answer=correct - ;; - esac - else - $ECHO "$error - $ECHOTXT" - echo " " - if test "$deletelog" = no - then - $ECHO "$error - $ECHOTXT" >> $jid.log - echo " " >> $jid.log - fi - answer=quit - fi -else - if test $verify = yes - then - $ECHO " -Are these parameters correct (yes,no,quit,)? $ECHOTXT" - read answer - case $answer in - q* | Q*) - answer=quit - ;; - y* | Y*) - answer=yes - ;; - *) - answer=no - ;; - esac - else - answer=yes - fi -fi - -case $answer in - no | correct) - -############################################################################## -# prompt for each value # -############################################################################## - - $ECHO " -Program name ($prog)? $ECHOTXT" - read value - if test "$value" - then - prog=$value - fi - $ECHO "Job ID ($jid)? $ECHOTXT" - read value - if test "$value" - then - jid=`$BASENAME $value $dotdat` - DIRJID=`dirname $value` - case $DIRJID in - \/*) - ;; - *) - DIRJID=`pwd`/$DIRJID - ;; - esac - fi - $ECHO "User subroutine name ($user)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - user= - ;; - *) - user=$value - case $user in - \/*) - ;; - *) - user=`pwd`/$user - ;; - esac - usernoext=$user - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - ;; - esac - fi - $ECHO "User objects or libraries ($objs)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - objs= - ;; - *) - objs="$value" - ;; - esac - fi - $ECHO "Restart File Job ID ($rid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - rid= - ;; - *) - rid=`$BASENAME $value .t08` - DIRRID=`dirname $value` - case $DIRRID in - \/*) - ;; - *) - DIRRID=`pwd`/$DIRRID - ;; - esac - ;; - esac - fi - $ECHO "Substructure File ID ($sid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - sid= - ;; - *) - sid=$value - DIRSID=`dirname $value` - case $DIRSID in - \/*) - ;; - *) - DIRSID=`pwd`/$DIRSID - ;; - esac - ;; - esac - fi - $ECHO "Post File Job ID ($pid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - pid= - ;; - *) - pid=$value - DIRPID=`dirname $value` - case $DIRPID in - \/*) - ;; - *) - DIRPID=`pwd`/$DIRPID - ;; - esac - ;; - esac - fi - $ECHO "Defaults File ID ($did)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - did= - ;; - *) - did=`$BASENAME $value $dotdat` - DIRDID=`dirname $value` - case $DIRDID in - \/*) - ;; - *) - DIRDID=`pwd`/$DIRDID - ;; - esac - ;; - esac - fi - $ECHO "View Factor File ID ($vid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - vid= - ;; - *) - vid=`$BASENAME $value .vfs` - DIRVID=`dirname $value` - case $DIRVID in - \/*) - ;; - *) - DIRVID=`pwd`/$DIRVID - ;; - esac - ;; - esac - fi - $ECHO "Save generated module ($prgsav)? $ECHOTXT" - read value - if test "$value" - then - prgsav=$value - fi - $ECHO "Run on tasks ($nprocdddm) tasks? $ECHOTXT" - read value - if test "$value" - then - nprocdddm=$value - nprocdddmprint=$value - fi - $ECHO "Run on ($nte) Element loop threads ? $ECHOTXT" - read value - if test "$value" - then - nte=$value - fi - $ECHO "Run on ($nsolver) solvers ? $ECHOTXT" - read value - if test "$value" - then - nsolver=$value - fi - $ECHO "Run on ($nts) Solver threads ? $ECHOTXT" - read value - if test "$value" - then - nts=$value - fi -# - if test $nprocdddm -gt 0 - then - nprocd=$nprocdddm - fi - if test $nsolver -gt 0 - then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi - fi -# Element loop threads. - if test $nte -eq -1 - then - nte=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nte -lt 0 - then - nte=0 - fi - nteprint=$nte -# Copy from ddm - if test $nprocdddm -gt 1 - then - nteprint=$nprocdddm - fi -# override with -nthread_elem option - if test $nte -ne 0 - then - nteprint=$nte - fi -# check for minimum 1 threads per processes for DDM - if test $nprocdddm -ne 0 - then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi - fi - nte=$nteprint -# Solver threads. - if test $nts -eq -1 - then - nts=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nts -lt 0 - then - nts=0 - fi - ntsprint=$nts -# Copy from ddm - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -# override with -nthread_solver option - if test $nts -ne 0 - then - ntsprint=$nts - fi -# check for minimum 1 threads per solver process. - if test $nsolver -lt $nprocdddm - then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi - else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi - fi - if test $ntsprint -eq 1 - then - set ntsprint=0 - fi - nts=$ntsprint -# Update print variable for -nsolver option - nsolverprint=$nsolver - if test $nsolver -eq 0 - then - nsolverprint= - fi - $ECHO "GPGPU id option ($gpuids)? $ECHOTXT" - read value - if test "$value" - then - gpuids=$value - fi - if test "$gpuids" = "" ; then - gpuoption= - else - gpuoption="-gp $gpuids" - fi - if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH - fi - if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" - then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" - fi -# - if test $nprocd -gt 1 - then - $ECHO "Message passing type ($itree)? $ECHOTXT" - read value - if test "$value" - then - itree=$value - fi - $ECHO "Host file name ($host)? $ECHOTXT" - read value - if test "$value" - then - host=$value - fi - if test $nprocdddm -gt 1 - then - $ECHO "Single input file? $ECHOTXT" - read value - case $value in - y* | Y*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - $ECHO "Compatible machines for DDM ($compatible)? $ECHOTXT" - read value - if test "$value" - then - compatible=$value - fi - $ECHO "Copy input files to remote hosts ($cpinput)? $ECHOTXT" - read value - if test "$value" - then - cpinput=$value - fi - $ECHO "Copy post files from remote hosts ($cpresults)? $ECHOTXT" - read value - if test "$value" - then - cpresults=$value - fi - fi - fi - $ECHO "Run the job in the queue ($qid)? $ECHOTXT" - read value - if test "$value" - then - qid=$value - fi - case $qid in - s* | S* | l* | L* | v* | V* ) - $ECHO "Queue priority ($priority)? $ECHOTXT" - read value - if test "$value" - then - priority=$value - fi - $ECHO "Job starts at ($att)? $ECHOTXT" - read value - if test "$value" - then - att=$value - fi - $ECHO "Queue CPU limit ($cpu)? $ECHOTXT" - read value - if test "$value" - then - cpu=$value - fi - ;; - * ) - ;; - esac - $ECHO "Auto Restart option ($nauto)? $ECHOTXT" - read value - if test "$value" - then - nauto=$value - fi - $ECHO "Run directory ($DIRJOB)? $ECHOTXT" - read value - if test "$value" - then - DIRJOB=$value - DIRSCR=$DIRJOB - fi - $ECHO "Scratch directory ($DIRSCR)? $ECHOTXT" - read value - if test "$value" - then - DIRSCR=$value - fi - ;; - quit) - exit 1 - ;; - *) - break - ;; - -esac - - if test $nt -eq -1 - then - nt=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nt -lt 0 - then - nt=0 - fi - -done -# -if test $nt -eq 0 -then - ntarg= -fi -if test $nt -eq 0 -then - ntprint= -fi -if test $nt -eq 0 -then - nt= -fi - -if test $nte -eq 0 -then - ntearg= -fi -if test $nte -eq 0 -then - nteprint= -fi -if test $nte -eq 0 -then - nte= -fi - -if test $nts -eq 0 -then - ntsarg= -fi -if test $nts -eq 0 -then - ntsprint= -fi -if test $nts -eq 0 -then - nts= -fi -# -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - pathdll=yes - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - fi - - if test "$pathdll"; then -# -# reset share lib path -# - if test $MACHINENAME = "HP" - then - SHLIB_PATH=$DIRJOB:$SHLIB_PATH - export SHLIB_PATH - fi - if test $MACHINENAME = "IBM" - then - LIBPATH=$DIRJOB:$LIBPATH - export LIBPATH - fi -# - LD_LIBRARY_PATH=$DIRJOB:$LD_LIBRARY_PATH - LD_LIBRARY64_PATH=$DIRJOB:$LD_LIBRARY64_PATH - LD_LIBRARYN32_PATH=$DIRJOB:$LD_LIBRARYN32_PATH - export LD_LIBRARY_PATH - export LD_LIBRARY64_PATH - export LD_LIBRARYN32_PATH - fi -fi -# end of dllrun>0 - - -if test $program = $exefile -o $program = $prog.marc -then - -# delete the old .log file unless we run in the background -if test "$deletelog" = yes -then - if test "$jid" - then - /bin/rm $jid.log 2>/dev/null - fi -else - echo - echo running the job in the background, see $jid.log - echo -fi - -# -# check if this is an autoforge or rezoning or radiation job -# -if test $nprocd -eq 1 -a "$jid" - -then - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^autoforge"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^rezoning"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^radiation"` - if test "$line" - then - autoforge=1 - fi -fi -# -# check that jobname for restarted run is not the same -# as restart file basename -# -if test "$rid" -then - if test "$jid" = "$rid" - then - echo " " - echo "ERROR: job name of current run is the same as job name" - echo " of the restarted job" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "ERROR: job name of current run is the same as job name" >> $jid.log - echo " of the restarted job" >> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi -fi - -# -# user objects/libraries used -# - - if test "$objs" - then - program="$DIRJOB/$jid.marc" - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# user subroutine used -# -# add DAMASK options for linking - DAMASK="-lstdc++" - - if test "$user" - then - program=$usernoext.marc - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# Special case for IBM using POE but not an SP machine -# in this case we always need a host file, also for serial jobs. -# -if test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP -then - MP_HOSTFILE=${jid}.host - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $nprocd -gt 1 - then - numdom=$nprocd - while test $numdom -gt 0 - do - hostname -s >> $MP_HOSTFILE - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - else - hostname -s > $MP_HOSTFILE - fi -fi -# -# check ssh for all hosts in host file -# -if test $nprocd -gt 1 -then -if test $MPITYPE = "intelmpi" -a "$INTELMPI_VERSION" = "HYDRA" - then -# get host list - if test "$host" - then - line=`grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' | uniq` -# count failing hosts - counter=0 - for i in $line - do - $RSH -o BatchMode=yes -o ConnectTimeout=10 $i uname -n - status=$? - if [[ $status != 0 ]] ; then - counter=$((counter+1)) - if [ "$counter" = "1" ]; then - echo " " - echo " error - connection test failed... " - echo " " - fi - echo " " - echo " connection test with ssh failed on host $i" - echo " check the following command: ssh $i uname -n " - echo " " - fi - done -# echo error message and quit - if test $counter -ne 0 - then - echo " " - echo " A parallel job using IntelMPI cannot be started. " - echo " The ssh command must be working correctly between " - echo " the computers used in the analysis. Furthermore, " - echo " it must be set up such that it does not prompt the " - echo " user for a password. " - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo " A parallel job using IntelMPI cannot be started. ">> $jid.log - echo " The ssh command must be working correctly between ">> $jid.log - echo " the computers used in the analysis. Furthermore, ">> $jid.log - echo " it must be set up such that it does not prompt the ">> $jid.log - echo " user for a password. ">> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi -fi -fi -# -# check correctness of host file; fix for user sub -# - if test $nprocd -gt 1 - then - -# construct the path name to the executable (execpath) - execpath=$MARC_BIN/$exefile - usersub=0 - if test $program = $prog.marc - then - execpath=$prog.marc - usersub=1 - fi - if test "$objs" - then - execpath="$DIRJOB/$jid.marc" - usersub=1 - fi - if test "$user" - then - execpath=$usernoext.marc - usersub=1 - fi - export execpath - execname=`$BASENAME $execpath` - - if test "$host" - then - userhost=$host - case $userhost in - \/* | \.\/*) - ;; - *) - userhost=`pwd`/$userhost - ;; - esac - -# check that the number of processes specified in the hostfile is -# equal to nprocd specified by -nprocd. - numproc=`grep -v '^#' $host | $AWK -v sum=0 '{sum=sum+$2}; END {print sum}'` - if test $nprocd -ne $numproc - then - echo " " - echo "error, the number of processes specified in the host file" - echo "must be equal to the number of processes given by -nprocd/-nsolver" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, the number of processes specified in the host file" >> $jid.log - echo "must be equal to the number of processes given by -nprocd/-nsolver" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - -# check for Myrinet that the number of processes per host is -# less than number of available user ports, 5 -# .gmpi directory must exist in user's home directory -# and must have write permission from remote hosts - if test $MPITYPE = "myrinet" - then - numproc=`grep -v '^#' $host | $AWK -v sum=1 '{if( $2 > 5) sum=6}; END {print sum}'` - if test $numproc -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes specified " - echo "in the hostfile must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes specified " >> $jid.log - echo "in the hostfile must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - if test ! -d ~/.gmpi - then - echo " " - echo "error, for Myrinet a .gmpi directory must exist " - echo "under the user's home directory" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a .gmpi directory must exist " >> $jid.log - echo "under the user's home directory" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - homedir=`echo ~` - for i in `grep -v '^#' $host | $AWK '{if (NF > 0) print $1}'` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - $RSH $i /bin/touch $homedir/.gmpi/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - echo " " - echo "error, for Myrinet a shared .gmpi directory must exist " - echo "under the user's home directory " - echo "with remote write permission" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a shared .gmpi directory must exist " >> $jid.log - echo "under the user's home directory " >> $jid.log - echo "with remote write permission" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - else - /bin/rm tmp.$$ - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - fi - fi - done - fi - fi - -# construct the host file $jid.host which is used by mpirun -# skip lines starting with # and only consider lines with more than -# one word in them. Note that the hostfile given to this script -# has two columns: the host name and the number of shared processes -# to run on this host. mpirun wants the number of _other_ -# processes to run in addition to the one being run on the machine -# on which the job is started. hence the $2-1 for fnr == 1. - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then -# HPMPI or HP hardware MPI - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ - -v mpihpspecial="$MPIHPSPECIAL" \ -'{if ( NF > 0) {\ - fnr++ ; \ - printf("-h %s -np %s",$1,$2); \ - printf(" %s",mpihpspecial); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF >= 3 ) printf(" -e MPI_WORKDIR=%s", $3);\ - if ( NF >= 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) \ - }\ - }' > $jid.host -# end HPMPI or HP hardware MPI - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then -# IBM using hardware MPI (POE) - MP_HOSTFILE=$jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.host -# end IBM using hardware MPI (POE) -# for Intel MPI, need to create a machinefile for DMP - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then -# Intel MPI - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - /bin/cp $host $jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Intel MPI for DMP -# for Solaris HPC 7.1, need to create a machinefile for DMP - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then -# Solaris HPC 7.1 - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Solaris HPC 7.1 for DMP -# for Myrinet, construct a configuration file in ~/.gmpi -# this must be readable by each process -# format is (hostname) (port number) for each process - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - grep -v '^#' $host | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ -{if ( NF > 0 ) \ - for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc]); \ -}' >> ~/.gmpi/$jid.host - else -# this is for mpich-1.2.5 and later, using the -pg option -# format: host nproc executable user arguments -# the arguments are added later - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub -v user=`whoami` \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s %s\n",path,user);\ - if ( NF == 3 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s %s\n",path,user) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s/bin/%s %s\n",$4,en,user) \ - }\ - }' > $jid.host - fi -# end Myrinet - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then -# Compaq MPI via Memory Channel - grep -v '^#' $host | $AWK '{if (NF > 0) print $1}' > $jid.host -# end Compaq MPI - else -# MPICH - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF == 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s/bin/%s\n",$4,en) \ - }\ - }' > $jid.host - fi -# define the variable host and host_filt -# host_filt is used for loops over hosts -# for Myrinet we need to use a filtered variant of userhost -# for others we can use $host - if test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - host=~/.gmpi/$jid.host - host_filt=$jid.host_tMp - grep -v '^#' $userhost | $AWK '{if (NF > 0) print $1}' > $host_filt - else - host=$jid.host - host_filt=$host - fi - else - host=$jid.host - host_filt=$host - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - host_filt=$jid.mfile - fi - fi -# figure out if the machines in the hostfile are nfs mounted -# or distributed and set the variable "dirstatus" accordingly. -# only perform the check if user subroutine is used -# or a user subroutine executable is used - - numfield=1 - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - numfield=2 - fi - DIR1=$DIRJOB - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - counter=0 - echo " " - echo "checking if local or shared directories for host" - if test "$deletelog" = no - then - echo "checking if local or shared directories for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - dirstatus[$counter]="shared" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - $RSH $i /bin/touch $DIR1/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - dirstatus[$counter]="local" - /bin/rm tmp.$$ - else - if test ! -f $jid.$$ - then - dirstatus[$counter]="local" - $RSH $i /bin/rm $DIR1/$jid.$$ - else - /bin/rm $jid.$$ - fi - fi - if test -f tmp.$$ - then - /bin/rm tmp.$$ - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - echo " ${dirstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${dirstatus[$counter]}" >> $jid.log - fi - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - fi - -# figure out if this is a compatible set of machines -# unless explicitly specified with flag -comp -# only perform the check if user subroutine is used -# or a user subroutine executable is used -# Myrinet does not support heterogeneous - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - if test $compatible = "unknown" - then - thisname=$ARCH - compatible=yes - counter=0 - echo "checking if machines are compatible for host" - if test "$deletelog" = no - then - echo "checking if machines are compatible for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]="yes" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - othername=`$RSH $i uname -a | cut -f 1 -d " "` - if test $thisname != $othername - then - compatible=no - compstatus[$counter]="no" - fi - fi - echo " ${compstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${compstatus[$counter]}" >> $jid.log - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - else - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]=$compatible - fi - done - if test $compatible = "no" - then - echo "all machines assumed incompatible" - if test "$deletelog" = no - then - echo "all machines assumed incompatible" >> $jid.log - fi - else - echo "all machines compatible" - if test "$deletelog" = no - then - echo "all machines compatible" >> $jid.log - fi - fi - fi -# error out if user objects or libraries are used on incompatible machines - if test "$compatible" = "no" -a -n "$objs" - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" - if test "$deletelog" = no - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" >> $jid.log - fi - exit 1 - fi -# modify new host file if NFS mounted heterogeneous machine - doit= - if test $program = $prog.marc - then - doit=yes - fi - if test "$user" - then - doit=yes - fi - if test "$doit" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - $AWK -v hst=$i '{fnr++ ; \ -if ($1 ~ hst) {if ( fnr == 1 ) printf("%s\n",$0); else \ -printf("%s %s %s_%s\n",$1,$2,$3,$1) } else print}' $jid.host > $jid.host{$$} - /bin/mv $jid.host{$$} $jid.host - host=$jid.host - fi - fi - done - fi - fi # if test $program = $prog.marc -o $user -o $obj - - else # if test $host - # assume shared memory machine if no hostfile given and - # MPITYPE is set to mpich or Myrinet - # check for Myrinet that the total number of processes is - # less than number of available user ports, 5 - if test $MPITYPE = "mpich" -o $MPITYPE = "scali" - then - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - host=$jid.host - elif test $MPITYPE = "myrinet" - then - if test $nprocd -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes " - echo "must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes " >> $jid.log - echo "must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - echo `hostname` $nprocd | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ - {for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc])} \ -' >> ~/.gmpi/$jid.host - host=~/.gmpi/$jid.host - else - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - - fi - fi # if test myrinet - - fi # if test $host - - fi # if test $nprocd -gt 1 - -fi # if test $program = $exefile -o $program = $prog.marc - -############################################################################## -# construct run stream (Marc only) # -############################################################################## - -# set maximum message length for ddm to a large number -# for vendor provided mpi -if test $itree -eq 0 -a $MPITYPE = hardware -then - itree=100000000 - if test $MACHINENAME = SGI - then - itree=100000001 - fi -fi -if test $itree -eq 0 -a $MPITYPE = hpmpi -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = myrinet -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = nec -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = scali -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = intelmpi -then - itree=100000000 -fi -if test $nprocdddm -lt 2 -then - nprocdarg= -else - nprocdarg="$nprocdarg $nprocdddm" -fi -if test $nsolver -eq 0 -then - nsolverarg= -else - nsolverarg="$nsolverarg $nsolver" -fi -if test $nprocdddm -lt 2 -a $nsolver -eq 0 -then -nprocd=0 -fi -if test $nprocd -gt 0 -then - if test "$host" - then - if test -z "$RUN_JOB2" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $host -- -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then - RUN_JOB="$RUN_JOB2 $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB_TMP="$RUN_JOB2 $host $bd$program" - RUN_JOB=" -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $nprocd -hf $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - numhost=`uniq $jid.mfile | wc -l` - if test "$INTELMPI_VERSION" = "HYDRA" - then - RUN_JOB_TMP="$RUN_JOB2 -configfile $jid.cfile" - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n $numhost -r $RSH -f $jid.mfile - RUN_JOB_TMP="$RUN_JOB2 $jid.cfile" - fi - -# intelmpi uses configfile. format: -# -host host1 -n n1 executable marcargs -# one such line per host -# collect the marcargs in RUN_JOB and construct the config file later -# collect the run stream in RUN_JOB_TMP - RUN_JOB="-jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - - - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then - RUN_JOB="$RUN_JOB2 $jid.mfile -n $nprocd $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test "$userhost" - then - RUN_JOB="$RUN_JOB -mhost $userhost" - fi - if test $MPITYPE = "scali" - then -# set default working directory to /tmp to allow -# different directory names - SCAMPI_WORKING_DIRECTORY=/tmp - export SCAMPI_WORKING_DIRECTORY - fi - else - if test -z "$RUN_JOB1" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - RUNNPROCD=$nprocd - if test $MACHINENAME = "IBM" -a $MPITYPE = "hardware" - then - RUNNPROCD= - MP_PROCS=$nprocd - export MP_PROCS - fi - if test $MPITYPE = "myrinet" - then - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - echo " " > /dev/null - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n 1 -f $jid.hosts - fi - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - fi -else - if test $nauto -gt 0 -o $ndcoup -gt 0 - then - RUN_JOB="$RUN_JOB0 $BINDIR/exe_auto $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else -# this is for a serial job without auto restart: - RUN_JOB="$RUN_JOB0 $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi -fi -if test "$rid" -then - RUN_JOB="$RUN_JOB -rid $rid -dirrid $DIRRID" -fi -if test "$pid" -then - RUN_JOB="$RUN_JOB -pid $pid -dirpid $DIRPID" -fi -if test "$sid" -then - RUN_JOB="$RUN_JOB -sid $sid -dirsid $DIRSID" -fi -if test "$did" -then - RUN_JOB="$RUN_JOB -def $did -dirdid $DIRDID" -fi -if test "$vid" -then - RUN_JOB="$RUN_JOB -vf $vid -dirvid $DIRVID" -fi -if test $nauto -gt 0 -then - RUN_JOB="$RUN_JOB -autorst $nauto " -fi -if test $ndcoup -gt 0 -then - RUN_JOB="$RUN_JOB -dcoup $ndcoup " -fi -if test $ndytran -gt 0 -then - RUN_JOB="$RUN_JOB -dytran $ndytran " -fi -if test $mesh -gt 0 -then - RUN_JOB="$RUN_JOB -me $mesh " -fi -if test $noutcore -gt 0 -then - RUN_JOB="$RUN_JOB -outcore $noutcore " -fi -if test "$dllrun" -gt 0 -then - RUN_JOB="$RUN_JOB -dll $dllrun " -fi -if test "$trkrun" -gt 0 -then - RUN_JOB="$RUN_JOB -trk $trkrun " -fi -if test "$iam" -then - RUN_JOB="$RUN_JOB -iam $iam " -fi -if test "$justlist" -then - RUN_JOB="$RUN_JOB -list 1 " -fi -if test "$feature" -then - RUN_JOB="$RUN_JOB -feature $feature " -fi -if test "$memlimit" -ne 0 -then - RUN_JOB="$RUN_JOB -ml $memlimit " -fi -if test "$cpinput" -then - RUN_JOB="$RUN_JOB -ci $cpinput " -fi -if test "$cpresults" -then - RUN_JOB="$RUN_JOB -cr $cpresults " -fi -if test "$DIRSCR" != "$DIRJOB" -then - RUN_JOB="$RUN_JOB -dirscr $DIRSCR" -else - DIRSCR=$DIRJOB -fi -if test "$makebdf" -then - RUN_JOB="$RUN_JOB -bdf $makebdf " -fi -if test $MPITYPE = "myrinet" -a "$host" -a "$MPIVERSION" != "MPICH-GM1.2.1..7" -then - # append $RUN_JOB to all lines of the host file - # and set RUN_JOB - $AWK -v args="$RUN_JOB" '{print $0,args}' $host > $host.$$ - /bin/mv $host.$$ $host - RUN_JOB=$RUN_JOB_TMP -fi -if test $MPITYPE = "intelmpi" -a "$host" -then - # construct config file, append $RUN_JOB to all lines of the config file - # and set RUN_JOB - if test "$INTELMPI_VERSION" = "HYDRA" - then - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf(" -host %s",$1); \ - printf(" -n %s",$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - else - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf("-host %s -n %s",$1,$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - fi - RUN_JOB=$RUN_JOB_TMP -fi -echo " " -echo "Final run stream value" -echo " RUNJOB="$RUN_JOB -if test "$deletelog" = no -then -echo " " >> $jid.log -echo "Final run stream value" >> $jid.log -echo " RUNJOB="$RUN_JOB >> $jid.log -fi - - -############################################################################## -# run marc using valgrind # -############################################################################## -#RUN_JOB="valgrind $RUN_JOB" -#RUN_JOB="valgrind --read-var-info=yes --gen-suppressions=yes $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=all -v $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=yes --error-limit=no $RUN_JOB" -############################################################################## - - -############################################################################## -# run the requested program in a queue # -############################################################################## - -if test "$deletelog" = yes -then - echo - date -else - echo >> $jid.log - date >> $jid.log -fi -if [ $qid = short -o $qid = long -o $qid = verylong -o $qid = at ] -then - -/bin/rm -f $jid.runmarcscript - - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - userobj=$usermoext.o - fi - cat > $jid.runmarcscript << END4 - if test "$user" - then - if test $MACHINENAME = "CRAY" - then - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTHIGH $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - $SOLVERLIBS \ - $MARCCUDALIBS \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } -END4 -else - prgsav=yes -fi -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc -# - -cat >> $jid.runmarcscript << END5 - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# first remove all .out files and incremental restart files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - /bin/rm $DIRJOB/$numdom${jid}_i_*.t08 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null - /bin/rm $DIRJOB/${jid}_i_*.t08 2>/dev/null -fi - -if test $nprocdddm -gt 1 -then - $RUN_JOB 2>>$jid.log -else - $RUN_JOB 2>>$jid.log -fi - -if test $dllrun -eq 0; then - if test $prgsav = no - then - /bin/rm -f $bd$program 2>/dev/null - fi -else - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes - then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -fi -END5 - - -# Submit to marc batch queue -# -if [ $qid = at ] -then -QUENAME=at -SUBMCMD= -else -# -# Submit to qsub queue -# -QUENAME=qsub -SUBMCMD="-q $qid -o /dev/null -e $jid.batch_err_log -x -r $jid" -if test "$priority" -then - SUBMCMD=$SUBMCMD" -p $priority" -fi -if test "$att" -then - SUBMCMD=$SUBMCMD" -a $att" -fi -if test "$cpu" -then - SUBMCMD=$SUBMCMD" -lt $cpu" -fi - -fi -echo $QUENAME $SUBMCMD -#cat $jid.runmarcscript -$QUENAME $SUBMCMD < $jid.runmarcscript - -/bin/rm -f $jid.runmarcscript - -############################################################################## -# run the requested program in the background # -############################################################################## - -else -if test $qid = background -then - -# -# first remove all old .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi -# -# compile user subroutine if present -# -( -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_h $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - echo " $PRODUCT Exit number 3" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTHIGH $user -o $userobj || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - echo " $PRODUCT Exit number 3" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc - -# - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - -$RUN_JOB & - -marcpid=$! -echo $marcpid > $DIRJOB/$jid.pid -wait $marcpid - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - fi - fi - fi -fi - - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi -) 1>>$jid.log 2>&1 & - - -############################################################################## -# run the requested program in the foreground # -############################################################################## - -else - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_h $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTHIGH $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTHIGH $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null -# done if no job id given -if test -z "$jid" -then - echo - echo only compilation requested - echo - exit -fi -# -# run marc -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi -# first remove all .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - $RUN_JOB - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - else - echo " " > /dev/null - fi - else - if test "$host" - then - mpdcleanup -a -f $jid.mfile - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.mfile 2> /dev/null - else - mpdcleanup -a -f $jid.hosts - /bin/rm $jid.hosts 2> /dev/null - fi - fi - fi -fi - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi - - -fi -fi diff --git a/installation/mods_MarcMentat/2017/Marc_tools/run_damask_l b/installation/mods_MarcMentat/2017/Marc_tools/run_damask_l deleted file mode 100644 index d159655db..000000000 --- a/installation/mods_MarcMentat/2017/Marc_tools/run_damask_l +++ /dev/null @@ -1,4122 +0,0 @@ -#!/bin/ksh -############################################################################## -# # -# run_marc - run a marc job # -# ------------------------- # -# # -# usage: run_marc -j jid { options } # -# # -# where standard options are: required: defaults: # -# -------------------------- # -# # -# -j* jid job id number. ** YES ** . # -# -pr* prog program name. . marc # -# -v* y|n do or do not verify inputs. . yes # -# -q* s|l|v|b|f batch queue name or background, . short # -# foreground. # -# -b* as alternative to option -q* # -# # -# ( batch queues only : # -# -pq* intra queue priority. . . # -# -at DATE/TIME delay start of job. . . # -# format : January,1,1990,12:31 # -# or : today,5pm # -# -cpu* secs job CPU limit . . ) # -# # -# -r* rid restart file job id. . . # -# -si* sid substructure file id. . . # -# -pi* post post file job id. . . # -# -de* did defaults file . no # -# -vf vid viewfactor . no # -# # -# -u* user user subroutine. . . # -# -obj obj user objects or libraries. . . # -# -sa* y|n do or do not save load module. . no # -# -autorst auto restart flag for auto forge . no # -# -me manual remeshing control . no # -# -ml memory limit in Mbyte # -# -mo This option is deprecated. As of Marc 2015, only # -# the integer*8 version is available. # -# -mpi selects MPI version # -# each platform has a default MPI version and some # -# have an alternative version. see the include file # -# for the respective platform # -# MPI_DEFAULT defines the default MPI version # -# MPI_OTHER defines versions one can switch to # -# -dcoup for contact decoupling # -# currently not supported # -# -dir directory where the job i/o should take place. # -# defaults to current directory. # -# -sdir directory where scratch files are created # -# defaults to current directory. # -# # -# -alloc only perform memory allocation test, no analysis # -# -list y only list options in the input file, no analysis # -# -fe num set feature number "num" for the run. only one allowed # -# -dytran flag to switch from Dytran to Marc # -# dytran = 0, program will run w/o Marc-Dytran Switch # -# = 1, program will restart Marc after Dytran run # -# >= 2, Not supported yet. # -# currently not supported # -# -ou force analysis to use out-of-core control # -# =0, not used # -# =1, element storage out-of-core # -# -dll run marc using shared library libmarc.so and exe_marc # -# =1, used # -# =2, do not free streaming input memory # -# =3, run with marc input deck # -# -trk run marc for post-tracking # -# -gpuid run marc using GPGPU capability # -# specify gpuid on to be used in the analysis. Multiple # -# IDs may be assigned for DDM runs. # -# Separate a list of IDs with a colon. Each DMP # -# process will be assigned a GPU ID in round robin fastion# -# = 0 # -# = 0:1 etc... # -# # -# where parallel options are: # -# -------------------------- # -# # -# itree, host, and comp options are available for the domain # -# decomposition only. # -# MARC_NUMBER_OF_THREADS, nthread, and dir options always available. # -# # -# # -# -nprocd number of domains. # -# defaults to single domain solution. # -# -nprocds number of domains if single input file. # -# defaults to single domain solution. # -# -nps same as -nprocds. # -# -nsolver number of solver tasks for solver types 12 and 13 # -# these are distributed tasks operating via MPI # -# -nthread_elem number of threads for element assembly and recovery # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by element assembly # -# recovery. # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_elem option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_elem specified. # -# -nthread_solver number of threads for solver types 6, 8, and 11 # -# = 0: use defaults. # -# defaults to 1 for single domain solution. # -# defaults to number of domains for multi-domain # -# solution. # -# > 1: number of threads to be used by 6, 8, and 11 # -# Also can be set through MARC_NUMBER_OF_THREADS # -# environment variable. # -# if both specified, -nthread_solver option will be used. # -# defaults if neither MARC_NUMBER_OF_THREADS environment # -# variable set nor -nthread_solver specified. # -# -nthread Same as -nthread_solver. # -# -itree message passing tree type for domain decomposition. # -# for debugging purposes; should not normally be used. # -# -host hostfile name for distributed execution on network. # -# defaults to no hostfile, unless jobid.defhost exists. # -# if jobid.defhost exists, only -np(s) necessary # -# -comp* y|n to be used with user routines on a network of # -# incompatible machines. # -# if set to no, a separate executable will be created # -# for each machine on the network. # -# if set to yes, the executable located on the machine # -# from which marc is started will be used on all machines.# -# defaults to no if O/S versions different on machines. # -# # -# -ci y|n copy input files to remote hosts (default: yes) # -# if "yes", input files are automatically copied to # -# remote hosts for a network run if necessary. # -# -cr y|n copy post files from remote hosts (default: yes) # -# if "yes", post files are automatically copied back from # -# remote hosts for a network run if necessary. # -############################################################################## -# set DIR to the directory in which this script is -REALCOM="`/bin/ls -l $0 |awk '{ print $NF; }'`" -DIR=`dirname $REALCOM` -# make sure DIR has an absolute path -case $DIR in - \/*) - ;; - *) - DIR=`pwd`/$DIR - ;; -esac -DIRSCRIPT=$DIR -AWK=awk -ARCH=`uname -a | cut -f 1 -d " "` -# Sun has a bad awk, use nawk instead -if test $ARCH = "SunOS" -then - AWK=nawk -fi -BASENAME=basename -# Sun has an incorrect /bin/basename, check if /usr/ucb/basename exists -if test $ARCH = "SunOS" -then - if test -x /usr/ucb/basename - then - BASENAME=/usr/ucb/basename - fi -fi - -# echo command line in the case of ECHO_COMMAND is true -if test "$ECHO_COMMAND" = true ; then - echo command "$0" "$@" -fi - -# -# "mode" selects version, i4 or i8 -# default is i4 -# this can be changed by a file run_marc_defaults -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MODE i8 -# it can also be set by the environmental variable MARC_INTEGER_SIZE -# and by the command line option "-mo" -# -mode= -modeerror= -modeoption= -if test -f $DIRSCRIPT/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $DIRSCRIPT/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $DIRSCRIPT/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $DIRSCRIPT/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -f $HOME/run_marc_defaults; then - line=`$AWK '{if ($1 == "MARC_MODE") {print $1}}' $HOME/run_marc_defaults` - if test "$line" = "MARC_MODE"; then - echo - echo warning: the option MARC_MODE is deprecated, as of Marc 2015, only the integer*8 version is available - echo - line= - fi - line=`$AWK '{if ($1 == "MARC_MODE") {print $2}}' $HOME/run_marc_defaults` - line=`echo $line | $AWK '{print $NF}'` - if test "$line" = "i4"; then - modeerror="defaults file $HOME/run_marc_defaults used mode $line ; this must be i8" - modeoption=error - echo $modeerror - fi - if test "$line" = "i8"; then - mode=i8 - fi -fi -if test -n "$MARC_INTEGER_SIZE" ; then - mode=$MARC_INTEGER_SIZE -fi -if test -z "$mode" ; then - mode=i8 -fi -case $mode in - i4) - modeerror="bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - modeoption=error - echo $modeerror - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo "bad value for MARC_INTEGER_SIZE variable; only i8 is supported." - exit - ;; -esac - -setmode=false -for arg in $* ; do - if $setmode ; then - mode=$arg - case $mode in - i4) - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - ;; - i8) - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - ;; - *) - echo " " - echo "error, version mode must be i8" - echo " " - echo " use -mo i8 " - echo " " - exit - ;; - esac - setmode=false - fi - if [ ${arg}X = -moX -o ${arg}X = -MOX ] ; then - echo - echo warning: the option -mo is deprecated, as of Marc 2015, only the integer*8 version is available - echo - setmode=true - fi - if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - MARC_INTEGER_SIZE=i8 - export MARC_INTEGER_SIZE - fi - if [ ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - modeerror="bad value for mode option; only i8 is supported." - modeoption=error - echo - echo $modeerror - echo - fi -done - -# set to i4 version for 32 bit Linux -if test "`uname -s`" = "Linux"; then - if test "`uname -m`" = "i686"; then - mode=i4 - MARC_INTEGER_SIZE=i4 - export MARC_INTEGER_SIZE - fi -fi - - -. "$DIR/getarch" - - -# getting user subroutine file name -found=0 -for i in "$@"; do - if test $found = 1; then - DAMASK_USER=$i - found=0 - fi - case $i in - -u* | -U*) - found=1 - ;; - esac -done -# sourcing include_linux64 (needs DAMASK_USER to be set) -. $MARC_INCLUDE - -# - -# -# Dynamically determine the echo syntax -# - -case "`echo '\c'`" in - '\c') - ECHO='echo -n' - ECHOTXT=' ' - ;; - *) - ECHO='echo' - ECHOTXT=' \c' - ;; -esac - -# -# Variables for the MARC environment -# - -PRODUCT="Marc" -EXITMSG=$MARC_TOOLS/MESSAGES -export EXITMSG -FLEXDIR=$DIR/../flexlm/licenses -export FLEXDIR -TIMCHK=3600 -export TIMCHK -BINDIR=$MARC_BIN -export BINDIR -AFMATDAT=$MARC_RUNTIME/AF_flowmat/ -export AFMATDAT -export MESHERDIR -MSC_LICENSE_FINPROC=0 -export MSC_LICENSE_FINPROC -# -# define directory path to global unified material database -# -MATFILE= -export MATFILE - -# -# define memory limit -# first set to MEMLIMIT from include -# -ml option overrules if specified -memlimit=$MEMLIMIT -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -# -if test $MACHINENAME = "HP" -then - SHLIB_PATH=$MARC_LIB:$MARC_LIB_SHARED:$SHLIB_PATH - export SHLIB_PATH -fi -# the one for IBM is defined futher down - -LD_LIBRARY_PATH=$MARC_LIB_SHARED:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MARC_LIB:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$MESHERDIR:$LD_LIBRARY_PATH -LD_LIBRARY_PATH=$SFMATDIR:$LD_LIBRARY_PATH -LD_LIBRARY64_PATH=$MARC_LIB:$LD_LIBRARY64_PATH -LD_LIBRARYN32_PATH=$MARC_LIB:$LD_LIBRARYN32_PATH -export LD_LIBRARY_PATH -export LD_LIBRARY64_PATH -export LD_LIBRARYN32_PATH - -atexit() { -kill -15 $$ -# -if test $MPITYPE = "myrinet" -then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi -fi -} - -trap "atexit" 2 - -# -# defaults -# - -prog=marc -exefile=marc -jid= -rid= -pid= -sid= -did= -vid= -user= -usernoext= -objs= -qid=background -cpu= -priority= -att= -trk= -verify=yes -prgsav=no -rmdll=no -cpdll=no -progdll= -pathdll= -error= -nprocd=0 -nprocdddm=1 -nprocdddmprint= -icreated=0 -nprocdarg= -nsolver=0 -nsolverarg=-ns -if test $nprocds -then - if test $nprocds -gt 1 - then - nprocdddm=$nprocds - nprocdddmprint=$nprocds - icreated=1 - nprocdarg=-nprocds - fi -fi -ntprint=0 -nt=-1 -nte=-1 -nts=-1 -ntarg=-nt -ntearg=-nte -ntsarg=-nts -nteprint= -ntsprint= -gpuids= -nauto=0 -ndcoup=0 -ndytran=0 -noutcore=0 -dllrun=0 -mesh=0 -itree=0 -iam= -ddm_arc=0 -link= -trkrun=0 -DIRJOB=`pwd` -DIRSCR=$DIRJOB -DIRSCRSET= -autoforge=0 -dotdat=.dat -dotdefhost=.defhost -host= -numhost= -mfile= -userhost= -makebdf= -cpinput=yes -cpresults=yes -marcdll=libmarc.$EXT_DLL -# define hostname and strip off extensions (alpha.aaa.com) -thishost=`hostname` -thishost=${thishost%%.*} -compatible=unknown -numfield=1 -justlist= -feature= -mpioption=false -iprintsimufact= -MDSRCLIB=$MARC_LIB/mdsrc.a -# -# check run_marc_defaults file for default MPI setting -# located in the tools directory of the Marc installation -# or in the user's home directory -# format: -# MARC_MPI -# -value= -file= -if test -f $DIRSCRIPT/run_marc_defaults; then - value=`$AWK '{if ($1 == "MARC_MPI") {print $2}}' $DIRSCRIPT/run_marc_defaults` - value=`echo $value | $AWK '{print $NF}'` - if test -n "$value"; then - file=$DIRSCRIPT/run_marc_defaults - fi -fi -if test -f $HOME/run_marc_defaults; then - value=`$AWK '{if ($1 == "MARC_MPI") {print $2}}' $HOME/run_marc_defaults` - value=`echo $value | $AWK '{print $NF}'` - if test -n "$value"; then - file=$HOME/run_marc_defaults - fi -fi -if test -n "$value"; then - MARC_MPITYPE=$value - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - echo " " - echo " error, incorrect option for MARC_MPI" - echo " defined in $file: $MARC_MPITYPE" - echo " valid options: $MPI_DEFAULT $MPI_OTHER" - echo " " - exit - fi - if test "$value" != "$MPI_DEFAULT"; then - exefile=marc_$value - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a_$value - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a_$value" - fi - fi -fi -# -# -# allow scratch directory to be specified with environmental variable -# MARCSCRATCH -if test $MARCSCRATCH -then - if test -d $MARCSCRATCH - then - DIRSCR=$MARCSCRATCH - else - echo "error, scratch directory '$MARCSCRATCH'" - echo " specified via environmental variable MARCSCRATCH does not exist" - exit - fi -fi -# -############################################################################## -# parse input - arguments always come in pairs # -############################################################################## - -arg=$1 -if [ ${arg}X = -i8X -o ${arg}X = -I8X ] ; then - shift - arg=$1 -fi -while [ -n "$arg" ] -do - shift - value=$1 - case $arg in - -al* | -AL*) - LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - export LD_LIBRARY_PATH - $MARC_BIN/marc -alloc 1 - exit - ;; - -li* | -LI*) - justlist=yes - ;; - -fe* | -FE*) - feature=$value - - ;; - -pr* | -PR*) - if test `dirname $value` = '.' - then - prog=`$BASENAME $value .marc` - progdll=`$BASENAME $value` - else - prog=`dirname $value`/`$BASENAME $value .marc` - progdll=`dirname $value`/`$BASENAME $value` - fi - prdir=`dirname $value` - case $prdir in - \/*) - ;; - *) - prog=`pwd`/$prdir/$prog - ;; - esac - ;; - -j* | -J*) - jid=`$BASENAME $value $dotdat` - DIRJID=`dirname $value` - case $DIRJID in - \/*) - ;; - *) - DIRJID=`pwd`/$DIRJID - ;; - esac - ;; - -r* | -R*) - rid=`$BASENAME $value .t08` - DIRRID=`dirname $value` - case $DIRRID in - \/*) - ;; - *) - DIRRID=`pwd`/$DIRRID - ;; - esac - ;; - -si* | -SI*) - sid=$value - DIRSID=`dirname $value` - case $DIRSID in - \/*) - ;; - *) - DIRSID=`pwd`/$DIRSID - ;; - esac - ;; - -pi* | -PI*) - if test -f $value.t19 - then - pid=`$BASENAME $value .t19` - else - pid=`$BASENAME $value .t16` - fi - DIRPID=`dirname $value` - case $DIRPID in - \/*) - ;; - *) - DIRPID=`pwd`/$DIRPID - ;; - esac - ;; - -bdf | -BDF) - makebdf=1 - ;; - -de* | -DE*) - did=`$BASENAME $value $dotdat` - DIRDID=`dirname $value` - case $DIRDID in - \/*) - ;; - *) - DIRDID=`pwd`/$DIRDID - ;; - esac - ;; - -vf | -VF) - vid=`$BASENAME $value .vfs` - DIRVID=`dirname $value` - case $DIRVID in - \/*) - ;; - *) - DIRVID=`pwd`/$DIRVID - ;; - esac - ;; - -u* | -U*) - user=$value - case $user in - \/*) - ;; - *) - user=`pwd`/$user - ;; - esac - usernoext=$user - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .F` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .for` - usernoext=`dirname $usernoext`/`$BASENAME $usernoext .f90` - ;; - -obj | -OBJ) - objs="$value" - ;; - -q* | -Q*) - qid=$value - ;; - -b* | -B*) - case $value in - y* | Y*) - qid=background - ;; - n* | N*) - qid=foreground - ;; - *) - ;; - esac - ;; - -at | -AT) - att=$value - ;; - -cpu* | -CPU*) - cpu=$value - ;; - -pq | -PQ*) - priority=$value - ;; - -v* | -V*) - verify=$value - ;; - -sa* | -SA*) - prgsav=$value - ;; - -np* | -NP*) - nprocdddm=$value - nprocdddmprint=$value - case $arg in - -nps* | -NPS* | -nprocds* | -NPROCDS*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - case $arg in - -np | -NP | -nprocd | -NPROCD) - icreated=0 - nprocdarg=-nprocd - ;; - esac - ;; - -ns* | -NS*) - nsolver=$value - ;; - -nt* | -NT*) - case $arg in - -nte | -NTE | -nthread_e* | -NTHREAD_E*) - nte=$value - ;; - esac - case $arg in - -nts | -NTS | -nthread_s* | -NTHREAD_S*) - nts=$value - ;; - esac - case $arg in - -nt | -NT | -nth* | -NTH* | -nthread* | -NTHREAD*) - nt=$value - ;; - esac - ;; - -gp* | -GP*) - gpuids=$value - ;; - -it* | -IT*) - itree=$value - ;; - -iam | -IAM) - iam=$value - case $value in - sfg | sfm | sim) - iprintsimufact=true - ;; - esac - ;; - -au* | -AU*) - nauto=$value - ;; - -dc* | -DC*) - ndcoup=$value - ;; - -dy* | -DY*) - ndytran=$value - ;; - -ou* | -OU*) - noutcore=$value - ;; - -dll | -DLL) - dllrun=$value - ;; - -trk | -TRK) - trkrun=$value - ;; - -ddm | -DDM) - ddm_arc=$value - ;; - -me | -ME ) - mesh=$value - ;; - -ml | -ML ) - memlimit=$value - ;; - -mo | -MO ) - ;; - -mpi | -MPI ) - mpioption=true - MARC_MPITYPE=$value - if test "$value" != "$MPI_DEFAULT"; then - exefile=marc_$value - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a_$value - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a_$value" - fi - else - exefile=marc - . $MARC_INCLUDE - MDSRCLIB=$MARC_LIB/mdsrc.a - if test "$MUMPSSOLVER" = MUMPS; then - MUMPSSOLVERLIBS="$MARC_LIB/libmumps.a" - fi - fi - ;; - -dir* | -DIR*) - DIRJOB=$value - case $DIRJOB in - \/*) - ;; - *) - DIRJOB=`pwd`/$DIRJOB - ;; - esac - if test -z "$DIRSCRSET" - then - DIRSCR=$DIRJOB - fi - ;; - -sd* | -SD*) - DIRSCR=$value - DIRSCRSET=yes - case $DIRSCR in - \/*) - ;; - *) - DIRSCR=`pwd`/$DIRSCR - ;; - esac - ;; - -ho* | -HO*) - host=$value - ;; - -co* | -CO*) - compatible=$value - ;; - -ci* | -CI*) - cpinput=$value - ;; - -cr* | -CR*) - cpresults=$value - ;; - *) - error="$error -$arg: invalid option" - break - ;; - esac - case $value in - -*) - error="$error -$arg: invalid name $value" - break - ;; - esac - shift - arg=$1 - if [ ${arg}X = -i8X -o ${arg}X = -I8X -o ${arg}X = -i4X -o ${arg}X = -I4X ] ; then - shift - arg=$1 - fi -done -argc=`expr $# % 2` -if test $argc -eq 1 -then -# -# odd number of arguments -# - error="$error -argument list incomplete" -fi - -if test $nprocdddm -gt 0 -then -nprocd=$nprocdddm -fi - -if test $nsolver -gt 0 -then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi -fi -# Set defaults -if test $nt -eq -1 -then -nt=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nt -lt 0 -then -nt=0 -fi -if test $nte -eq -1 -then -nte=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nte -lt 0 -then -nte=0 -fi -if test $nts -eq -1 -then -nts=${MARC_NUMBER_OF_THREADS:-0} -fi -if test $nts -lt 0 -then -nts=0 -fi -# -# set number of element loop threads -# -ntprint=$nt -nteprint=$nte -# copy from -nprocd[s] -if test $nprocdddm -gt 1 -then - nteprint=$nprocdddm -fi -# override with -nthread_elem option -if test $nte -ne 0 -then -nteprint=$nte -fi -# check for minimum 1 threads per processes for DDM -if test $nprocdddm -gt 1 -then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi -fi -nte=$nteprint -# -# set number of Solver threads -# -ntsprint=$nts -# copy from -nthread or -nprocd[s] -if test $ntprint -ne 0 -then - ntsprint=$ntprint -else - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -fi -# override with -nthread_solver option -if test $nts -ne 0 -then - ntsprint=$nts -fi -# check for minimum 1 threads per solver process. -if test $nsolver -lt $nprocdddm -then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi -else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi -fi -if test $ntsprint -eq 1 -then - set ntsprint=0 -fi -nts=$ntsprint - -# set stack size for multi-threading. -export KMP_MONITOR_STACKSIZE=7M -export OMP_STACKSIZE=7M - -# -# deprecate -nthread option at arugment of marc -nt=0 -# Reset nprocdddmm, nsolver and threads if not given. -if test $nprocdddm -eq 0 -then - nprocdarg= -fi -if test $nprocdddm -eq 0 -then - nprocdddmprint= -fi -if test $nprocdddm -eq 0 -then - nprocdddm= -fi - -nsolverprint=$nsolver -if test $nsolver -eq 0 -then - nsolverprint= -fi -# end of threads setting. -gpuoption= -if test "$gpuids" = "" ; then - gpuoption= -else - gpuoption="-gp $gpuids" -fi - -if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH -else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH -fi -# Linux 64 + HPMPI, Below code is taken from include_linux64 -if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" -then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" -fi - -if test $nprocd -gt 1; then - if test -f $jid$dotdefhost; then - if test "$host" = ""; then - host=$jid$dotdefhost - fi - fi - if test -f hostfile_qa_$nprocd; then - if test "$host" = ""; then - host=hostfile_qa_$nprocd - fi - fi -fi - -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$dllrun" -eq 1 || test "$dllrun" -eq 2; then - dotdat=.inp - fi - - if test "$progdll"; then - /bin/cp ${progdll}_$marcdll $DIRJOB/$marcdll - rmdll=yes - pathdll=yes - progdll=${progdll}_$marcdll - else - progdll=$marcdll - fi - - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - pathdll=yes - fi -fi - -############################################################################## -# check parameter validity # -############################################################################## - -while test forever; do - -# -# check for input file existence -# -if test $nprocdddm -gt 1 -a $icreated -eq 0; then - if test ! -f $DIRJID/1$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/1$jid$dotdat not accessible" - fi - fi -else - if test ! -f $DIRJID/$jid$dotdat; then - if test "$jid" != "" ; then - error="$error -input file $DIRJID/$jid$dotdat not accessible" - fi - fi -fi - if test $nprocd -gt 1; then - if test "$host" ; then - if test ! -f $host; then - error="$error -host name file $host not accessible" - fi - fi - fi - -# -# check if the job is already running in the background -# -if test -f $DIRJOB/$jid.pid; then - error="$error -job is already running (the file $jid.pid exists)" -fi - -# -# if the program name is other than marc, then -# assume that this is a program in the users local directory -# - -bd=$MARC_BIN/ - -case $prog in - marc | MARC | $exefile) - program=$exefile - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 or $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - if test ! -f $user - then - error="$error -user subroutine file $user not accessible" - fi - fi - if test "$objs" - then - missingobjs= - for o in $objs - do - if test ! -f "$o" - then - if test -z "$missingobjs" - then - missingobjs="$o" - else - missingobjs="$missingobjs $o" - fi - fi - done - if test -n "$missingobjs" - then - error="$error -user object/library file(s) $missingobjs not accessible" - fi - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$vid" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRVID/1$vid.vfs - then - error="$error -view factor file $DIRVID/1$vid.vfs not accessible" - fi - else - if test ! -f $DIRVID/$vid.vfs - then - error="$error -view factor file $DIRVID/$vid.vfs not accessible" - fi - fi - fi - if $mpioption - then - notok=true - for i in "$MPI_OTHER"; do - if test "$MARC_MPITYPE" = "$i"; then - notok=false - fi - done - if test "$MARC_MPITYPE" = "$MPI_DEFAULT"; then - notok=false - fi - if $notok; then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE (valid: $MPI_OTHER)" - fi - fi - ;; - *) - program=$prog.marc - case $prog in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - if test "$rid" - then - if test ! -f $DIRRID/$rid.t08 - then - error="$error -restart file $DIRRID/$rid.t08 not accessible" - fi - fi - if test "$pid" - then - if test ! -f $DIRPID/$pid.t16 - then - if test ! -f $DIRPID/$pid.t19 - then - error="$error -post file $DIRPID/$pid.t16 and $DIRPID/$pid.t19 not accessible" - fi - fi - fi - if test "$user" - then - error="$error -program option may not be used with user subroutine" - fi - if test "$objs" - then - error="$error -program option may not be used with user objects or libraries" - fi - if test "$did" - then - if test $nprocdddm -gt 1 -a $icreated -eq 0 - then - if test ! -f $DIRDID/1$did$dotdat - then - error="$error -defaults file $DIRDID/1$did$dotdat not accessible" - fi - else - if test ! -f $DIRDID/$did$dotdat - then - error="$error -defaults file $DIRDID/$did$dotdat not accessible" - fi - fi - fi - if test "$nauto" - then - if test $nauto -gt 2 - then - error="$error -incorrect option for auto restart " - fi - fi - if test "$ndcoup" - then - if test $ndcoup -gt 3 - then - error="$error -incorrect option for contact decoupling " - fi - fi - if test "$ndytran" - then - if test $ndytran -gt 1 - then - error="$error -incorrect option for Marc-Dytran Switch " - fi - fi - if $mpioption - then - if test ! -x $MARC_BIN/$exefile - then - error="$error -incorrect option for -mpi option: $MARC_MPITYPE " - fi - fi - ;; -esac - -############################################################################## -# check argument integrity # -############################################################################## - -if test "$jid" -then - : -else - if test "$user" - then -# allow user sub without giving job id - qid=foreground - verify=no - else - error="$error -job id required" -fi -fi - -if test $nprocd -gt 1 -then - if test $nauto -gt 0 - then - error="$error -cannot run DDM job with auto restart (-au) option " - fi -fi -case $qid in - S* | s*) - qid=short - ;; - L* | l*) - qid=long - ;; - V* | v*) - qid=verylong - ;; - B* | b*) - qid=background - ;; - F* | f*) - qid=foreground - ;; - A* | a*) - qid=at - ;; - *) - error="$error -bad value for queue_id option" - ;; -esac - -case $prgsav in - N* | n*) - prgsav=no - ;; - Y* | y*) - prgsav=yes - ;; - *) - error="$error -bad value for save option" - ;; -esac - -case $verify in - N* | n*) - verify=no - ;; - Y* | y*) - verify=yes - ;; - *) - error="$error -bad value for verify option" - ;; 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- *) - sid=$value - DIRSID=`dirname $value` - case $DIRSID in - \/*) - ;; - *) - DIRSID=`pwd`/$DIRSID - ;; - esac - ;; - esac - fi - $ECHO "Post File Job ID ($pid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - pid= - ;; - *) - pid=$value - DIRPID=`dirname $value` - case $DIRPID in - \/*) - ;; - *) - DIRPID=`pwd`/$DIRPID - ;; - esac - ;; - esac - fi - $ECHO "Defaults File ID ($did)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - did= - ;; - *) - did=`$BASENAME $value $dotdat` - DIRDID=`dirname $value` - case $DIRDID in - \/*) - ;; - *) - DIRDID=`pwd`/$DIRDID - ;; - esac - ;; - esac - fi - $ECHO "View Factor File ID ($vid)? $ECHOTXT" - read value - if test "$value" - then - case $value in - -*) - vid= - ;; - *) - vid=`$BASENAME $value .vfs` - DIRVID=`dirname $value` - case $DIRVID in - \/*) - ;; - *) - DIRVID=`pwd`/$DIRVID - ;; - esac - ;; - esac - fi - $ECHO "Save generated module ($prgsav)? $ECHOTXT" - read value - if test "$value" - then - prgsav=$value - fi - $ECHO "Run on tasks ($nprocdddm) tasks? $ECHOTXT" - read value - if test "$value" - then - nprocdddm=$value - nprocdddmprint=$value - fi - $ECHO "Run on ($nte) Element loop threads ? $ECHOTXT" - read value - if test "$value" - then - nte=$value - fi - $ECHO "Run on ($nsolver) solvers ? $ECHOTXT" - read value - if test "$value" - then - nsolver=$value - fi - $ECHO "Run on ($nts) Solver threads ? $ECHOTXT" - read value - if test "$value" - then - nts=$value - fi -# - if test $nprocdddm -gt 0 - then - nprocd=$nprocdddm - fi - if test $nsolver -gt 0 - then - if test $nsolver -gt $nprocd - then - nprocd=$nsolver - fi - fi -# Element loop threads. - if test $nte -eq -1 - then - nte=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nte -lt 0 - then - nte=0 - fi - nteprint=$nte -# Copy from ddm - if test $nprocdddm -gt 1 - then - nteprint=$nprocdddm - fi -# override with -nthread_elem option - if test $nte -ne 0 - then - nteprint=$nte - fi -# check for minimum 1 threads per processes for DDM - if test $nprocdddm -ne 0 - then - if test $nteprint -lt $nprocdddm - then - nteprint=$nprocdddm - fi - fi - nte=$nteprint -# Solver threads. - if test $nts -eq -1 - then - nts=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nts -lt 0 - then - nts=0 - fi - ntsprint=$nts -# Copy from ddm - if test $nprocdddm -gt 1 - then - ntsprint=$nprocdddm - fi -# override with -nthread_solver option - if test $nts -ne 0 - then - ntsprint=$nts - fi -# check for minimum 1 threads per solver process. - if test $nsolver -lt $nprocdddm - then - if test $ntsprint -lt $nsolver - then - ntsprint=$nsolver - fi - else - if test $ntsprint -lt $nprocdddm - then - ntsprint=$nprocdddm - fi - fi - if test $ntsprint -eq 1 - then - set ntsprint=0 - fi - nts=$ntsprint -# Update print variable for -nsolver option - nsolverprint=$nsolver - if test $nsolver -eq 0 - then - nsolverprint= - fi - $ECHO "GPGPU id option ($gpuids)? $ECHOTXT" - read value - if test "$value" - then - gpuids=$value - fi - if test "$gpuids" = "" ; then - gpuoption= - else - gpuoption="-gp $gpuids" - fi - if test "$gpuids" = "" ; then - export LD_LIBRARY_PATH=$CUDALIB1:$LD_LIBRARY_PATH - else - MARCCUDALIBS=$MARCCUDALIBS2 - export LD_LIBRARY_PATH=$CUDALIB2:$LD_LIBRARY_PATH - fi - if test $MPITYPE = hpmpi -a "$ARCHITECTURE" = "linux_amd64" - then - export MPIHPSPECIAL="$MPIHPSPECIAL -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH" - fi -# - if test $nprocd -gt 1 - then - $ECHO "Message passing type ($itree)? $ECHOTXT" - read value - if test "$value" - then - itree=$value - fi - $ECHO "Host file name ($host)? $ECHOTXT" - read value - if test "$value" - then - host=$value - fi - if test $nprocdddm -gt 1 - then - $ECHO "Single input file? $ECHOTXT" - read value - case $value in - y* | Y*) - icreated=1 - nprocdarg=-nprocds - ;; - esac - $ECHO "Compatible machines for DDM ($compatible)? $ECHOTXT" - read value - if test "$value" - then - compatible=$value - fi - $ECHO "Copy input files to remote hosts ($cpinput)? $ECHOTXT" - read value - if test "$value" - then - cpinput=$value - fi - $ECHO "Copy post files from remote hosts ($cpresults)? $ECHOTXT" - read value - if test "$value" - then - cpresults=$value - fi - fi - fi - $ECHO "Run the job in the queue ($qid)? $ECHOTXT" - read value - if test "$value" - then - qid=$value - fi - case $qid in - s* | S* | l* | L* | v* | V* ) - $ECHO "Queue priority ($priority)? $ECHOTXT" - read value - if test "$value" - then - priority=$value - fi - $ECHO "Job starts at ($att)? $ECHOTXT" - read value - if test "$value" - then - att=$value - fi - $ECHO "Queue CPU limit ($cpu)? $ECHOTXT" - read value - if test "$value" - then - cpu=$value - fi - ;; - * ) - ;; - esac - $ECHO "Auto Restart option ($nauto)? $ECHOTXT" - read value - if test "$value" - then - nauto=$value - fi - $ECHO "Run directory ($DIRJOB)? $ECHOTXT" - read value - if test "$value" - then - DIRJOB=$value - DIRSCR=$DIRJOB - fi - $ECHO "Scratch directory ($DIRSCR)? $ECHOTXT" - read value - if test "$value" - then - DIRSCR=$value - fi - ;; - quit) - exit 1 - ;; - *) - break - ;; - -esac - - if test $nt -eq -1 - then - nt=${MARC_NUMBER_OF_THREADS:-0} - fi - if test $nt -lt 0 - then - nt=0 - fi - -done -# -if test $nt -eq 0 -then - ntarg= -fi -if test $nt -eq 0 -then - ntprint= -fi -if test $nt -eq 0 -then - nt= -fi - -if test $nte -eq 0 -then - ntearg= -fi -if test $nte -eq 0 -then - nteprint= -fi -if test $nte -eq 0 -then - nte= -fi - -if test $nts -eq 0 -then - ntsarg= -fi -if test $nts -eq 0 -then - ntsprint= -fi -if test $nts -eq 0 -then - nts= -fi -# -if test "$dllrun" -gt 0; then - exefile=exe_marc - prog=exe_marc - program=$exefile - bd=$MARC_BIN/ - if test "$user"; then - . $MARC_TOOLS/make_marc_user_dll $DIRJOB $user - user= - pathdll=yes - if test $prgsav = no; then - rmdll=yes - fi - if test $prgsav = yes; then - cpdll=yes - rmdll=yes - fi - fi - - if test "$pathdll"; then -# -# reset share lib path -# - if test $MACHINENAME = "HP" - then - SHLIB_PATH=$DIRJOB:$SHLIB_PATH - export SHLIB_PATH - fi - if test $MACHINENAME = "IBM" - then - LIBPATH=$DIRJOB:$LIBPATH - export LIBPATH - fi -# - LD_LIBRARY_PATH=$DIRJOB:$LD_LIBRARY_PATH - LD_LIBRARY64_PATH=$DIRJOB:$LD_LIBRARY64_PATH - LD_LIBRARYN32_PATH=$DIRJOB:$LD_LIBRARYN32_PATH - export LD_LIBRARY_PATH - export LD_LIBRARY64_PATH - export LD_LIBRARYN32_PATH - fi -fi -# end of dllrun>0 - - -if test $program = $exefile -o $program = $prog.marc -then - -# delete the old .log file unless we run in the background -if test "$deletelog" = yes -then - if test "$jid" - then - /bin/rm $jid.log 2>/dev/null - fi -else - echo - echo running the job in the background, see $jid.log - echo -fi - -# -# check if this is an autoforge or rezoning or radiation job -# -if test $nprocd -eq 1 -a "$jid" - -then - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^autoforge"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^rezoning"` - if test "$line" - then - autoforge=1 - fi - line=`$AWK '/^[eE][nN][dD]/ {exit} ; {print}' $DIRJID/${jid}$dotdat | grep -i "^radiation"` - if test "$line" - then - autoforge=1 - fi -fi -# -# check that jobname for restarted run is not the same -# as restart file basename -# -if test "$rid" -then - if test "$jid" = "$rid" - then - echo " " - echo "ERROR: job name of current run is the same as job name" - echo " of the restarted job" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "ERROR: job name of current run is the same as job name" >> $jid.log - echo " of the restarted job" >> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi -fi - -# -# user objects/libraries used -# - - if test "$objs" - then - program="$DIRJOB/$jid.marc" - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# user subroutine used -# -# add DAMASK options for linking - DAMASK="-lstdc++" - - if test "$user" - then - program=$usernoext.marc - case $program in - \/* | \.\/*) - bd= - ;; - *) - bd=`pwd`/ - ;; - esac - link=yes - fi - -# -# Special case for IBM using POE but not an SP machine -# in this case we always need a host file, also for serial jobs. -# -if test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP -then - MP_HOSTFILE=${jid}.host - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $nprocd -gt 1 - then - numdom=$nprocd - while test $numdom -gt 0 - do - hostname -s >> $MP_HOSTFILE - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - else - hostname -s > $MP_HOSTFILE - fi -fi -# -# check ssh for all hosts in host file -# -if test $nprocd -gt 1 -then -if test $MPITYPE = "intelmpi" -a "$INTELMPI_VERSION" = "HYDRA" - then -# get host list - if test "$host" - then - line=`grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' | uniq` -# count failing hosts - counter=0 - for i in $line - do - $RSH -o BatchMode=yes -o ConnectTimeout=10 $i uname -n - status=$? - if [[ $status != 0 ]] ; then - counter=$((counter+1)) - if [ "$counter" = "1" ]; then - echo " " - echo " error - connection test failed... " - echo " " - fi - echo " " - echo " connection test with ssh failed on host $i" - echo " check the following command: ssh $i uname -n " - echo " " - fi - done -# echo error message and quit - if test $counter -ne 0 - then - echo " " - echo " A parallel job using IntelMPI cannot be started. " - echo " The ssh command must be working correctly between " - echo " the computers used in the analysis. Furthermore, " - echo " it must be set up such that it does not prompt the " - echo " user for a password. " - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo " A parallel job using IntelMPI cannot be started. ">> $jid.log - echo " The ssh command must be working correctly between ">> $jid.log - echo " the computers used in the analysis. Furthermore, ">> $jid.log - echo " it must be set up such that it does not prompt the ">> $jid.log - echo " user for a password. ">> $jid.log - echo " " >> $jid.log - echo " Exit number 8" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi -fi -fi -# -# check correctness of host file; fix for user sub -# - if test $nprocd -gt 1 - then - -# construct the path name to the executable (execpath) - execpath=$MARC_BIN/$exefile - usersub=0 - if test $program = $prog.marc - then - execpath=$prog.marc - usersub=1 - fi - if test "$objs" - then - execpath="$DIRJOB/$jid.marc" - usersub=1 - fi - if test "$user" - then - execpath=$usernoext.marc - usersub=1 - fi - export execpath - execname=`$BASENAME $execpath` - - if test "$host" - then - userhost=$host - case $userhost in - \/* | \.\/*) - ;; - *) - userhost=`pwd`/$userhost - ;; - esac - -# check that the number of processes specified in the hostfile is -# equal to nprocd specified by -nprocd. - numproc=`grep -v '^#' $host | $AWK -v sum=0 '{sum=sum+$2}; END {print sum}'` - if test $nprocd -ne $numproc - then - echo " " - echo "error, the number of processes specified in the host file" - echo "must be equal to the number of processes given by -nprocd/-nsolver" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, the number of processes specified in the host file" >> $jid.log - echo "must be equal to the number of processes given by -nprocd/-nsolver" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - -# check for Myrinet that the number of processes per host is -# less than number of available user ports, 5 -# .gmpi directory must exist in user's home directory -# and must have write permission from remote hosts - if test $MPITYPE = "myrinet" - then - numproc=`grep -v '^#' $host | $AWK -v sum=1 '{if( $2 > 5) sum=6}; END {print sum}'` - if test $numproc -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes specified " - echo "in the hostfile must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes specified " >> $jid.log - echo "in the hostfile must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - if test ! -d ~/.gmpi - then - echo " " - echo "error, for Myrinet a .gmpi directory must exist " - echo "under the user's home directory" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a .gmpi directory must exist " >> $jid.log - echo "under the user's home directory" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - homedir=`echo ~` - for i in `grep -v '^#' $host | $AWK '{if (NF > 0) print $1}'` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - $RSH $i /bin/touch $homedir/.gmpi/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - echo " " - echo "error, for Myrinet a shared .gmpi directory must exist " - echo "under the user's home directory " - echo "with remote write permission" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet a shared .gmpi directory must exist " >> $jid.log - echo "under the user's home directory " >> $jid.log - echo "with remote write permission" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - else - /bin/rm tmp.$$ - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - fi - fi - done - fi - fi - -# construct the host file $jid.host which is used by mpirun -# skip lines starting with # and only consider lines with more than -# one word in them. Note that the hostfile given to this script -# has two columns: the host name and the number of shared processes -# to run on this host. mpirun wants the number of _other_ -# processes to run in addition to the one being run on the machine -# on which the job is started. hence the $2-1 for fnr == 1. - if test -f $jid.host - then - /bin/rm $jid.host 2> /dev/null - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then -# HPMPI or HP hardware MPI - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ - -v mpihpspecial="$MPIHPSPECIAL" \ -'{if ( NF > 0) {\ - fnr++ ; \ - printf("-h %s -np %s",$1,$2); \ - printf(" %s",mpihpspecial); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF >= 3 ) printf(" -e MPI_WORKDIR=%s", $3);\ - if ( NF >= 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) \ - }\ - }' > $jid.host -# end HPMPI or HP hardware MPI - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then -# IBM using hardware MPI (POE) - MP_HOSTFILE=$jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.host -# end IBM using hardware MPI (POE) -# for Intel MPI, need to create a machinefile for DMP - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then -# Intel MPI - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - /bin/cp $host $jid.host - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Intel MPI for DMP -# for Solaris HPC 7.1, need to create a machinefile for DMP - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then -# Solaris HPC 7.1 - if test -f $jid.mfile - then - /bin/rm $jid.mfile 2> /dev/null - fi - grep -v '^#' $host | $AWK '{host=$1;num=$2;for (i=1;i<=num;i++) print host}' > $jid.mfile -# end Solaris HPC 7.1 for DMP -# for Myrinet, construct a configuration file in ~/.gmpi -# this must be readable by each process -# format is (hostname) (port number) for each process - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - grep -v '^#' $host | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ -{if ( NF > 0 ) \ - for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc]); \ -}' >> ~/.gmpi/$jid.host - else -# this is for mpich-1.2.5 and later, using the -pg option -# format: host nproc executable user arguments -# the arguments are added later - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub -v user=`whoami` \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s %s\n",path,user);\ - if ( NF == 3 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s %s\n",path,user) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s %s\n",$3,en,user); else printf(" %s/bin/%s %s\n",$4,en,user) \ - }\ - }' > $jid.host - fi -# end Myrinet - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then -# Compaq MPI via Memory Channel - grep -v '^#' $host | $AWK '{if (NF > 0) print $1}' > $jid.host -# end Compaq MPI - else -# MPICH - grep -v '^#' $host | $AWK -v path=$execpath -v en=$execname -v us=$usersub \ -'{if ( NF > 0) {\ - fnr++ ; \ - if ( fnr == 1 ) printf("%s %d",$1,$2-1); \ - else printf("%s %s",$1,$2); \ - if ( NF == 2 ) printf(" %s\n",path);\ - if ( NF == 3 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s\n",path) ;\ - if ( NF == 4 ) if (us) printf(" %s/%s\n",$3,en); else printf(" %s/bin/%s\n",$4,en) \ - }\ - }' > $jid.host - fi -# define the variable host and host_filt -# host_filt is used for loops over hosts -# for Myrinet we need to use a filtered variant of userhost -# for others we can use $host - if test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - host=~/.gmpi/$jid.host - host_filt=$jid.host_tMp - grep -v '^#' $userhost | $AWK '{if (NF > 0) print $1}' > $host_filt - else - host=$jid.host - host_filt=$host - fi - else - host=$jid.host - host_filt=$host - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - host_filt=$jid.mfile - fi - fi -# figure out if the machines in the hostfile are nfs mounted -# or distributed and set the variable "dirstatus" accordingly. -# only perform the check if user subroutine is used -# or a user subroutine executable is used - - numfield=1 - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - numfield=2 - fi - DIR1=$DIRJOB - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - counter=0 - echo " " - echo "checking if local or shared directories for host" - if test "$deletelog" = no - then - echo "checking if local or shared directories for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - dirstatus[$counter]="shared" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - $RSH $i /bin/touch $DIR1/$jid.$$ 2> tmp.$$ - if test -s tmp.$$ - then - dirstatus[$counter]="local" - /bin/rm tmp.$$ - else - if test ! -f $jid.$$ - then - dirstatus[$counter]="local" - $RSH $i /bin/rm $DIR1/$jid.$$ - else - /bin/rm $jid.$$ - fi - fi - if test -f tmp.$$ - then - /bin/rm tmp.$$ - fi - if test -f $jid.$$ - then - /bin/rm $jid.$$ - fi - echo " ${dirstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${dirstatus[$counter]}" >> $jid.log - fi - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - fi - -# figure out if this is a compatible set of machines -# unless explicitly specified with flag -comp -# only perform the check if user subroutine is used -# or a user subroutine executable is used -# Myrinet does not support heterogeneous - if test $program = $prog.marc -o -n "$user" -o -n "$objs" - then - if test $compatible = "unknown" - then - thisname=$ARCH - compatible=yes - counter=0 - echo "checking if machines are compatible for host" - if test "$deletelog" = no - then - echo "checking if machines are compatible for host" >> $jid.log - fi - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]="yes" - $ECHO " $i $ECHOTXT" - if test "$deletelog" = no - then - $ECHO " $i $ECHOTXT" >> $jid.log - fi - othername=`$RSH $i uname -a | cut -f 1 -d " "` - if test $thisname != $othername - then - compatible=no - compstatus[$counter]="no" - fi - fi - echo " ${compstatus[$counter]}" - if test "$deletelog" = no - then - echo " ${compstatus[$counter]}" >> $jid.log - fi - done - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - fi - else - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - compstatus[$counter]=$compatible - fi - done - if test $compatible = "no" - then - echo "all machines assumed incompatible" - if test "$deletelog" = no - then - echo "all machines assumed incompatible" >> $jid.log - fi - else - echo "all machines compatible" - if test "$deletelog" = no - then - echo "all machines compatible" >> $jid.log - fi - fi - fi -# error out if user objects or libraries are used on incompatible machines - if test "$compatible" = "no" -a -n "$objs" - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" - if test "$deletelog" = no - then - echo "User object/libraries cannot be used in a parallel job on incompatible machines" >> $jid.log - fi - exit 1 - fi -# modify new host file if NFS mounted heterogeneous machine - doit= - if test $program = $prog.marc - then - doit=yes - fi - if test "$user" - then - doit=yes - fi - if test "$doit" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - $AWK -v hst=$i '{fnr++ ; \ -if ($1 ~ hst) {if ( fnr == 1 ) printf("%s\n",$0); else \ -printf("%s %s %s_%s\n",$1,$2,$3,$1) } else print}' $jid.host > $jid.host{$$} - /bin/mv $jid.host{$$} $jid.host - host=$jid.host - fi - fi - done - fi - fi # if test $program = $prog.marc -o $user -o $obj - - else # if test $host - # assume shared memory machine if no hostfile given and - # MPITYPE is set to mpich or Myrinet - # check for Myrinet that the total number of processes is - # less than number of available user ports, 5 - if test $MPITYPE = "mpich" -o $MPITYPE = "scali" - then - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - host=$jid.host - elif test $MPITYPE = "myrinet" - then - if test $nprocd -gt 5 - then - echo " " - echo "error, for Myrinet the number of processes " - echo "must not exceed 5 for a hostname" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error, for Myrinet the number of processes " >> $jid.log - echo "must not exceed 5 for a hostname" >> $jid.log - echo " " >> $jid.log - fi - exit 1 - fi - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - echo $nprocd > ~/.gmpi/$jid.host - echo `hostname` $nprocd | $AWK \ -'BEGIN {iport[0] = 2; \ - iport[1] = 4; \ - iport[2] = 5; \ - iport[3] = 6; \ - iport[4] = 7 \ - } \ - {for(iproc = 0; iproc < $2; iproc++) printf("%s %d\n",$1,iport[iproc])} \ -' >> ~/.gmpi/$jid.host - host=~/.gmpi/$jid.host - else - numproc=`echo $nprocd | $AWK '{sum=$1-1}; {print sum}'` - echo `hostname` $numproc $execpath > $jid.host - - fi - fi # if test myrinet - - fi # if test $host - - fi # if test $nprocd -gt 1 - -fi # if test $program = $exefile -o $program = $prog.marc - -############################################################################## -# construct run stream (Marc only) # -############################################################################## - -# set maximum message length for ddm to a large number -# for vendor provided mpi -if test $itree -eq 0 -a $MPITYPE = hardware -then - itree=100000000 - if test $MACHINENAME = SGI - then - itree=100000001 - fi -fi -if test $itree -eq 0 -a $MPITYPE = hpmpi -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = myrinet -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = nec -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = scali -then - itree=100000000 -fi -if test $itree -eq 0 -a $MPITYPE = intelmpi -then - itree=100000000 -fi -if test $nprocdddm -lt 2 -then - nprocdarg= -else - nprocdarg="$nprocdarg $nprocdddm" -fi -if test $nsolver -eq 0 -then - nsolverarg= -else - nsolverarg="$nsolverarg $nsolver" -fi -if test $nprocdddm -lt 2 -a $nsolver -eq 0 -then -nprocd=0 -fi -if test $nprocd -gt 0 -then - if test "$host" - then - if test -z "$RUN_JOB2" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - if test $MPITYPE = hpmpi -o $MACHINENAME = HP -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $host -- -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = IBM -a $MPITYPE = hardware -a "$MACHINETYPE" = NONSP - then - RUN_JOB="$RUN_JOB2 $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MPITYPE = "myrinet" - then - if test $MPIVERSION = "MPICH-GM1.2.1..7" - then - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB_TMP="$RUN_JOB2 $host $bd$program" - RUN_JOB=" -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - elif test $MACHINENAME = DEC -a $MPITYPE = hardware - then - RUN_JOB="$RUN_JOB2 $nprocd -hf $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - elif test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - numhost=`uniq $jid.mfile | wc -l` - if test "$INTELMPI_VERSION" = "HYDRA" - then - RUN_JOB_TMP="$RUN_JOB2 -configfile $jid.cfile" - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n $numhost -r $RSH -f $jid.mfile - RUN_JOB_TMP="$RUN_JOB2 $jid.cfile" - fi - -# intelmpi uses configfile. format: -# -host host1 -n n1 executable marcargs -# one such line per host -# collect the marcargs in RUN_JOB and construct the config file later -# collect the run stream in RUN_JOB_TMP - RUN_JOB="-jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - - - elif test $MACHINENAME = "SUN" -a $MPITYPE = "hardware" - then - RUN_JOB="$RUN_JOB2 $jid.mfile -n $nprocd $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB2 $host $bd$program -jid $jid -dirjid $DIRJID \ -$nprocdarg \ -$nsolverarg \ --maxnum $MAXNUM -itree $itree \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test "$userhost" - then - RUN_JOB="$RUN_JOB -mhost $userhost" - fi - if test $MPITYPE = "scali" - then -# set default working directory to /tmp to allow -# different directory names - SCAMPI_WORKING_DIRECTORY=/tmp - export SCAMPI_WORKING_DIRECTORY - fi - else - if test -z "$RUN_JOB1" - then - echo " " - echo "error: parallel job attempted on non-parallel version," - echo " or, if parallel version is installed, the include " - echo " file is probably corrupted" - echo " " - if test "$deletelog" = no - then - echo " " >> $jid.log - echo "error: parallel job attempted on non-parallel version," >> $jid.log - echo " or, if parallel version is installed, the include " >> $jid.log - echo " file is probably corrupted" >> $jid.log - echo " " >> $jid.log - fi - exit - fi - RUNNPROCD=$nprocd - if test $MACHINENAME = "IBM" -a $MPITYPE = "hardware" - then - RUNNPROCD= - MP_PROCS=$nprocd - export MP_PROCS - fi - if test $MPITYPE = "myrinet" - then - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - echo " " > /dev/null - else - export I_MPI_JOB_CONTEXT=$$ - mpdboot -n 1 -f $jid.hosts - fi - RUN_JOB="$RUN_JOB1 $RUNNPROCD $bd$program -jid $jid -dirjid $DIRJID \ - $nprocdarg \ - $nsolverarg \ - -maxnum $MAXNUM -itree $itree \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi - fi -else - if test $nauto -gt 0 -o $ndcoup -gt 0 - then - RUN_JOB="$RUN_JOB0 $BINDIR/exe_auto $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ - $ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - else -# this is for a serial job without auto restart: - RUN_JOB="$RUN_JOB0 $bd$program -jid $jid -dirjid $DIRJID \ --maxnum $MAXNUM \ -$ntearg $nte $ntsarg $nts $gpuoption -dirjob $DIRJOB " - fi -fi -if test "$rid" -then - RUN_JOB="$RUN_JOB -rid $rid -dirrid $DIRRID" -fi -if test "$pid" -then - RUN_JOB="$RUN_JOB -pid $pid -dirpid $DIRPID" -fi -if test "$sid" -then - RUN_JOB="$RUN_JOB -sid $sid -dirsid $DIRSID" -fi -if test "$did" -then - RUN_JOB="$RUN_JOB -def $did -dirdid $DIRDID" -fi -if test "$vid" -then - RUN_JOB="$RUN_JOB -vf $vid -dirvid $DIRVID" -fi -if test $nauto -gt 0 -then - RUN_JOB="$RUN_JOB -autorst $nauto " -fi -if test $ndcoup -gt 0 -then - RUN_JOB="$RUN_JOB -dcoup $ndcoup " -fi -if test $ndytran -gt 0 -then - RUN_JOB="$RUN_JOB -dytran $ndytran " -fi -if test $mesh -gt 0 -then - RUN_JOB="$RUN_JOB -me $mesh " -fi -if test $noutcore -gt 0 -then - RUN_JOB="$RUN_JOB -outcore $noutcore " -fi -if test "$dllrun" -gt 0 -then - RUN_JOB="$RUN_JOB -dll $dllrun " -fi -if test "$trkrun" -gt 0 -then - RUN_JOB="$RUN_JOB -trk $trkrun " -fi -if test "$iam" -then - RUN_JOB="$RUN_JOB -iam $iam " -fi -if test "$justlist" -then - RUN_JOB="$RUN_JOB -list 1 " -fi -if test "$feature" -then - RUN_JOB="$RUN_JOB -feature $feature " -fi -if test "$memlimit" -ne 0 -then - RUN_JOB="$RUN_JOB -ml $memlimit " -fi -if test "$cpinput" -then - RUN_JOB="$RUN_JOB -ci $cpinput " -fi -if test "$cpresults" -then - RUN_JOB="$RUN_JOB -cr $cpresults " -fi -if test "$DIRSCR" != "$DIRJOB" -then - RUN_JOB="$RUN_JOB -dirscr $DIRSCR" -else - DIRSCR=$DIRJOB -fi -if test "$makebdf" -then - RUN_JOB="$RUN_JOB -bdf $makebdf " -fi -if test $MPITYPE = "myrinet" -a "$host" -a "$MPIVERSION" != "MPICH-GM1.2.1..7" -then - # append $RUN_JOB to all lines of the host file - # and set RUN_JOB - $AWK -v args="$RUN_JOB" '{print $0,args}' $host > $host.$$ - /bin/mv $host.$$ $host - RUN_JOB=$RUN_JOB_TMP -fi -if test $MPITYPE = "intelmpi" -a "$host" -then - # construct config file, append $RUN_JOB to all lines of the config file - # and set RUN_JOB - if test "$INTELMPI_VERSION" = "HYDRA" - then - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf(" -host %s",$1); \ - printf(" -n %s",$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - else - grep -v '^#' $host | $AWK -v args="$RUN_JOB" -v path=$execpath -v en=$execname -v us=$usersub \ - '{if ( NF > 0) {\ - printf("-host %s -n %s",$1,$2); \ - if ( NF == 2 ) printf(" %s",path);\ - if ( NF >= 3 ) printf(" -wdir %s ",$3); \ - if ( NF >= 3 ) if (us) printf(" %s/%s",$3,en); else printf(" %s",path); \ - printf(" %s\n",args); \ - }\ - }' > $jid.cfile - fi - RUN_JOB=$RUN_JOB_TMP -fi -echo " " -echo "Final run stream value" -echo " RUNJOB="$RUN_JOB -if test "$deletelog" = no -then -echo " " >> $jid.log -echo "Final run stream value" >> $jid.log -echo " RUNJOB="$RUN_JOB >> $jid.log -fi - - -############################################################################## -# run marc using valgrind # -############################################################################## -#RUN_JOB="valgrind $RUN_JOB" -#RUN_JOB="valgrind --read-var-info=yes --gen-suppressions=yes $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=all -v $RUN_JOB" -#RUN_JOB="valgrind --gen-suppressions=yes --error-limit=no $RUN_JOB" -############################################################################## - - -############################################################################## -# run the requested program in a queue # -############################################################################## - -if test "$deletelog" = yes -then - echo - date -else - echo >> $jid.log - date >> $jid.log -fi -if [ $qid = short -o $qid = long -o $qid = verylong -o $qid = at ] -then - -/bin/rm -f $jid.runmarcscript - - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - userobj=$usermoext.o - fi - cat > $jid.runmarcscript << END4 - if test "$user" - then - if test $MACHINENAME = "CRAY" - then - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTLOW $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - $SOLVERLIBS \ - $MARCCUDALIBS \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } -END4 -else - prgsav=yes -fi -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc -# - -cat >> $jid.runmarcscript << END5 - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# first remove all .out files and incremental restart files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - /bin/rm $DIRJOB/$numdom${jid}_i_*.t08 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null - /bin/rm $DIRJOB/${jid}_i_*.t08 2>/dev/null -fi - -if test $nprocdddm -gt 1 -then - $RUN_JOB 2>>$jid.log -else - $RUN_JOB 2>>$jid.log -fi - -if test $dllrun -eq 0; then - if test $prgsav = no - then - /bin/rm -f $bd$program 2>/dev/null - fi -else - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes - then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test \$numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - numdom=\`echo \$numdom | $AWK '{sum=\$1-1}; {print sum}'\` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null -fi -END5 - - -# Submit to marc batch queue -# -if [ $qid = at ] -then -QUENAME=at -SUBMCMD= -else -# -# Submit to qsub queue -# -QUENAME=qsub -SUBMCMD="-q $qid -o /dev/null -e $jid.batch_err_log -x -r $jid" -if test "$priority" -then - SUBMCMD=$SUBMCMD" -p $priority" -fi -if test "$att" -then - SUBMCMD=$SUBMCMD" -a $att" -fi -if test "$cpu" -then - SUBMCMD=$SUBMCMD" -lt $cpu" -fi - -fi -echo $QUENAME $SUBMCMD -#cat $jid.runmarcscript -$QUENAME $SUBMCMD < $jid.runmarcscript - -/bin/rm -f $jid.runmarcscript - -############################################################################## -# run the requested program in the background # -############################################################################## - -else -if test $qid = background -then - -# -# first remove all old .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi -# -# compile user subroutine if present -# -( -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_l $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - echo " $PRODUCT Exit number 3" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTLOW $user -o $userobj || \ - { - echo "$0: compile failed for $user" - echo " $PRODUCT Exit number 3" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - echo " $PRODUCT Exit number 3" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null - -# -# run marc - -# - -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - -$RUN_JOB & - -marcpid=$! -echo $marcpid > $DIRJOB/$jid.pid -wait $marcpid - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - fi - fi - fi -fi - - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi -) 1>>$jid.log 2>&1 & - - -############################################################################## -# run the requested program in the foreground # -############################################################################## - -else - -# -# compile user subroutine if present -# -if test "$link" -then - if test -z "$FCOMPROOT"; then - echo "$0: No compiler available" - echo - echo " $PRODUCT Exit number 3" - exit 1 - fi - echo - echo "Using compiler from: $FCOMPROOT" - echo - if test "$user" - then - # compile and link on other hosts in $host if compstatus=no - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${compstatus[$counter]} = "no" - then - DIR1=$DIRJOB - DIR2=$DIR - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - marcdir=`echo $line | $AWK '{print $4}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - if test -n "$marcdir" - then - DIR2=$marcdir - fi - # first copy over the user sub if local directories - if test ${dirstatus[$counter]} = "local" - then - $RCP $user $i:$DIR1/ - fi - # do the compilation on the other machine - if test ${dirstatus[$counter]} = "shared" - then - hname=_$ibase - else - hname= - fi - remoteprog=$DIR1/${execname}$hname - remoteuser=$DIR1/`$BASENAME $user` - $RSH $i /bin/rm $remoteprog 2> /dev/null - echo - $RSH $i $DIR2/tools/comp_damask_l $DIR2 $DIR1 $remoteuser $remoteprog - # check if successful, the new executable should be there - line=`$RSH $i /bin/ls $remoteprog 2> /dev/null` - if test "$line" - then - echo compilation and linking successful on host $i - else - echo "$0: compile failed for $user on host $i" - exit 1 - fi - # remove the user subroutine on remote machine - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $remoteuser 2> /dev/null - fi - fi - fi - done - fi - fi - if test "$userhost" - then - echo - echo "Compiling and linking user subroutine $user on host `hostname`" - fi - userobj=$usernoext.o - if test $MACHINENAME = "CRAY" - then - $DFORTLOW $user || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - else - $DFORTLOW $user -o $userobj || \ - { - echo "$0: compile failed for $user" - exit 1 - } - /bin/rm $program 2>/dev/null - fi - fi # if test $user - - - $LOAD $bd${program} $MARC_LIB/main.o \ - $MARC_LIB/blkdta.o $MARC_LIB/comm?.o \ - ${userobj-} \ - $objs \ - $MARC_LIB/srclib.a \ - $MNFLIBS \ - $MDUSER \ - ${MUMPSSOLVERLIBS} \ - $MDSRCLIB \ - $MARC_LIB/mcvfit.a \ - $STUBS \ - ${SOLVERLIBS} \ - ${MARCCUDALIBS} \ - $TKLIBS \ - $MRCLIBS \ - $METISLIBS \ - $DAMASK \ - $OPENSSL_LIB \ - $SYSLIBS \ - $SFLIB \ - $SECLIBS || \ - { - echo "$0: link failed for ${user:+$userobj }$objs" - exit 1 - } - # copy user subroutine executable for hosts using local working dir - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - if test ${dirstatus[$counter]} = "local" -a ${compstatus[$counter]} = "yes" - then - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - echo "Copying executable to host ${i}" - $RCP $program ${i}:${DIR1}/ - fi - fi - done - fi - fi -else # if test $link - prgsav=yes -fi # if test $link -/bin/rm $userobj 2>/dev/null -/bin/rm $DIRJOB/*.mod 2>/dev/null -# done if no job id given -if test -z "$jid" -then - echo - echo only compilation requested - echo - exit -fi -# -# run marc -# -# Define share library path based on platforms -# This is required for using the Patran Mesher -if test $MACHINENAME = "IBM" -then - LIBPATH=$MARC_LIB:$MARC_LIB_SHARED:$LIBPATH - export LIBPATH -fi -# first remove all .out files -# the ones for ddm are removed in the code -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRJOB/$numdom$jid.out 2>/dev/null - /bin/rm $DIRJOB/$numdom$jid.log 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done -else - /bin/rm $DIRJOB/$jid.out 2>/dev/null -fi - -# for DDM with ARC support - -if test $ddm_arc -gt 0; then - RUN_JOB="$MESHERDIR/sf_exeddm $RUN_JOB -ddm $ddm_arc " -fi - - $RUN_JOB - -if test $nprocd -gt 1 -then - if test $MACHINENAME = "LINUX" -a $MPITYPE = "intelmpi" - then - if test "$INTELMPI_VERSION" = "HYDRA" - then - if test "$host" - then - /bin/rm $jid.mfile 2> /dev/null - /bin/rm $jid.hosts 2> /dev/null - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.cfile 2> /dev/null - else - echo " " > /dev/null - fi - else - if test "$host" - then - mpdcleanup -a -f $jid.mfile - /bin/rm $jid.host 2> /dev/null - /bin/rm $jid.mfile 2> /dev/null - else - mpdcleanup -a -f $jid.hosts - /bin/rm $jid.hosts 2> /dev/null - fi - fi - fi -fi - -if test $dllrun -eq 0; then -if test $prgsav = no -then - /bin/rm -f $bd$program 2>/dev/null - # for network run, remove executable on remote machines - # and executables with modified name - if test $nprocd -gt 1 - then - if test "$userhost" - then - counter=0 - if test -f "$host_filt" - then - for i in `$AWK -v n=$numfield '{print $n}' $host_filt` - do - ibase=${i%%.*} - if test $ibase != $thishost - then - counter=$((counter+1)) - DIR1=$DIRJOB - line=`grep -v '^#' $userhost | grep "^$ibase "` - workdir=`echo $line | $AWK '{print $3}'` - if test -n "$workdir" - then - DIR1=$workdir - fi - # if an incompatible host uses shared directory, - # then the root machine deletes the executable - if test ${dirstatus[$counter]} = "shared" -a ${compstatus[$counter]} = "no" - then - hname=_$ibase - /bin/rm ${execname}$hname - fi - # if local directory used, the remote machine - # deletes the executable - if test ${dirstatus[$counter]} = "local" - then - $RSH $i /bin/rm $DIR1/${execname} 2>/dev/null - fi - fi - done - fi - fi -fi -fi -else -#dllrun >0 - if test $cpdll = yes; then - filename=$usernoext - /bin/cp $DIRJOB/$marcdll $DIRJOB/${filename}_$marcdll 2>/dev/null - fi - if test $rmdll = yes;then - /bin/rm -f $DIRJOB/$marcdll 2>/dev/null - fi -fi - -if test $nprocdddm -gt 1 -then - numdom=$nprocdddm - while test $numdom -gt 0 - do - /bin/rm $DIRSCR/$numdom$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t74 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t75 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t76 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t77 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t78 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t79 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t84 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t85 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t86 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t87 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t88 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.t90 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sle 2>/dev/null - /bin/rm $DIRSCR/$numdom$jid.sin 2>/dev/null - numdom=`echo $numdom | $AWK '{sum=$1-1}; {print sum}'` - done - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - if test $MPITYPE = "myrinet" - then - if test -f "$host_filt" - then - /bin/rm $host_filt - fi - fi -else - /bin/rm $DIRSCR/$jid.t02 2>/dev/null - /bin/rm $DIRSCR/$jid.t03 2>/dev/null - /bin/rm $DIRSCR/$jid.t11 2>/dev/null - /bin/rm $DIRSCR/$jid.t12 2>/dev/null - /bin/rm $DIRSCR/$jid.t13 2>/dev/null - /bin/rm $DIRSCR/$jid.t14 2>/dev/null - /bin/rm $DIRSCR/$jid.t15 2>/dev/null - /bin/rm $DIRSCR/$jid.t22 2>/dev/null - /bin/rm $DIRSCR/$jid.t23 2>/dev/null - /bin/rm $DIRSCR/$jid.t32 2>/dev/null - /bin/rm $DIRSCR/$jid.t33 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t81* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t82* 2>/dev/null - /bin/rm $DIRSCR/$jid.*.t83* 2>/dev/null - /bin/rm $DIRSCR/$jid.t84 2>/dev/null - /bin/rm $DIRJOB/$jid.pid 2>/dev/null - /bin/rm $DIRJOB/$jid.sle 2>/dev/null - /bin/rm $DIRJOB/$jid.sin 2>/dev/null -fi - - -fi -fi diff --git a/installation/mods_MarcMentat/2017/Mentat_bin/kill7 b/installation/mods_MarcMentat/2017/Mentat_bin/kill7 deleted file mode 100644 index 6d1ff84bf..000000000 --- a/installation/mods_MarcMentat/2017/Mentat_bin/kill7 +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/sh - -if [ "$1" = "" ]; then - echo "usage: $0 job_name" - exit 1 -fi - -echo STOP > $1.cnt diff --git a/installation/mods_MarcMentat/2017/Mentat_bin/kill8 b/installation/mods_MarcMentat/2017/Mentat_bin/kill8 deleted file mode 100644 index 6d1ff84bf..000000000 --- a/installation/mods_MarcMentat/2017/Mentat_bin/kill8 +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/sh - -if [ "$1" = "" ]; then - echo "usage: $0 job_name" - exit 1 -fi - -echo STOP > $1.cnt diff --git a/installation/mods_MarcMentat/2017/Mentat_bin/kill9 b/installation/mods_MarcMentat/2017/Mentat_bin/kill9 deleted file mode 100644 index 6d1ff84bf..000000000 --- a/installation/mods_MarcMentat/2017/Mentat_bin/kill9 +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/sh - -if [ "$1" = "" ]; then - echo "usage: $0 job_name" - exit 1 -fi - -echo STOP > $1.cnt diff --git a/installation/mods_MarcMentat/2017/Mentat_bin/submit7 b/installation/mods_MarcMentat/2017/Mentat_bin/submit7 deleted file mode 100644 index d0e3be475..000000000 --- a/installation/mods_MarcMentat/2017/Mentat_bin/submit7 +++ /dev/null @@ -1,187 +0,0 @@ -#!/bin/sh -# -# The exit status of this script is read by Mentat. -# Normal exit status is 0. -# - -DIR=%INSTALLDIR%/marc%VERSION% -if test $MARCDIR1 -then - DIR=$MARCDIR1 -fi - -if test -z "$DIR"; then - REALCOM="`ls -l $0 |awk '{ print $NF; }'`" - DIRSCRIPT=`dirname $REALCOM` - case $DIRSCRIPT in - \/*) - ;; - *) - DIRSCRIPT=`pwd`/$DIRSCRIPT - ;; - esac - . $DIRSCRIPT/getarch - - DIR="$MENTAT_MARCDIR" -fi - -SRCEXT=.f -SRCEXTC=.F -RSTEXT=.t08 -PSTEXT=.t19 -PSTEXTB=.t16 -VWFCEXT=.vfs - -slv=$1 -version=$2 -ndom_fea_solver=$3 -ndom_preprocessor=$4 -hostfile=$5 -compat=$6 -job=$7 -srcfile=$8 -srcmeth=$9 -shift 9 # cannot use $10, $11, ... -restart=$1 -postfile=$2 -viewfactorsfile=$3 -autorst=$4 -copy_datfile="-ci $5" -copy_postfile="-cr $6" -scr_dir=$7 -dcoup=$8 -assem_recov_nthread=$9 -shift 9 # cannot use $10, $11, ... -nthread=$1 -nsolver=$2 -mode=$3 -gpu=$4 - -if [ "$slv" != "" -a "$slv" != "marc" ]; then - slv="-iam sfm" -else - slv="" -fi - -if [ "$ndom_fea_solver" != "" -a "$ndom_fea_solver" != "1" ]; then - nprocds="-nprocds $ndom_fea_solver" -else - nprocd="" - if [ "$ndom_preprocessor" != "" -a "$ndom_preprocessor" != "1" ]; then - nprocd="-nprocd $ndom_preprocessor" - else - nprocd="" - fi -fi - -if [ "$srcfile" != "" -a "$srcfile" != "-" ]; then - srcfile=`echo $srcfile | sed "s/$SRCEXT$//" | sed "s/$SRCEXTC$//"` - case "$srcmeth" in - -) - srcfile="-u $srcfile" - ;; - compsave) - srcfile="-u $srcfile -save y" - ;; - runsaved) - srcfile=${srcfile%.*}".marc" - srcfile="-prog $srcfile" - ;; - esac -else - srcfile="" -fi - -if [ "$restart" != "" -a "$restart" != "-" ]; then - restart=`echo $restart | sed "s/$RSTEXT$//"` - restart="-r $restart" -else - restart="" -fi - -if [ "$postfile" != "" -a "$postfile" != "-" ]; then - postfile=`echo $postfile | sed "s/$PSTEXT$//"` - postfile=`echo $postfile | sed "s/$PSTEXTB$//"` - postfile="-pid $postfile" -else - postfile="" -fi - -if [ "$viewfactorsfile" != "" -a "$viewfactorsfile" != "-" ]; then - viewfactorsfile=`echo $viewfactorsfile | sed "s/$VWFCEXT$//"` - viewfactorsfile="-vf $viewfactorsfile" -else - viewfactorsfile="" -fi - -if [ "$hostfile" != "" -a "$hostfile" != "-" ]; then - hostfile="-ho $hostfile" -else - hostfile="" -fi - -if [ "$compat" != "" -a "$compat" != "-" ]; then - compat="-co $compat" -else - compat="" -fi - -if [ "$scr_dir" != "" -a "$scr_dir" != "-" ]; then - scr_dir="-sd $scr_dir" -else - scr_dir="" -fi - -if [ "$dcoup" != "" -a "$dcoup" != "0" ]; then - dcoup="-dcoup $dcoup" -else - dcoup="" -fi - -if [ "$assem_recov_nthread" != "" -a "$assem_recov_nthread" != "1" ]; then - assem_recov_nthread="-nthread_elem $assem_recov_nthread" -else - assem_recov_nthread="" -fi - -if [ "$nthread" != "" -a "$nthread" != "0" -a "$nthread" != "1" ]; then - nthread="-nthread $nthread" -else - nthread="" -fi - -if [ "$nsolver" != "" -a "$nsolver" != "0" ]; then - nsolver="-nsolver $nsolver" -else - nsolver="" -fi - -case "$mode" in - 4) mode="-mo i4" ;; - 8) mode="-mo i8" ;; - *) mode= ;; -esac - -if [ "$gpu" != "" -a "$gpu" != "-" ]; then - gpu="-gpu $gpu" -else - gpu="" -fi - -rm -f $job.cnt -rm -f $job.sts -rm -f $job.out -rm -f $job.log - -# To prevent a mismatch with the python version used by the solver -# do *not* prepend $MENTAT_INSTALL_DIR/python/bin to environment variable PATH -# unset environment variables PYTHONHOME and PYTHONPATH -unset PYTHONHOME -unset PYTHONPATH - -"${DIR}/tools/run_damask_h" $slv -j $job -v n -b y $nprocds $nprocd -autorst $autorst \ - $srcfile $restart $postfile $viewfactorsfile $hostfile \ - $compat $copy_datfile $copy_postfile $scr_dir $dcoup \ - $assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1 -sleep 1 -exit 0 diff --git a/installation/mods_MarcMentat/2017/Mentat_bin/submit8 b/installation/mods_MarcMentat/2017/Mentat_bin/submit8 deleted file mode 100644 index d466fc6ab..000000000 --- a/installation/mods_MarcMentat/2017/Mentat_bin/submit8 +++ /dev/null @@ -1,187 +0,0 @@ -#!/bin/sh -# -# The exit status of this script is read by Mentat. -# Normal exit status is 0. -# - -DIR=%INSTALLDIR%/marc%VERSION% -if test $MARCDIR1 -then - DIR=$MARCDIR1 -fi - -if test -z "$DIR"; then - REALCOM="`ls -l $0 |awk '{ print $NF; }'`" - DIRSCRIPT=`dirname $REALCOM` - case $DIRSCRIPT in - \/*) - ;; - *) - DIRSCRIPT=`pwd`/$DIRSCRIPT - ;; - esac - . $DIRSCRIPT/getarch - - DIR="$MENTAT_MARCDIR" -fi - -SRCEXT=.f -SRCEXTC=.F -RSTEXT=.t08 -PSTEXT=.t19 -PSTEXTB=.t16 -VWFCEXT=.vfs - -slv=$1 -version=$2 -ndom_fea_solver=$3 -ndom_preprocessor=$4 -hostfile=$5 -compat=$6 -job=$7 -srcfile=$8 -srcmeth=$9 -shift 9 # cannot use $10, $11, ... -restart=$1 -postfile=$2 -viewfactorsfile=$3 -autorst=$4 -copy_datfile="-ci $5" -copy_postfile="-cr $6" -scr_dir=$7 -dcoup=$8 -assem_recov_nthread=$9 -shift 9 # cannot use $10, $11, ... -nthread=$1 -nsolver=$2 -mode=$3 -gpu=$4 - -if [ "$slv" != "" -a "$slv" != "marc" ]; then - slv="-iam sfm" -else - slv="" -fi - -if [ "$ndom_fea_solver" != "" -a "$ndom_fea_solver" != "1" ]; then - nprocds="-nprocds $ndom_fea_solver" -else - nprocd="" - if [ "$ndom_preprocessor" != "" -a "$ndom_preprocessor" != "1" ]; then - nprocd="-nprocd $ndom_preprocessor" - else - nprocd="" - fi -fi - -if [ "$srcfile" != "" -a "$srcfile" != "-" ]; then - srcfile=`echo $srcfile | sed "s/$SRCEXT$//" | sed "s/$SRCEXTC$//"` - case "$srcmeth" in - -) - srcfile="-u $srcfile" - ;; - compsave) - srcfile="-u $srcfile -save y" - ;; - runsaved) - srcfile=${srcfile%.*}".marc" - srcfile="-prog $srcfile" - ;; - esac -else - srcfile="" -fi - -if [ "$restart" != "" -a "$restart" != "-" ]; then - restart=`echo $restart | sed "s/$RSTEXT$//"` - restart="-r $restart" -else - restart="" -fi - -if [ "$postfile" != "" -a "$postfile" != "-" ]; then - postfile=`echo $postfile | sed "s/$PSTEXT$//"` - postfile=`echo $postfile | sed "s/$PSTEXTB$//"` - postfile="-pid $postfile" -else - postfile="" -fi - -if [ "$viewfactorsfile" != "" -a "$viewfactorsfile" != "-" ]; then - viewfactorsfile=`echo $viewfactorsfile | sed "s/$VWFCEXT$//"` - viewfactorsfile="-vf $viewfactorsfile" -else - viewfactorsfile="" -fi - -if [ "$hostfile" != "" -a "$hostfile" != "-" ]; then - hostfile="-ho $hostfile" -else - hostfile="" -fi - -if [ "$compat" != "" -a "$compat" != "-" ]; then - compat="-co $compat" -else - compat="" -fi - -if [ "$scr_dir" != "" -a "$scr_dir" != "-" ]; then - scr_dir="-sd $scr_dir" -else - scr_dir="" -fi - -if [ "$dcoup" != "" -a "$dcoup" != "0" ]; then - dcoup="-dcoup $dcoup" -else - dcoup="" -fi - -if [ "$assem_recov_nthread" != "" -a "$assem_recov_nthread" != "1" ]; then - assem_recov_nthread="-nthread_elem $assem_recov_nthread" -else - assem_recov_nthread="" -fi - -if [ "$nthread" != "" -a "$nthread" != "0" -a "$nthread" != "1" ]; then - nthread="-nthread $nthread" -else - nthread="" -fi - -if [ "$nsolver" != "" -a "$nsolver" != "0" ]; then - nsolver="-nsolver $nsolver" -else - nsolver="" -fi - -case "$mode" in - 4) mode="-mo i4" ;; - 8) mode="-mo i8" ;; - *) mode= ;; -esac - -if [ "$gpu" != "" -a "$gpu" != "-" ]; then - gpu="-gpu $gpu" -else - gpu="" -fi - -rm -f $job.cnt -rm -f $job.sts -rm -f $job.out -rm -f $job.log - -# To prevent a mismatch with the python version used by the solver -# do *not* prepend $MENTAT_INSTALL_DIR/python/bin to environment variable PATH -# unset environment variables PYTHONHOME and PYTHONPATH -unset PYTHONHOME -unset PYTHONPATH - -"${DIR}/tools/run_damask" $slv -j $job -v n -b y $nprocds $nprocd -autorst $autorst \ - $srcfile $restart $postfile $viewfactorsfile $hostfile \ - $compat $copy_datfile $copy_postfile $scr_dir $dcoup \ - $assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1 -sleep 1 -exit 0 diff --git a/installation/mods_MarcMentat/2017/Mentat_bin/submit9 b/installation/mods_MarcMentat/2017/Mentat_bin/submit9 deleted file mode 100644 index 207a61803..000000000 --- a/installation/mods_MarcMentat/2017/Mentat_bin/submit9 +++ /dev/null @@ -1,187 +0,0 @@ -#!/bin/sh -# -# The exit status of this script is read by Mentat. -# Normal exit status is 0. -# - -DIR=%INSTALLDIR%/marc%VERSION% -if test $MARCDIR1 -then - DIR=$MARCDIR1 -fi - -if test -z "$DIR"; then - REALCOM="`ls -l $0 |awk '{ print $NF; }'`" - DIRSCRIPT=`dirname $REALCOM` - case $DIRSCRIPT in - \/*) - ;; - *) - DIRSCRIPT=`pwd`/$DIRSCRIPT - ;; - esac - . $DIRSCRIPT/getarch - - DIR="$MENTAT_MARCDIR" -fi - -SRCEXT=.f -SRCEXTC=.F -RSTEXT=.t08 -PSTEXT=.t19 -PSTEXTB=.t16 -VWFCEXT=.vfs - -slv=$1 -version=$2 -ndom_fea_solver=$3 -ndom_preprocessor=$4 -hostfile=$5 -compat=$6 -job=$7 -srcfile=$8 -srcmeth=$9 -shift 9 # cannot use $10, $11, ... -restart=$1 -postfile=$2 -viewfactorsfile=$3 -autorst=$4 -copy_datfile="-ci $5" -copy_postfile="-cr $6" -scr_dir=$7 -dcoup=$8 -assem_recov_nthread=$9 -shift 9 # cannot use $10, $11, ... -nthread=$1 -nsolver=$2 -mode=$3 -gpu=$4 - -if [ "$slv" != "" -a "$slv" != "marc" ]; then - slv="-iam sfm" -else - slv="" -fi - -if [ "$ndom_fea_solver" != "" -a "$ndom_fea_solver" != "1" ]; then - nprocds="-nprocds $ndom_fea_solver" -else - nprocd="" - if [ "$ndom_preprocessor" != "" -a "$ndom_preprocessor" != "1" ]; then - nprocd="-nprocd $ndom_preprocessor" - else - nprocd="" - fi -fi - -if [ "$srcfile" != "" -a "$srcfile" != "-" ]; then - srcfile=`echo $srcfile | sed "s/$SRCEXT$//" | sed "s/$SRCEXTC$//"` - case "$srcmeth" in - -) - srcfile="-u $srcfile" - ;; - compsave) - srcfile="-u $srcfile -save y" - ;; - runsaved) - srcfile=${srcfile%.*}".marc" - srcfile="-prog $srcfile" - ;; - esac -else - srcfile="" -fi - -if [ "$restart" != "" -a "$restart" != "-" ]; then - restart=`echo $restart | sed "s/$RSTEXT$//"` - restart="-r $restart" -else - restart="" -fi - -if [ "$postfile" != "" -a "$postfile" != "-" ]; then - postfile=`echo $postfile | sed "s/$PSTEXT$//"` - postfile=`echo $postfile | sed "s/$PSTEXTB$//"` - postfile="-pid $postfile" -else - postfile="" -fi - -if [ "$viewfactorsfile" != "" -a "$viewfactorsfile" != "-" ]; then - viewfactorsfile=`echo $viewfactorsfile | sed "s/$VWFCEXT$//"` - viewfactorsfile="-vf $viewfactorsfile" -else - viewfactorsfile="" -fi - -if [ "$hostfile" != "" -a "$hostfile" != "-" ]; then - hostfile="-ho $hostfile" -else - hostfile="" -fi - -if [ "$compat" != "" -a "$compat" != "-" ]; then - compat="-co $compat" -else - compat="" -fi - -if [ "$scr_dir" != "" -a "$scr_dir" != "-" ]; then - scr_dir="-sd $scr_dir" -else - scr_dir="" -fi - -if [ "$dcoup" != "" -a "$dcoup" != "0" ]; then - dcoup="-dcoup $dcoup" -else - dcoup="" -fi - -if [ "$assem_recov_nthread" != "" -a "$assem_recov_nthread" != "1" ]; then - assem_recov_nthread="-nthread_elem $assem_recov_nthread" -else - assem_recov_nthread="" -fi - -if [ "$nthread" != "" -a "$nthread" != "0" -a "$nthread" != "1" ]; then - nthread="-nthread $nthread" -else - nthread="" -fi - -if [ "$nsolver" != "" -a "$nsolver" != "0" ]; then - nsolver="-nsolver $nsolver" -else - nsolver="" -fi - -case "$mode" in - 4) mode="-mo i4" ;; - 8) mode="-mo i8" ;; - *) mode= ;; -esac - -if [ "$gpu" != "" -a "$gpu" != "-" ]; then - gpu="-gpu $gpu" -else - gpu="" -fi - -rm -f $job.cnt -rm -f $job.sts -rm -f $job.out -rm -f $job.log - -# To prevent a mismatch with the python version used by the solver -# do *not* prepend $MENTAT_INSTALL_DIR/python/bin to environment variable PATH -# unset environment variables PYTHONHOME and PYTHONPATH -unset PYTHONHOME -unset PYTHONPATH - -"${DIR}/tools/run_damask_l" $slv -j $job -v n -b y $nprocds $nprocd -autorst $autorst \ - $srcfile $restart $postfile $viewfactorsfile $hostfile \ - $compat $copy_datfile $copy_postfile $scr_dir $dcoup \ - $assem_recov_nthread $nthread $nsolver $mode $gpu > /dev/null 2>&1 -sleep 1 -exit 0 diff --git a/installation/mods_MarcMentat/apply_DAMASK_modifications.sh b/installation/mods_MarcMentat/apply_DAMASK_modifications.sh index 74abaf29c..d6cd6b171 100755 --- a/installation/mods_MarcMentat/apply_DAMASK_modifications.sh +++ b/installation/mods_MarcMentat/apply_DAMASK_modifications.sh @@ -58,15 +58,9 @@ echo "Editor: $EDITOR" echo '' echo 'adapting Marc tools...' theDIR=$INSTALLDIR/marc$VERSION/tools -for filename in 'comp_damask' \ - 'comp_damask_l' \ - 'comp_damask_h' \ - 'comp_damask_mp' \ +for filename in 'comp_damask_mp' \ 'comp_damask_lmp' \ 'comp_damask_hmp' \ - 'run_damask' \ - 'run_damask_l' \ - 'run_damask_h' \ 'run_damask_mp' \ 'run_damask_lmp' \ 'run_damask_hmp' \ @@ -85,15 +79,9 @@ for filename in 'edit_window' \ 'submit4' \ 'submit5' \ 'submit6' \ - 'submit7' \ - 'submit8' \ - 'submit9' \ 'kill4' \ 'kill5' \ - 'kill6' \ - 'kill7' \ - 'kill8' \ - 'kill9'; do + 'kill6'; do cp $SCRIPTLOCATION/$VERSION/Mentat_bin/$filename $theDIR echo $theDIR/$filename | xargs perl -pi -e "s:%INSTALLDIR%:${INSTALLDIR}:g" echo $theDIR/$filename | xargs perl -pi -e "s:%VERSION%:${VERSION}:g" @@ -122,8 +110,8 @@ echo '' echo 'setting file access rights...' for filename in marc$VERSION/tools/run_damask* \ marc$VERSION/tools/comp_damask* \ - mentat$VERSION/bin/submit{4..9} \ - mentat$VERSION/bin/kill{4..9} ; do + mentat$VERSION/bin/submit{4..6} \ + mentat$VERSION/bin/kill{4..6} ; do chmod 755 $INSTALLDIR/${filename} done @@ -142,10 +130,7 @@ if [ -d "$BIN_DIR" ]; then echo 'creating symlinks ...' echo'' theDIR=$INSTALLDIR/marc$VERSION/tools - for filename in 'run_damask' \ - 'run_damask_l' \ - 'run_damask_h' \ - 'run_damask_mp' \ + for filename in 'run_damask_mp' \ 'run_damask_lmp' \ 'run_damask_hmp'; do echo ${filename:4}$VERSION diff --git a/installation/mods_MarcMentat/installation.txt b/installation/mods_MarcMentat/installation.txt index ae1bca772..c2b56b3e6 100644 --- a/installation/mods_MarcMentat/installation.txt +++ b/installation/mods_MarcMentat/installation.txt @@ -21,16 +21,10 @@ The structure of this directory should be (VERSION = 20XX or 20XX.Y) ./installation.txt this text ./apply_MPIE_modifications script file to apply modifications to the installation ./VERSION/Marc_tools/comp_user.original original file from installation -./VERSION/Marc_tools/comp_damask modified version using -O1 optimization -./VERSION/Marc_tools/comp_damask_l modified version using -O0 optimization -./VERSION/Marc_tools/comp_damask_h modified version using -O2 optimization ./VERSION/Marc_tools/comp_damask_mp modified version using -O1 optimization and OpenMP ./VERSION/Marc_tools/comp_damask_lmp modified version using -O0 optimization and OpenMP ./VERSION/Marc_tools/comp_damask_hmp modified version using -O2 optimization and OpenMP ./VERSION/Marc_tools/run_marc.original original file from installation -./VERSION/Marc_tools/run_damask modified version using -O1 optimization -./VERSION/Marc_tools/run_damask_l modified version using -O0 optimization -./VERSION/Marc_tools/run_damask_h modified version using -O2 optimization ./VERSION/Marc_tools/run_damask_mp modified version using -O1 optimization and OpenMP ./VERSION/Marc_tools/run_damask_lmp modified version using -O0 optimization and OpenMP ./VERSION/Marc_tools/run_damask_hmp modified version using -O2 optimization and OpenMP @@ -42,14 +36,8 @@ The structure of this directory should be (VERSION = 20XX or 20XX.Y) ./VERSION/Mentat_bin/submit4 modified version of original calling run_h_marc ./VERSION/Mentat_bin/submit5 modified version of original calling run_marc ./VERSION/Mentat_bin/submit6 modified version of original calling run_l_marc -./VERSION/Mentat_bin/submit7 modified version of original calling run_hmp_marc -./VERSION/Mentat_bin/submit8 modified version of original calling run_mp_marc -./VERSION/Mentat_bin/submit9 modified version of original calling run_lmp_marc ./VERSION/Mentat_bin/kill4 kill file for submit4, identical to original kill1 ./VERSION/Mentat_bin/kill5 kill file for submit5, identical to original kill1 ./VERSION/Mentat_bin/kill6 kill file for submit6, identical to original kill1 -./VERSION/Mentat_bin/kill7 kill file for submit7, identical to original kill1 -./VERSION/Mentat_bin/kill8 kill file for submit8, identical to original kill1 -./VERSION/Mentat_bin/kill9 kill file for submit9, identical to original kill1 ./VERSION/Mentat_menus/job_run.ms.original original file from installation ./VERSION/Mentat_menus/job_run.ms modified version adding DAMASK menu to run menu From 732022d4f0c9c87cb09ca71a586945df6297f129 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 31 Aug 2018 08:58:13 +0200 Subject: [PATCH 47/67] functions from IO does not add any value here only prevents the automated selection of a new unit --- src/DAMASK_spectral.f90 | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index 72db08564..8c908465f 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -27,9 +27,7 @@ program DAMASK_spectral getSolverJobName, & interface_restartInc use IO, only: & - IO_read, & IO_isBlank, & - IO_open_file, & IO_stringPos, & IO_stringValue, & IO_floatValue, & @@ -38,8 +36,7 @@ program DAMASK_spectral IO_lc, & IO_intOut, & IO_warning, & - IO_timeStamp, & - IO_EOF + IO_timeStamp use debug, only: & debug_level, & debug_spectral, & @@ -90,7 +87,7 @@ program DAMASK_spectral ! variables related to information from load case and geom file real(pReal), dimension(9) :: temp_valueVector = 0.0_pReal !< temporarily from loadcase file when reading in tensors (initialize to 0.0) logical, dimension(9) :: temp_maskVector = .false. !< temporarily from loadcase file when reading in tensors - integer(pInt), parameter :: FILEUNIT = 234_pInt !< file unit, DAMASK IO does not support newunit feature + integer(pInt) :: fileUnit, myStat integer(pInt), allocatable, dimension(:) :: chunkPos integer(pInt) :: & @@ -191,11 +188,11 @@ program DAMASK_spectral !-------------------------------------------------------------------------------------------------- ! reading basic information from load case file and allocate data structure containing load cases - call IO_open_file(FILEUNIT,trim(loadCaseFile)) - rewind(FILEUNIT) + open(newunit=fileunit,iostat=myStat,file=trim(loadCaseFile),action='read') + if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=trim(loadCaseFile)) do - line = IO_read(FILEUNIT) - if (trim(line) == IO_EOF) exit + read(fileUnit, '(A)', iostat=myStat) line + if ( myStat /= 0_pInt) exit if (IO_isBlank(line)) cycle ! skip empty lines chunkPos = IO_stringPos(line) do i = 1_pInt, chunkPos(1) ! reading compulsory parameters for loadcase @@ -233,8 +230,8 @@ program DAMASK_spectral ! reading the load case and assign values to the allocated data structure rewind(FILEUNIT) do - line = IO_read(FILEUNIT) - if (trim(line) == IO_EOF) exit + read(fileUnit, '(A)', iostat=myStat) line + if ( myStat /= 0_pInt) exit if (IO_isBlank(line)) cycle ! skip empty lines currentLoadCase = currentLoadCase + 1_pInt chunkPos = IO_stringPos(line) From c0ac05aa889d255849e468c99a638b80ad119046 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 31 Aug 2018 09:11:09 +0200 Subject: [PATCH 48/67] no need to use two loops --- src/DAMASK_spectral.f90 | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index 8c908465f..73f047860 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -133,6 +133,7 @@ program DAMASK_spectral incInfo, & !< string parsed to solution with information about current load case workingDir type(tLoadCase), allocatable, dimension(:) :: loadCases !< array of all load cases + type(tLoadCase) :: newLoadCase type(tSolutionState), allocatable, dimension(:) :: solres integer(MPI_OFFSET_KIND) :: fileOffset integer(MPI_OFFSET_KIND), dimension(:), allocatable :: outputSize @@ -188,6 +189,7 @@ program DAMASK_spectral !-------------------------------------------------------------------------------------------------- ! reading basic information from load case file and allocate data structure containing load cases + allocate (loadCases(0)) ! array of load cases open(newunit=fileunit,iostat=myStat,file=trim(loadCaseFile),action='read') if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=trim(loadCaseFile)) do @@ -205,29 +207,27 @@ program DAMASK_spectral N_n = N_n + 1_pInt end select enddo ! count all identifiers to allocate memory and do sanity check - enddo - - if ((N_def /= N_n) .or. (N_n /= N_t) .or. N_n < 1_pInt) & ! sanity check - call IO_error(error_ID=837_pInt,ext_msg = trim(loadCaseFile)) ! error message for incomplete loadcase - allocate (loadCases(N_n)) ! array of load cases - loadCases%stress%myType='stress' - - do i = 1, size(loadCases) - allocate(loadCases(i)%ID(nActiveFields)) + if ((N_def /= N_n) .or. (N_n /= N_t) .or. N_n < 1_pInt) & ! sanity check + call IO_error(error_ID=837_pInt,ext_msg = trim(loadCaseFile)) ! error message for incomplete loadcase + loadCases = [loadCases,newLoadCase] + currentLoadCase = currentLoadCase + 1_pInt + loadCases(currentLoadCase)%stress%myType='stress' + allocate(loadCases(currentLoadCase)%ID(nActiveFields)) field = 1 - loadCases(i)%ID(field) = FIELD_MECH_ID ! mechanical active by default + loadCases(currentLoadCase)%ID(field) = FIELD_MECH_ID ! mechanical active by default thermalActive: if (any(thermal_type == THERMAL_conduction_ID)) then field = field + 1 - loadCases(i)%ID(field) = FIELD_THERMAL_ID + loadCases(currentLoadCase)%ID(field) = FIELD_THERMAL_ID endif thermalActive damageActive: if (any(damage_type == DAMAGE_nonlocal_ID)) then field = field + 1 - loadCases(i)%ID(field) = FIELD_DAMAGE_ID + loadCases(currentLoadCase)%ID(field) = FIELD_DAMAGE_ID endif damageActive enddo !-------------------------------------------------------------------------------------------------- ! reading the load case and assign values to the allocated data structure + currentLoadCase = 0_pInt rewind(FILEUNIT) do read(fileUnit, '(A)', iostat=myStat) line @@ -380,7 +380,7 @@ program DAMASK_spectral case(FIELD_MECH_ID) call mech_init - case(FIELD_THERMAL_ID) + case(FIELD_THERMAL_ID) call spectral_thermal_init case(FIELD_DAMAGE_ID) From 017563e0615e073c11e19a29089685d915952170 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 31 Aug 2018 09:14:16 +0200 Subject: [PATCH 49/67] one more loop not needed --- src/DAMASK_spectral.f90 | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index 73f047860..92012dcfa 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -223,18 +223,7 @@ program DAMASK_spectral field = field + 1 loadCases(currentLoadCase)%ID(field) = FIELD_DAMAGE_ID endif damageActive - enddo -!-------------------------------------------------------------------------------------------------- -! reading the load case and assign values to the allocated data structure - currentLoadCase = 0_pInt - rewind(FILEUNIT) - do - read(fileUnit, '(A)', iostat=myStat) line - if ( myStat /= 0_pInt) exit - if (IO_isBlank(line)) cycle ! skip empty lines - currentLoadCase = currentLoadCase + 1_pInt - chunkPos = IO_stringPos(line) do i = 1_pInt, chunkPos(1) select case (IO_lc(IO_stringValue(line,chunkPos,i))) case('fdot','dotf','l','velocitygrad','velgrad','velocitygradient','f') ! assign values for the deformation BC matrix @@ -303,8 +292,10 @@ program DAMASK_spectral enddo loadCases(currentLoadCase)%rotation = math_plain9to33(temp_valueVector) end select - enddo; enddo - close(FILEUNIT) + enddo + enddo + + close(fileUnit) !-------------------------------------------------------------------------------------------------- ! consistency checks and output of load case From 3cb279b083efe798bacffb0e648d7bedc3996b21 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 31 Aug 2018 09:39:33 +0200 Subject: [PATCH 50/67] one more loop not needed --- src/DAMASK_spectral.f90 | 158 +++++++++++++++++++--------------------- 1 file changed, 74 insertions(+), 84 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index 92012dcfa..fb67d575d 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -115,7 +115,7 @@ program DAMASK_spectral stagIterate integer(pInt) :: & i, j, k, l, field, & - errorID, & + errorID = 0_pInt, & cutBackLevel = 0_pInt, & !< cut back level \f$ t = \frac{t_{inc}}{2^l} \f$ stepFraction = 0_pInt !< fraction of current time interval integer(pInt) :: & @@ -166,6 +166,7 @@ program DAMASK_spectral if (any(thermal_type == THERMAL_conduction_ID )) nActiveFields = nActiveFields + 1 if (any(damage_type == DAMAGE_nonlocal_ID )) nActiveFields = nActiveFields + 1 allocate(solres(nActiveFields)) + allocate(newLoadCase%ID(nActiveFields)) !-------------------------------------------------------------------------------------------------- ! assign mechanics solver depending on selected type @@ -188,7 +189,7 @@ program DAMASK_spectral end select !-------------------------------------------------------------------------------------------------- -! reading basic information from load case file and allocate data structure containing load cases +! reading information from load case file and to sanity checks allocate (loadCases(0)) ! array of load cases open(newunit=fileunit,iostat=myStat,file=trim(loadCaseFile),action='read') if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=trim(loadCaseFile)) @@ -209,19 +210,17 @@ program DAMASK_spectral enddo ! count all identifiers to allocate memory and do sanity check if ((N_def /= N_n) .or. (N_n /= N_t) .or. N_n < 1_pInt) & ! sanity check call IO_error(error_ID=837_pInt,ext_msg = trim(loadCaseFile)) ! error message for incomplete loadcase - loadCases = [loadCases,newLoadCase] - currentLoadCase = currentLoadCase + 1_pInt - loadCases(currentLoadCase)%stress%myType='stress' - allocate(loadCases(currentLoadCase)%ID(nActiveFields)) + + newLoadCase%stress%myType='stress' field = 1 - loadCases(currentLoadCase)%ID(field) = FIELD_MECH_ID ! mechanical active by default + newLoadCase%ID(field) = FIELD_MECH_ID ! mechanical active by default thermalActive: if (any(thermal_type == THERMAL_conduction_ID)) then field = field + 1 - loadCases(currentLoadCase)%ID(field) = FIELD_THERMAL_ID + newLoadCase%ID(field) = FIELD_THERMAL_ID endif thermalActive damageActive: if (any(damage_type == DAMAGE_nonlocal_ID)) then field = field + 1 - loadCases(currentLoadCase)%ID(field) = FIELD_DAMAGE_ID + newLoadCase%ID(field) = FIELD_DAMAGE_ID endif damageActive do i = 1_pInt, chunkPos(1) @@ -230,46 +229,43 @@ program DAMASK_spectral temp_valueVector = 0.0_pReal if (IO_lc(IO_stringValue(line,chunkPos,i)) == 'fdot'.or. & ! in case of Fdot, set type to fdot IO_lc(IO_stringValue(line,chunkPos,i)) == 'dotf') then - loadCases(currentLoadCase)%deformation%myType = 'fdot' + newLoadCase%deformation%myType = 'fdot' else if (IO_lc(IO_stringValue(line,chunkPos,i)) == 'f') then - loadCases(currentLoadCase)%deformation%myType = 'f' + newLoadCase%deformation%myType = 'f' else - loadCases(currentLoadCase)%deformation%myType = 'l' + newLoadCase%deformation%myType = 'l' endif do j = 1_pInt, 9_pInt temp_maskVector(j) = IO_stringValue(line,chunkPos,i+j) /= '*' ! true if not a * if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j) ! read value where applicable enddo - loadCases(currentLoadCase)%deformation%maskLogical = & ! logical mask in 3x3 notation - transpose(reshape(temp_maskVector,[ 3,3])) - loadCases(currentLoadCase)%deformation%maskFloat = & ! float (1.0/0.0) mask in 3x3 notation - merge(ones,zeros,loadCases(currentLoadCase)%deformation%maskLogical) - loadCases(currentLoadCase)%deformation%values = math_plain9to33(temp_valueVector) ! values in 3x3 notation + newLoadCase%deformation%maskLogical = transpose(reshape(temp_maskVector,[ 3,3])) ! logical mask in 3x3 notation + newLoadCase%deformation%maskFloat = merge(ones,zeros,newLoadCase%deformation%maskLogical)! float (1.0/0.0) mask in 3x3 notation + newLoadCase%deformation%values = math_plain9to33(temp_valueVector) ! values in 3x3 notation case('p','pk1','piolakirchhoff','stress', 's') temp_valueVector = 0.0_pReal do j = 1_pInt, 9_pInt temp_maskVector(j) = IO_stringValue(line,chunkPos,i+j) /= '*' ! true if not an asterisk if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j) ! read value where applicable enddo - loadCases(currentLoadCase)%stress%maskLogical = transpose(reshape(temp_maskVector,[ 3,3])) - loadCases(currentLoadCase)%stress%maskFloat = merge(ones,zeros,& - loadCases(currentLoadCase)%stress%maskLogical) - loadCases(currentLoadCase)%stress%values = math_plain9to33(temp_valueVector) + newLoadCase%stress%maskLogical = transpose(reshape(temp_maskVector,[ 3,3])) + newLoadCase%stress%maskFloat = merge(ones,zeros,newLoadCase%stress%maskLogical) + newLoadCase%stress%values = math_plain9to33(temp_valueVector) case('t','time','delta') ! increment time - loadCases(currentLoadCase)%time = IO_floatValue(line,chunkPos,i+1_pInt) + newLoadCase%time = IO_floatValue(line,chunkPos,i+1_pInt) case('n','incs','increments','steps') ! number of increments - loadCases(currentLoadCase)%incs = IO_intValue(line,chunkPos,i+1_pInt) + newLoadCase%incs = IO_intValue(line,chunkPos,i+1_pInt) case('logincs','logincrements','logsteps') ! number of increments (switch to log time scaling) - loadCases(currentLoadCase)%incs = IO_intValue(line,chunkPos,i+1_pInt) - loadCases(currentLoadCase)%logscale = 1_pInt + newLoadCase%incs = IO_intValue(line,chunkPos,i+1_pInt) + newLoadCase%logscale = 1_pInt case('freq','frequency','outputfreq') ! frequency of result writings - loadCases(currentLoadCase)%outputfrequency = IO_intValue(line,chunkPos,i+1_pInt) + newLoadCase%outputfrequency = IO_intValue(line,chunkPos,i+1_pInt) case('r','restart','restartwrite') ! frequency of writing restart information - loadCases(currentLoadCase)%restartfrequency = & + newLoadCase%restartfrequency = & max(0_pInt,IO_intValue(line,chunkPos,i+1_pInt)) case('guessreset','dropguessing') - loadCases(currentLoadCase)%followFormerTrajectory = .false. ! do not continue to predict deformation along former trajectory - case('euler') ! rotation of currentLoadCase given in euler angles + newLoadCase%followFormerTrajectory = .false. ! do not continue to predict deformation along former trajectory + case('euler') ! rotation of load case given in euler angles temp_valueVector = 0.0_pReal l = 1_pInt ! assuming values given in degrees k = 1_pInt ! assuming keyword indicating degree/radians present @@ -284,87 +280,79 @@ program DAMASK_spectral temp_valueVector(j) = IO_floatValue(line,chunkPos,i+k+j) enddo if (l == 1_pInt) temp_valueVector(1:3) = temp_valueVector(1:3) * inRad ! convert to rad - loadCases(currentLoadCase)%rotation = math_EulerToR(temp_valueVector(1:3)) ! convert rad Eulers to rotation matrix - case('rotation','rot') ! assign values for the rotation of currentLoadCase matrix + newLoadCase%rotation = math_EulerToR(temp_valueVector(1:3)) ! convert rad Eulers to rotation matrix + case('rotation','rot') ! assign values for the rotation matrix temp_valueVector = 0.0_pReal do j = 1_pInt, 9_pInt temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j) enddo - loadCases(currentLoadCase)%rotation = math_plain9to33(temp_valueVector) + newLoadCase%rotation = math_plain9to33(temp_valueVector) end select enddo - enddo + currentLoadCase = currentLoadCase + 1_pInt + if(currentLoadCase == 1_pInt) newLoadCase%followFormerTrajectory = .false. ! cannot guess along trajectory for first inc of first load case - close(fileUnit) - -!-------------------------------------------------------------------------------------------------- -! consistency checks and output of load case - loadCases(1)%followFormerTrajectory = .false. ! cannot guess along trajectory for first inc of first currentLoadCase - errorID = 0_pInt - if (worldrank == 0) then - checkLoadcases: do currentLoadCase = 1_pInt, size(loadCases) + reportAndCheck: if (worldrank == 0) then write (loadcase_string, '(i6)' ) currentLoadCase write(6,'(1x,a,i6)') 'load case: ', currentLoadCase - if (.not. loadCases(currentLoadCase)%followFormerTrajectory) & - write(6,'(2x,a)') 'drop guessing along trajectory' - if (loadCases(currentLoadCase)%deformation%myType == 'l') then + if (.not. newLoadCase%followFormerTrajectory) write(6,'(2x,a)') 'drop guessing along trajectory' + if (newLoadCase%deformation%myType == 'l') then do j = 1_pInt, 3_pInt - if (any(loadCases(currentLoadCase)%deformation%maskLogical(j,1:3) .eqv. .true.) .and. & - any(loadCases(currentLoadCase)%deformation%maskLogical(j,1:3) .eqv. .false.)) & - errorID = 832_pInt ! each row should be either fully or not at all defined + if (any(newLoadCase%deformation%maskLogical(j,1:3) .eqv. .true.) .and. & + any(newLoadCase%deformation%maskLogical(j,1:3) .eqv. .false.)) errorID = 832_pInt ! each row should be either fully or not at all defined enddo write(6,'(2x,a)') 'velocity gradient:' - else if (loadCases(currentLoadCase)%deformation%myType == 'f') then + else if (newLoadCase%deformation%myType == 'f') then write(6,'(2x,a)') 'deformation gradient at end of load case:' else write(6,'(2x,a)') 'deformation gradient rate:' endif do i = 1_pInt, 3_pInt; do j = 1_pInt, 3_pInt - if(loadCases(currentLoadCase)%deformation%maskLogical(i,j)) then - write(6,'(2x,f12.7)',advance='no') loadCases(currentLoadCase)%deformation%values(i,j) + if(newLoadCase%deformation%maskLogical(i,j)) then + write(6,'(2x,f12.7)',advance='no') newLoadCase%deformation%values(i,j) else write(6,'(2x,12a)',advance='no') ' * ' endif enddo; write(6,'(/)',advance='no') enddo - if (any(loadCases(currentLoadCase)%stress%maskLogical .eqv. & - loadCases(currentLoadCase)%deformation%maskLogical)) errorID = 831_pInt ! exclusive or masking only - if (any(loadCases(currentLoadCase)%stress%maskLogical .and. & - transpose(loadCases(currentLoadCase)%stress%maskLogical) .and. & + if (any(newLoadCase%stress%maskLogical .eqv. & + newLoadCase%deformation%maskLogical)) errorID = 831_pInt ! exclusive or masking only + if (any(newLoadCase%stress%maskLogical .and. & + transpose(newLoadCase%stress%maskLogical) .and. & reshape([ .false.,.true.,.true.,.true.,.false.,.true.,.true.,.true.,.false.],[ 3,3]))) & errorID = 838_pInt ! no rotation is allowed by stress BC write(6,'(2x,a)') 'stress / GPa:' do i = 1_pInt, 3_pInt; do j = 1_pInt, 3_pInt - if(loadCases(currentLoadCase)%stress%maskLogical(i,j)) then - write(6,'(2x,f12.7)',advance='no') loadCases(currentLoadCase)%stress%values(i,j)*1e-9_pReal + if(newLoadCase%stress%maskLogical(i,j)) then + write(6,'(2x,f12.7)',advance='no') newLoadCase%stress%values(i,j)*1e-9_pReal else write(6,'(2x,12a)',advance='no') ' * ' endif enddo; write(6,'(/)',advance='no') enddo - if (any(abs(math_mul33x33(loadCases(currentLoadCase)%rotation, & - math_transpose33(loadCases(currentLoadCase)%rotation))-math_I3) > & + if (any(abs(math_mul33x33(newLoadCase%rotation, & + transpose(newLoadCase%rotation))-math_I3) > & reshape(spread(tol_math_check,1,9),[ 3,3]))& - .or. abs(math_det33(loadCases(currentLoadCase)%rotation)) > & + .or. abs(math_det33(newLoadCase%rotation)) > & 1.0_pReal + tol_math_check) errorID = 846_pInt ! given rotation matrix contains strain - if (any(dNeq(loadCases(currentLoadCase)%rotation, math_I3))) & + if (any(dNeq(newLoadCase%rotation, math_I3))) & write(6,'(2x,a,/,3(3(3x,f12.7,1x)/))',advance='no') 'rotation of loadframe:',& - math_transpose33(loadCases(currentLoadCase)%rotation) - if (loadCases(currentLoadCase)%time < 0.0_pReal) errorID = 834_pInt ! negative time increment - write(6,'(2x,a,f12.6)') 'time: ', loadCases(currentLoadCase)%time - if (loadCases(currentLoadCase)%incs < 1_pInt) errorID = 835_pInt ! non-positive incs count - write(6,'(2x,a,i5)') 'increments: ', loadCases(currentLoadCase)%incs - if (loadCases(currentLoadCase)%outputfrequency < 1_pInt) errorID = 836_pInt ! non-positive result frequency - write(6,'(2x,a,i5)') 'output frequency: ', & - loadCases(currentLoadCase)%outputfrequency - write(6,'(2x,a,i5,/)') 'restart frequency: ', & - loadCases(currentLoadCase)%restartfrequency + transpose(newLoadCase%rotation) + if (newLoadCase%time < 0.0_pReal) errorID = 834_pInt ! negative time increment + write(6,'(2x,a,f12.6)') 'time: ', newLoadCase%time + if (newLoadCase%incs < 1_pInt) errorID = 835_pInt ! non-positive incs count + write(6,'(2x,a,i5)') 'increments: ', newLoadCase%incs + if (newLoadCase%outputfrequency < 1_pInt) errorID = 836_pInt ! non-positive result frequency + write(6,'(2x,a,i5)') 'output frequency: ', newLoadCase%outputfrequency + write(6,'(2x,a,i5,/)') 'restart frequency: ', newLoadCase%restartfrequency if (errorID > 0_pInt) call IO_error(error_ID = errorID, ext_msg = loadcase_string) ! exit with error message - enddo checkLoadcases - endif + endif reportAndCheck + loadCases = [loadCases,newLoadCase] ! load case is ok, append it + enddo + close(fileUnit) !-------------------------------------------------------------------------------------------------- -! doing initialization depending on selected solver +! doing initialization depending on active solvers call Utilities_init() do field = 1, nActiveFields select case (loadCases(1)%ID(field)) @@ -444,13 +432,13 @@ program DAMASK_spectral fileOffset = fileOffset + sum(outputSize) ! forward to current file position endif writeUndeformed !-------------------------------------------------------------------------------------------------- -! looping over loadcases +! looping over load cases loadCaseLooping: do currentLoadCase = 1_pInt, size(loadCases) - time0 = time ! currentLoadCase start time + time0 = time ! load case start time guess = loadCases(currentLoadCase)%followFormerTrajectory ! change of load case? homogeneous guess for the first inc !-------------------------------------------------------------------------------------------------- -! loop over incs defined in input file for current currentLoadCase +! loop over incs defined in input file for current load case incLooping: do inc = 1_pInt, loadCases(currentLoadCase)%incs totalIncsCounter = totalIncsCounter + 1_pInt @@ -460,13 +448,13 @@ program DAMASK_spectral if (loadCases(currentLoadCase)%logscale == 0_pInt) then ! linear scale timeinc = loadCases(currentLoadCase)%time/real(loadCases(currentLoadCase)%incs,pReal) else - if (currentLoadCase == 1_pInt) then ! 1st currentLoadCase of logarithmic scale - if (inc == 1_pInt) then ! 1st inc of 1st currentLoadCase of logarithmic scale + if (currentLoadCase == 1_pInt) then ! 1st load case of logarithmic scale + if (inc == 1_pInt) then ! 1st inc of 1st load case of logarithmic scale timeinc = loadCases(1)%time*(2.0_pReal**real( 1_pInt-loadCases(1)%incs ,pReal)) ! assume 1st inc is equal to 2nd - else ! not-1st inc of 1st currentLoadCase of logarithmic scale + else ! not-1st inc of 1st load case of logarithmic scale timeinc = loadCases(1)%time*(2.0_pReal**real(inc-1_pInt-loadCases(1)%incs ,pReal)) endif - else ! not-1st currentLoadCase of logarithmic scale + else ! not-1st load case of logarithmic scale timeinc = time0 * & ( (1.0_pReal + loadCases(currentLoadCase)%time/time0 )**(real( inc ,pReal)/& real(loadCases(currentLoadCase)%incs ,pReal))& @@ -633,8 +621,7 @@ program DAMASK_spectral convergedCounter, ' out of ', & notConvergedCounter + convergedCounter, ' (', & real(convergedCounter, pReal)/& - real(notConvergedCounter + convergedCounter,pReal)*100.0_pReal, & - ' %) increments converged!' + real(notConvergedCounter + convergedCounter,pReal)*100.0_pReal, ' %) increments converged!' flush(6) call MPI_file_close(resUnit,ierr) close(statUnit) @@ -655,10 +642,13 @@ end program DAMASK_spectral !-------------------------------------------------------------------------------------------------- subroutine quit(stop_id) #include - use MPI +#ifdef _OPENMP + use MPI, only: & + MPI_finalize +#endif use prec, only: & pInt - + implicit none integer(pInt), intent(in) :: stop_id integer, dimension(8) :: dateAndTime ! type default integer From f028e0529830d78e04eab8715016724a2232bc17 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 31 Aug 2018 10:14:33 +0200 Subject: [PATCH 51/67] guessing was not correctly set --- src/DAMASK_spectral.f90 | 57 +++++++++++++++++++++-------------------- 1 file changed, 29 insertions(+), 28 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index fb67d575d..b99fb1e1d 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -87,7 +87,6 @@ program DAMASK_spectral ! variables related to information from load case and geom file real(pReal), dimension(9) :: temp_valueVector = 0.0_pReal !< temporarily from loadcase file when reading in tensors (initialize to 0.0) logical, dimension(9) :: temp_maskVector = .false. !< temporarily from loadcase file when reading in tensors - integer(pInt) :: fileUnit, myStat integer(pInt), allocatable, dimension(:) :: chunkPos integer(pInt) :: & @@ -124,7 +123,8 @@ program DAMASK_spectral totalIncsCounter = 0_pInt, & !< total # of increments convergedCounter = 0_pInt, & !< # of converged increments notConvergedCounter = 0_pInt, & !< # of non-converged increments - resUnit = 0_pInt, & !< file unit for results writing + fileUnit = 0_pInt, & !< file unit for reading load case and writing results + myStat, & statUnit = 0_pInt, & !< file unit for statistics output lastRestartWritten = 0_pInt, & !< total increment # at which last restart information was written stagIter @@ -223,7 +223,7 @@ program DAMASK_spectral newLoadCase%ID(field) = FIELD_DAMAGE_ID endif damageActive - do i = 1_pInt, chunkPos(1) + readIn: do i = 1_pInt, chunkPos(1) select case (IO_lc(IO_stringValue(line,chunkPos,i))) case('fdot','dotf','l','velocitygrad','velgrad','velocitygradient','f') ! assign values for the deformation BC matrix temp_valueVector = 0.0_pReal @@ -288,9 +288,10 @@ program DAMASK_spectral enddo newLoadCase%rotation = math_plain9to33(temp_valueVector) end select - enddo + enddo readIn + currentLoadCase = currentLoadCase + 1_pInt - if(currentLoadCase == 1_pInt) newLoadCase%followFormerTrajectory = .false. ! cannot guess along trajectory for first inc of first load case + newLoadCase%followFormerTrajectory = merge(.true.,.false.,currentLoadCase > 1_pInt) ! by default, guess from previous load case reportAndCheck: if (worldrank == 0) then write (loadcase_string, '(i6)' ) currentLoadCase @@ -372,22 +373,22 @@ program DAMASK_spectral ! write header of output file if (worldrank == 0) then writeHeader: if (interface_restartInc < 1_pInt) then - open(newunit=resUnit,file=trim(getSolverJobName())//& + open(newunit=fileUnit,file=trim(getSolverJobName())//& '.spectralOut',form='UNFORMATTED',status='REPLACE') - write(resUnit) 'load:', trim(loadCaseFile) ! ... and write header - write(resUnit) 'workingdir:', trim(workingDir) - write(resUnit) 'geometry:', trim(geometryFile) - write(resUnit) 'grid:', grid - write(resUnit) 'size:', geomSize - write(resUnit) 'materialpoint_sizeResults:', materialpoint_sizeResults - write(resUnit) 'loadcases:', size(loadCases) - write(resUnit) 'frequencies:', loadCases%outputfrequency ! one entry per LoadCase - write(resUnit) 'times:', loadCases%time ! one entry per LoadCase - write(resUnit) 'logscales:', loadCases%logscale - write(resUnit) 'increments:', loadCases%incs ! one entry per LoadCase - write(resUnit) 'startingIncrement:', restartInc ! start with writing out the previous inc - write(resUnit) 'eoh' - close(resUnit) ! end of header + write(fileUnit) 'load:', trim(loadCaseFile) ! ... and write header + write(fileUnit) 'workingdir:', trim(workingDir) + write(fileUnit) 'geometry:', trim(geometryFile) + write(fileUnit) 'grid:', grid + write(fileUnit) 'size:', geomSize + write(fileUnit) 'materialpoint_sizeResults:', materialpoint_sizeResults + write(fileUnit) 'loadcases:', size(loadCases) + write(fileUnit) 'frequencies:', loadCases%outputfrequency ! one entry per LoadCase + write(fileUnit) 'times:', loadCases%time ! one entry per LoadCase + write(fileUnit) 'logscales:', loadCases%logscale + write(fileUnit) 'increments:', loadCases%incs ! one entry per LoadCase + write(fileUnit) 'startingIncrement:', restartInc ! start with writing out the previous inc + write(fileUnit) 'eoh' + close(fileUnit) ! end of header open(newunit=statUnit,file=trim(getSolverJobName())//& '.sta',form='FORMATTED',status='REPLACE') write(statUnit,'(a)') 'Increment Time CutbackLevel Converged IterationsNeeded' ! statistics file @@ -409,13 +410,13 @@ program DAMASK_spectral call MPI_file_open(PETSC_COMM_WORLD, trim(getSolverJobName())//'.spectralOut', & MPI_MODE_WRONLY + MPI_MODE_APPEND, & MPI_INFO_NULL, & - resUnit, & + fileUnit, & ierr) if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_open') - call MPI_file_get_position(resUnit,fileOffset,ierr) ! get offset from header + call MPI_file_get_position(fileUnit,fileOffset,ierr) ! get offset from header if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_get_position') fileOffset = fileOffset + sum(outputSize(1:worldrank)) ! offset of my process in file (header + processes before me) - call MPI_file_seek (resUnit,fileOffset,MPI_SEEK_SET,ierr) + call MPI_file_seek (fileUnit,fileOffset,MPI_SEEK_SET,ierr) if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_seek') writeUndeformed: if (interface_restartInc < 1_pInt) then @@ -423,7 +424,7 @@ program DAMASK_spectral do i = 1, size(materialpoint_results,3)/(maxByteOut/(materialpoint_sizeResults*pReal))+1 ! slice the output of my process in chunks not exceeding the limit for one output outputIndex = int([(i-1_pInt)*((maxRealOut)/materialpoint_sizeResults)+1_pInt, & ! QUESTION: why not starting i at 0 instead of murky 1? min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt) - call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)), & + call MPI_file_write(fileUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)), & [(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), & int((outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)), & MPI_DOUBLE, MPI_STATUS_IGNORE, ierr) @@ -565,7 +566,7 @@ program DAMASK_spectral write(6,'(/,a)') ' cutting back ' else ! no more options to continue call IO_warning(850_pInt) - call MPI_file_close(resUnit,ierr) + call MPI_file_close(fileUnit,ierr) close(statUnit) call quit(-1_pInt*(lastRestartWritten+1_pInt)) ! quit and provide information about last restart inc written endif @@ -588,12 +589,12 @@ program DAMASK_spectral write(6,'(1/,a)') ' ... writing results to file ......................................' flush(6) call materialpoint_postResults() - call MPI_file_seek (resUnit,fileOffset,MPI_SEEK_SET,ierr) + call MPI_file_seek (fileUnit,fileOffset,MPI_SEEK_SET,ierr) if (ierr /= 0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_seek') do i=1, size(materialpoint_results,3)/(maxByteOut/(materialpoint_sizeResults*pReal))+1 ! slice the output of my process in chunks not exceeding the limit for one output outputIndex=int([(i-1_pInt)*((maxRealOut)/materialpoint_sizeResults)+1_pInt, & min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt) - call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),& + call MPI_file_write(fileUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),& [(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), & int((outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)),& MPI_DOUBLE, MPI_STATUS_IGNORE, ierr) @@ -623,7 +624,7 @@ program DAMASK_spectral real(convergedCounter, pReal)/& real(notConvergedCounter + convergedCounter,pReal)*100.0_pReal, ' %) increments converged!' flush(6) - call MPI_file_close(resUnit,ierr) + call MPI_file_close(fileUnit,ierr) close(statUnit) if (notConvergedCounter > 0_pInt) call quit(3_pInt) ! error if some are not converged From 5330fb31adb79b27d1709d073f873c83c1301d7e Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Fri, 31 Aug 2018 10:19:37 +0200 Subject: [PATCH 52/67] more verbose error message --- src/DAMASK_spectral.f90 | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index b99fb1e1d..ee5af421c 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -190,13 +190,16 @@ program DAMASK_spectral !-------------------------------------------------------------------------------------------------- ! reading information from load case file and to sanity checks - allocate (loadCases(0)) ! array of load cases + allocate (loadCases(0)) ! array of load cases open(newunit=fileunit,iostat=myStat,file=trim(loadCaseFile),action='read') if (myStat /= 0_pInt) call IO_error(100_pInt,el=myStat,ext_msg=trim(loadCaseFile)) do read(fileUnit, '(A)', iostat=myStat) line if ( myStat /= 0_pInt) exit if (IO_isBlank(line)) cycle ! skip empty lines + + currentLoadCase = currentLoadCase + 1_pInt + chunkPos = IO_stringPos(line) do i = 1_pInt, chunkPos(1) ! reading compulsory parameters for loadcase select case (IO_lc(IO_stringValue(line,chunkPos,i))) @@ -207,13 +210,13 @@ program DAMASK_spectral case('n','incs','increments','steps','logincs','logincrements','logsteps') N_n = N_n + 1_pInt end select - enddo ! count all identifiers to allocate memory and do sanity check - if ((N_def /= N_n) .or. (N_n /= N_t) .or. N_n < 1_pInt) & ! sanity check - call IO_error(error_ID=837_pInt,ext_msg = trim(loadCaseFile)) ! error message for incomplete loadcase + enddo + if ((N_def /= N_n) .or. (N_n /= N_t) .or. N_n < 1_pInt) & ! sanity check + call IO_error(error_ID=837_pInt,el=currentLoadCase,ext_msg = trim(loadCaseFile)) ! error message for incomplete loadcase newLoadCase%stress%myType='stress' field = 1 - newLoadCase%ID(field) = FIELD_MECH_ID ! mechanical active by default + newLoadCase%ID(field) = FIELD_MECH_ID ! mechanical active by default thermalActive: if (any(thermal_type == THERMAL_conduction_ID)) then field = field + 1 newLoadCase%ID(field) = FIELD_THERMAL_ID @@ -290,7 +293,6 @@ program DAMASK_spectral end select enddo readIn - currentLoadCase = currentLoadCase + 1_pInt newLoadCase%followFormerTrajectory = merge(.true.,.false.,currentLoadCase > 1_pInt) ! by default, guess from previous load case reportAndCheck: if (worldrank == 0) then From 3e811108309c3474f973ccdc56447391642af5c4 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Fri, 31 Aug 2018 11:22:59 -0400 Subject: [PATCH 53/67] tell user whether DEBUG version or not --- src/DAMASK_spectral.f90 | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index 2ed94d06a..c60593912 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -154,6 +154,9 @@ program DAMASK_spectral ! init DAMASK (all modules) call CPFEM_initAll(el = 1_pInt, ip = 1_pInt) write(6,'(/,a)') ' <<<+- DAMASK_spectral init -+>>>' +#ifdef DEBUG + write(6,'(/,a)') ' <<<+- DEBUG version -+>>>' +#endif write(6,'(/,a,/)') ' Roters et al., Computational Materials Science, 2018' write(6,'(a15,a)') ' Current time: ',IO_timeStamp() #include "compilation_info.f90" From b66b01e65da6157c52177b61048ef48d4bded236 Mon Sep 17 00:00:00 2001 From: Test User Date: Fri, 31 Aug 2018 20:52:04 +0200 Subject: [PATCH 54/67] [skip ci] updated version information after successful test of v2.0.2-492-gb24ebb8a --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index c1e114a98..9615f9d5f 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-490-g29e55d20 +v2.0.2-492-gb24ebb8a From 36f0e9141d4e0ca06fe8e54cc3c978d81f47c53e Mon Sep 17 00:00:00 2001 From: Test User Date: Sat, 1 Sep 2018 12:39:08 +0200 Subject: [PATCH 55/67] [skip ci] updated version information after successful test of v2.0.2-494-g6a64637a --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index c1e114a98..79ff3e2f6 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-490-g29e55d20 +v2.0.2-494-g6a64637a From e8a0cd507b6cd6d005570fdabd71eb4cc467f540 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 5 Sep 2018 23:37:33 +0200 Subject: [PATCH 56/67] test compatible with new-style dislotwin --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index fa02113fa..b64eb647f 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit fa02113fa7a0af3376648e4320318ec337fe79aa +Subproject commit b64eb647f30766f3f58daf44e843b9f1e4e5f5e4 From 3966659ac990cef5f70a33a63ac7671d66a24df3 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 6 Sep 2018 16:18:06 +0200 Subject: [PATCH 57/67] to easily see start and end of each job --- .gitlab-ci.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index caa411bb8..5833fda97 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -29,7 +29,12 @@ before_script: done - source $DAMASKROOT/env/DAMASK.sh - cd $DAMASKROOT/PRIVATE/testing + - echo "Job start: $(date)" +################################################################################################### +after_script: + - echo "Job end: $(date)" +# ################################################################################################### variables: # =============================================================================================== From e70efd2608bcb1623e02e5702637f61168e4bbb8 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 6 Sep 2018 16:49:39 +0200 Subject: [PATCH 58/67] inform about debug versions indenpendently of the solver --- src/DAMASK_spectral.f90 | 3 --- src/debug.f90 | 3 +++ 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90 index c907abe07..ee5af421c 100644 --- a/src/DAMASK_spectral.f90 +++ b/src/DAMASK_spectral.f90 @@ -156,9 +156,6 @@ program DAMASK_spectral ! init DAMASK (all modules) call CPFEM_initAll(el = 1_pInt, ip = 1_pInt) write(6,'(/,a)') ' <<<+- DAMASK_spectral init -+>>>' -#ifdef DEBUG - write(6,'(/,a)') ' <<<+- DEBUG version -+>>>' -#endif write(6,'(/,a,/)') ' Roters et al., Computational Materials Science, 2018' write(6,'(a15,a)') ' Current time: ',IO_timeStamp() #include "compilation_info.f90" diff --git a/src/debug.f90 b/src/debug.f90 index 2a4edf28e..6debf84c2 100644 --- a/src/debug.f90 +++ b/src/debug.f90 @@ -109,6 +109,9 @@ subroutine debug_init character(len=65536) :: tag, line write(6,'(/,a)') ' <<<+- debug init -+>>>' +#ifdef DEBUG + write(6,'(a)') achar(27)//'[31m <<<+- DEBUG version -+>>>'//achar(27)//'[0m' +#endif write(6,'(a15,a)') ' Current time: ',IO_timeStamp() #include "compilation_info.f90" From 24fb2d0e5ccabadc2fe0c814db995f7af7e7c5eb Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 6 Sep 2018 16:54:35 +0200 Subject: [PATCH 59/67] testing compatible with 20-xxx branch --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index b64eb647f..2c40bb79f 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit b64eb647f30766f3f58daf44e843b9f1e4e5f5e4 +Subproject commit 2c40bb79f9a57d2178eb7be0e533fd5104f9f87e From 6beb74f6d12fc19c7c7902a3c03b7a19e85ddb27 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 6 Sep 2018 17:58:12 +0200 Subject: [PATCH 60/67] ticks caused trouble, not entirely clear why --- .gitlab-ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 5833fda97..61cad252f 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -29,12 +29,12 @@ before_script: done - source $DAMASKROOT/env/DAMASK.sh - cd $DAMASKROOT/PRIVATE/testing - - echo "Job start: $(date)" + - echo Job start: $(date) ################################################################################################### after_script: - - echo "Job end: $(date)" -# + - echo Job end: $(date) + ################################################################################################### variables: # =============================================================================================== From bfa56e9bffc2856bb4a8cf27e1d8e7c309159604 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 6 Sep 2018 18:07:40 +0200 Subject: [PATCH 61/67] a colon followed by a white space seems to be the problem --- .gitlab-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 61cad252f..29ded97dc 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -29,11 +29,11 @@ before_script: done - source $DAMASKROOT/env/DAMASK.sh - cd $DAMASKROOT/PRIVATE/testing - - echo Job start: $(date) + - echo Job start:" $(date)" ################################################################################################### after_script: - - echo Job end: $(date) + - echo Job end:" $(date)" ################################################################################################### variables: From 6c3b5f17eb6d05a8637f18e454fa03117b5b7fd0 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Thu, 6 Sep 2018 14:19:09 -0400 Subject: [PATCH 62/67] updated orientation/quaternion class to follow Rowenhorst_etal2015 --- lib/damask/orientation.py | 160 +++++++++++++------------------------- 1 file changed, 53 insertions(+), 107 deletions(-) diff --git a/lib/damask/orientation.py b/lib/damask/orientation.py index 7d97d2c81..17e5e3e58 100644 --- a/lib/damask/orientation.py +++ b/lib/damask/orientation.py @@ -30,12 +30,19 @@ class Quaternion: """ Orientation represented as unit quaternion. - All methods and naming conventions based on http://www.euclideanspace.com/maths/algebra/realNormedAlgebra/quaternions. + All methods and naming conventions based on Rowenhorst_etal2015 + Convention 1: coordinate frames are right-handed + Convention 2: a rotation angle ω is taken to be positive for a counterclockwise rotation + when viewing from the end point of the rotation axis unit vector towards the origin + Convention 3: rotations will be interpreted in the passive sense + Convention 4: Euler angle triplets are implemented using the Bunge convention, + with the angular ranges as [0, 2π],[0, π],[0, 2π] + Convention 5: the rotation angle ω is limited to the interval [0, π] w is the real part, (x, y, z) are the imaginary parts. - Representation of rotation is in ACTIVE form! - (Derived directly or through angleAxis, Euler angles, or active matrix) - Vector "a" (defined in coordinate system "A") is actively rotated to new coordinates "b". + + Vector "a" (defined in coordinate system "A") is passively rotated + resulting in new coordinates "b" when expressed in system "B". b = Q * a b = np.dot(Q.asMatrix(),a) """ @@ -309,10 +316,12 @@ class Quaternion: return np.outer([i for i in self],[i for i in self]) def asMatrix(self): - return np.array( - [[1.0-2.0*(self.y*self.y+self.z*self.z), 2.0*(self.x*self.y-self.z*self.w), 2.0*(self.x*self.z+self.y*self.w)], - [ 2.0*(self.x*self.y+self.z*self.w), 1.0-2.0*(self.x*self.x+self.z*self.z), 2.0*(self.y*self.z-self.x*self.w)], - [ 2.0*(self.x*self.z-self.y*self.w), 2.0*(self.x*self.w+self.y*self.z), 1.0-2.0*(self.x*self.x+self.y*self.y)]]) + qbarhalf = 0.5*(self.w**2 - self.x**2 - self.y**2 - self.z**2) + return 2.0*np.array( + [[ qbarhalf + self.x**2 , self.x*self.y - self.w*self.z, self.x*self.z + self.w*self.y], + [ self.x*self.y + self.w*self.z, qbarhalf + self.y**2 , self.y*self.z - self.w*self.x], + [ self.x*self.z - self.w*self.y, self.y*self.z + self.w*self.x, qbarhalf + self.z**2 ], + ]) def asAngleAxis(self, degrees = False): @@ -335,52 +344,28 @@ class Quaternion: return np.inf*np.ones(3) if self.w == 0.0 else np.array([self.x, self.y, self.z])/self.w def asEulers(self, - type = "bunge", degrees = False, - standardRange = False): + ): """ Orientation as Bunge-Euler angles. - Conversion of ACTIVE rotation to Euler angles taken from: - Melcher, A.; Unser, A.; Reichhardt, M.; Nestler, B.; Poetschke, M.; Selzer, M. - Conversion of EBSD data by a quaternion based algorithm to be used for grain structure simulations - Technische Mechanik 30 (2010) pp 401--413. """ - angles = [0.0,0.0,0.0] - if type.lower() == 'bunge' or type.lower() == 'zxz': - if abs(self.x) < 1e-4 and abs(self.y) < 1e-4: - x = self.w**2 - self.z**2 - y = 2.*self.w*self.z - angles[0] = math.atan2(y,x) - elif abs(self.w) < 1e-4 and abs(self.z) < 1e-4: - x = self.x**2 - self.y**2 - y = 2.*self.x*self.y - angles[0] = math.atan2(y,x) - angles[1] = math.pi - else: - chi = math.sqrt((self.w**2 + self.z**2)*(self.x**2 + self.y**2)) + q03 = self.w**2+self.z**2 + q12 = self.x**2+self.y**2 + chi = np.sqrt(q03*q12) + + if abs(chi) < 1e-10 and abs(q12) < 1e-10: + eulers = np.array([math.atan2(-2*self.w*self.z,self.w**2-self.z**2),0,0]) + elif abs(chi) < 1e-10 and abs(q03) < 1e-10: + eulers = np.array([math.atan2( 2*self.x*self.y,self.x**2-self.y**2),np.pi,0]) + else: + eulers = np.array([math.atan2((self.x*self.z-self.w*self.y)/chi,(-self.w*self.x-self.y*self.z)/chi), + math.atan2(2*chi,q03-q12), + math.atan2((self.w*self.y+self.x*self.z)/chi,( self.y*self.z-self.w*self.x)/chi), + ]) - x = (self.w * self.x - self.y * self.z)/2./chi - y = (self.w * self.y + self.x * self.z)/2./chi - angles[0] = math.atan2(y,x) - - x = self.w**2 + self.z**2 - (self.x**2 + self.y**2) - y = 2.*chi - angles[1] = math.atan2(y,x) - - x = (self.w * self.x + self.y * self.z)/2./chi - y = (self.z * self.x - self.y * self.w)/2./chi - angles[2] = math.atan2(y,x) - - if standardRange: - angles[0] %= 2*math.pi - if angles[1] < 0.0: - angles[1] += math.pi - angles[2] *= -1.0 - angles[2] %= 2*math.pi - - return np.degrees(angles) if degrees else angles + return np.degrees(eulers) if degrees else eulers # # Static constructors @@ -408,7 +393,7 @@ class Quaternion: halfangle = math.atan(np.linalg.norm(rodrigues)) c = math.cos(halfangle) w = c - x,y,z = c*rodrigues + x,y,z = rodrigues/c return cls([w,x,y,z]) @@ -431,24 +416,19 @@ class Quaternion: @classmethod def fromEulers(cls, eulers, - type = 'Bunge', degrees = False): if not isinstance(eulers, np.ndarray): eulers = np.array(eulers,dtype='d') eulers = np.radians(eulers) if degrees else eulers - c = np.cos(0.5 * eulers) - s = np.sin(0.5 * eulers) + sigma = 0.5*(eulers[0]+eulers[2]) + delta = 0.5*(eulers[0]-eulers[2]) + c = np.cos(0.5*eulers[1]) + s = np.sin(0.5*eulers[1]) - if type.lower() == 'bunge' or type.lower() == 'zxz': - w = c[0] * c[1] * c[2] - s[0] * c[1] * s[2] - x = c[0] * s[1] * c[2] + s[0] * s[1] * s[2] - y = - c[0] * s[1] * s[2] + s[0] * s[1] * c[2] - z = c[0] * c[1] * s[2] + s[0] * c[1] * c[2] - else: - w = c[0] * c[1] * c[2] - s[0] * s[1] * s[2] - x = s[0] * s[1] * c[2] + c[0] * c[1] * s[2] - y = s[0] * c[1] * c[2] + c[0] * s[1] * s[2] - z = c[0] * s[1] * c[2] - s[0] * c[1] * s[2] + w = c * np.cos(sigma) + x = -s * np.cos(delta) + y = -s * np.sin(delta) + z = -c * np.sin(sigma) return cls([w,x,y,z]) @@ -460,49 +440,16 @@ class Quaternion: if m.shape != (3,3) and np.prod(m.shape) == 9: m = m.reshape(3,3) - tr = np.trace(m) - if tr > 1e-8: - s = math.sqrt(tr + 1.0)*2.0 + w = 0.5*math.sqrt(1.+m[0,0]+m[1,1]+m[2,2]) + x = 0.5*math.sqrt(1.+m[0,0]-m[1,1]-m[2,2]) + y = 0.5*math.sqrt(1.-m[0,0]+m[1,1]-m[2,2]) + z = 0.5*math.sqrt(1.-m[0,0]-m[1,1]+m[2,2]) - return cls( - [ s*0.25, - (m[2,1] - m[1,2])/s, - (m[0,2] - m[2,0])/s, - (m[1,0] - m[0,1])/s, - ]) + x *= -1 if m[2,1] < m[1,2] else 1 + y *= -1 if m[0,2] < m[2,0] else 1 + z *= -1 if m[1,0] < m[0,1] else 1 - elif m[0,0] > m[1,1] and m[0,0] > m[2,2]: - t = m[0,0] - m[1,1] - m[2,2] + 1.0 - s = 2.0*math.sqrt(t) - - return cls( - [ (m[2,1] - m[1,2])/s, - s*0.25, - (m[0,1] + m[1,0])/s, - (m[2,0] + m[0,2])/s, - ]) - - elif m[1,1] > m[2,2]: - t = -m[0,0] + m[1,1] - m[2,2] + 1.0 - s = 2.0*math.sqrt(t) - - return cls( - [ (m[0,2] - m[2,0])/s, - (m[0,1] + m[1,0])/s, - s*0.25, - (m[1,2] + m[2,1])/s, - ]) - - else: - t = -m[0,0] - m[1,1] + m[2,2] + 1.0 - s = 2.0*math.sqrt(t) - - return cls( - [ (m[1,0] - m[0,1])/s, - (m[2,0] + m[0,2])/s, - (m[1,2] + m[2,1])/s, - s*0.25, - ]) + return cls( np.array([w,x,y,z])/math.sqrt(w**2 + x**2 + y**2 + z**2)) @classmethod @@ -829,7 +776,7 @@ class Orientation: else: self.quaternion = Quaternion.fromRandom(randomSeed=random) elif isinstance(Eulers, np.ndarray) and Eulers.shape == (3,): # based on given Euler angles - self.quaternion = Quaternion.fromEulers(Eulers,type='bunge',degrees=degrees) + self.quaternion = Quaternion.fromEulers(Eulers,degrees=degrees) elif isinstance(matrix, np.ndarray) : # based on given rotation matrix self.quaternion = Quaternion.fromMatrix(matrix) elif isinstance(angleAxis, np.ndarray) and angleAxis.shape == (4,): # based on given angle and rotation axis @@ -855,16 +802,15 @@ class Orientation: return 'Symmetry: %s\n' % (self.symmetry) + \ 'Quaternion: %s\n' % (self.quaternion) + \ 'Matrix:\n%s\n' % ( '\n'.join(['\t'.join(map(str,self.asMatrix()[i,:])) for i in range(3)]) ) + \ - 'Bunge Eulers / deg: %s' % ('\t'.join(map(str,self.asEulers('bunge',degrees=True))) ) + 'Bunge Eulers / deg: %s' % ('\t'.join(map(str,self.asEulers(degrees=True))) ) def asQuaternion(self): return self.quaternion.asList() def asEulers(self, - type = 'bunge', degrees = False, - standardRange = False): - return self.quaternion.asEulers(type, degrees, standardRange) + ): + return self.quaternion.asEulers(degrees) eulers = property(asEulers) def asRodrigues(self): From a16454f1f98a0ecd24cd800cff947c4aa22a7856 Mon Sep 17 00:00:00 2001 From: Satyapriya Gupta Date: Thu, 6 Sep 2018 16:43:29 -0400 Subject: [PATCH 63/67] fixed missing propagation of dependent state variables --- src/crystallite.f90 | 30 +++++++++++++++++++++++------- 1 file changed, 23 insertions(+), 7 deletions(-) diff --git a/src/crystallite.f90 b/src/crystallite.f90 index b9ae84a44..4b365c68d 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -174,10 +174,11 @@ subroutine crystallite_init use config, only: & config_deallocate, & config_crystallite, & - crystallite_name + crystallite_name, & + material_Nphase use constitutive, only: & constitutive_initialFi, & - constitutive_microstructure ! derived (shortcut) quantities of given state + constitutive_microstructure ! derived (shortcut) quantities of given state implicit none @@ -187,7 +188,8 @@ subroutine crystallite_init i, & !< counter in integration point loop e, & !< counter in element loop o = 0_pInt, & !< counter in output loop - r, & !< counter in crystallite loop + r, & + ph, & !< counter in crystallite loop cMax, & !< maximum number of integration point components iMax, & !< maximum number of integration points eMax, & !< maximum number of elements @@ -421,6 +423,19 @@ subroutine crystallite_init enddo !$OMP END PARALLEL DO + do ph = 1_pInt,material_Nphase +!-------------------------------------------------------------------------------------------------- +! propagate dependent states to materialpoint and boundary value problem level + plasticState(ph)%partionedState0(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & + plasticState(ph)%sizeState,:) & + = plasticState(ph)%state(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & + plasticState(ph)%sizeState,:) + plasticState(ph)%state0 (plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & + plasticState(ph)%sizeState,:) & + = plasticState(ph)%state(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & + plasticState(ph)%sizeState,:) + enddo + call crystallite_stressAndItsTangent(.true.) ! request elastic answers crystallite_fallbackdPdF = crystallite_dPdF ! use initial elastic stiffness as fallback @@ -614,6 +629,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco) if (crystallite_requested(c,i,e)) then plasticState (phaseAt(c,i,e))%subState0( :,phasememberAt(c,i,e)) = & plasticState (phaseAt(c,i,e))%partionedState0(:,phasememberAt(c,i,e)) + do mySource = 1_pInt, phase_Nsources(phaseAt(c,i,e)) sourceState(phaseAt(c,i,e))%p(mySource)%subState0( :,phasememberAt(c,i,e)) = & sourceState(phaseAt(c,i,e))%p(mySource)%partionedState0(:,phasememberAt(c,i,e)) @@ -990,7 +1006,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco) timeSyncing2: if(numerics_timeSyncing) then if (any(.not. crystallite_localPlasticity .and. .not. crystallite_todo .and. .not. crystallite_converged & - .and. crystallite_subStep <= subStepMinCryst)) then ! no way of rescuing a nonlocal ip that violated the lower time step limit, ... + .and. crystallite_subStep <= subStepMinCryst)) then ! no way of rescuing a nonlocal ip that violated the lower time step limit, ... if (iand(debug_level(debug_crystallite),debug_levelExtensive) /= 0_pInt) then elementLooping4: do e = FEsolving_execElem(1),FEsolving_execElem(2) myNcomponents = homogenization_Ngrains(mesh_element(3,e)) @@ -1004,7 +1020,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco) enddo elementLooping4 endif where(.not. crystallite_localPlasticity) - crystallite_todo = .false. ! ... so let all nonlocal ips die peacefully + crystallite_todo = .false. ! ... so let all nonlocal ips die peacefully crystallite_subStep = 0.0_pReal endwhere endif @@ -1056,9 +1072,9 @@ subroutine crystallite_stressAndItsTangent(updateJaco) elementLooping5: do e = FEsolving_execElem(1),FEsolving_execElem(2) myNcomponents = homogenization_Ngrains(mesh_element(3,e)) - do i = FEsolving_execIP(1,e),FEsolving_execIP(2,e) ! iterate over IPs of this element to be processed + do i = FEsolving_execIP(1,e),FEsolving_execIP(2,e) ! iterate over IPs of this element to be processed do c = 1,myNcomponents - if (.not. crystallite_converged(c,i,e)) then ! respond fully elastically (might be not required due to becoming terminally ill anyway) + if (.not. crystallite_converged(c,i,e)) then ! respond fully elastically (might be not required due to becoming terminally ill anyway) if(iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) & write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3,/)') '<< CRYST >> no convergence: respond fully elastic at el (elFE) ip ipc ', & e,'(',mesh_element(1,e),')',i,c From 0a8dd880d155f5f507c2b490fe136bf3eb6a8d38 Mon Sep 17 00:00:00 2001 From: Test User Date: Sat, 8 Sep 2018 05:32:52 +0200 Subject: [PATCH 64/67] [skip ci] updated version information after successful test of v2.0.2-514-gbfa56e9b --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 9615f9d5f..069730c70 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-492-gb24ebb8a +v2.0.2-514-gbfa56e9b From 07dcdc9fc62f1afa303447a813689bd6e6ad533a Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 11 Sep 2018 02:10:55 +0200 Subject: [PATCH 65/67] undoes commit 6c3b5f17eb6d05a8637f18e454fa03117b5b7fd0 tests fail, needs closer look. Changes incorporated into 10-consistent-orientation-conversions-in-the-damask-core-and-the-python-module --- lib/damask/orientation.py | 169 +++++++++++++++++++++++++------------- 1 file changed, 114 insertions(+), 55 deletions(-) diff --git a/lib/damask/orientation.py b/lib/damask/orientation.py index ea0986762..7d97d2c81 100644 --- a/lib/damask/orientation.py +++ b/lib/damask/orientation.py @@ -27,22 +27,15 @@ class Rodrigues: # ****************************************************************************************** class Quaternion: - u""" + """ Orientation represented as unit quaternion. - All methods and naming conventions based on Rowenhorst_etal2015 - Convention 1: coordinate frames are right-handed - Convention 2: a rotation angle ω is taken to be positive for a counterclockwise rotation - when viewing from the end point of the rotation axis unit vector towards the origin - Convention 3: rotations will be interpreted in the passive sense - Convention 4: Euler angle triplets are implemented using the Bunge convention, - with the angular ranges as [0, 2π],[0, π],[0, 2π] - Convention 5: the rotation angle ω is limited to the interval [0, π] + All methods and naming conventions based on http://www.euclideanspace.com/maths/algebra/realNormedAlgebra/quaternions. w is the real part, (x, y, z) are the imaginary parts. - - Vector "a" (defined in coordinate system "A") is passively rotated - resulting in new coordinates "b" when expressed in system "B". + Representation of rotation is in ACTIVE form! + (Derived directly or through angleAxis, Euler angles, or active matrix) + Vector "a" (defined in coordinate system "A") is actively rotated to new coordinates "b". b = Q * a b = np.dot(Q.asMatrix(),a) """ @@ -316,12 +309,10 @@ class Quaternion: return np.outer([i for i in self],[i for i in self]) def asMatrix(self): - qbarhalf = 0.5*(self.w**2 - self.x**2 - self.y**2 - self.z**2) - return 2.0*np.array( - [[ qbarhalf + self.x**2 , self.x*self.y - self.w*self.z, self.x*self.z + self.w*self.y], - [ self.x*self.y + self.w*self.z, qbarhalf + self.y**2 , self.y*self.z - self.w*self.x], - [ self.x*self.z - self.w*self.y, self.y*self.z + self.w*self.x, qbarhalf + self.z**2 ], - ]) + return np.array( + [[1.0-2.0*(self.y*self.y+self.z*self.z), 2.0*(self.x*self.y-self.z*self.w), 2.0*(self.x*self.z+self.y*self.w)], + [ 2.0*(self.x*self.y+self.z*self.w), 1.0-2.0*(self.x*self.x+self.z*self.z), 2.0*(self.y*self.z-self.x*self.w)], + [ 2.0*(self.x*self.z-self.y*self.w), 2.0*(self.x*self.w+self.y*self.z), 1.0-2.0*(self.x*self.x+self.y*self.y)]]) def asAngleAxis(self, degrees = False): @@ -344,23 +335,52 @@ class Quaternion: return np.inf*np.ones(3) if self.w == 0.0 else np.array([self.x, self.y, self.z])/self.w def asEulers(self, - degrees = False): - """Orientation as Bunge-Euler angles.""" - q03 = self.w**2+self.z**2 - q12 = self.x**2+self.y**2 - chi = np.sqrt(q03*q12) - - if abs(chi) < 1e-10 and abs(q12) < 1e-10: - eulers = np.array([math.atan2(-2*self.w*self.z,self.w**2-self.z**2),0,0]) - elif abs(chi) < 1e-10 and abs(q03) < 1e-10: - eulers = np.array([math.atan2( 2*self.x*self.y,self.x**2-self.y**2),np.pi,0]) - else: - eulers = np.array([math.atan2((self.x*self.z-self.w*self.y)/chi,(-self.w*self.x-self.y*self.z)/chi), - math.atan2(2*chi,q03-q12), - math.atan2((self.w*self.y+self.x*self.z)/chi,( self.y*self.z-self.w*self.x)/chi), - ]) + type = "bunge", + degrees = False, + standardRange = False): + """ + Orientation as Bunge-Euler angles. - return np.degrees(eulers) if degrees else eulers + Conversion of ACTIVE rotation to Euler angles taken from: + Melcher, A.; Unser, A.; Reichhardt, M.; Nestler, B.; Poetschke, M.; Selzer, M. + Conversion of EBSD data by a quaternion based algorithm to be used for grain structure simulations + Technische Mechanik 30 (2010) pp 401--413. + """ + angles = [0.0,0.0,0.0] + + if type.lower() == 'bunge' or type.lower() == 'zxz': + if abs(self.x) < 1e-4 and abs(self.y) < 1e-4: + x = self.w**2 - self.z**2 + y = 2.*self.w*self.z + angles[0] = math.atan2(y,x) + elif abs(self.w) < 1e-4 and abs(self.z) < 1e-4: + x = self.x**2 - self.y**2 + y = 2.*self.x*self.y + angles[0] = math.atan2(y,x) + angles[1] = math.pi + else: + chi = math.sqrt((self.w**2 + self.z**2)*(self.x**2 + self.y**2)) + + x = (self.w * self.x - self.y * self.z)/2./chi + y = (self.w * self.y + self.x * self.z)/2./chi + angles[0] = math.atan2(y,x) + + x = self.w**2 + self.z**2 - (self.x**2 + self.y**2) + y = 2.*chi + angles[1] = math.atan2(y,x) + + x = (self.w * self.x + self.y * self.z)/2./chi + y = (self.z * self.x - self.y * self.w)/2./chi + angles[2] = math.atan2(y,x) + + if standardRange: + angles[0] %= 2*math.pi + if angles[1] < 0.0: + angles[1] += math.pi + angles[2] *= -1.0 + angles[2] %= 2*math.pi + + return np.degrees(angles) if degrees else angles # # Static constructors @@ -388,7 +408,7 @@ class Quaternion: halfangle = math.atan(np.linalg.norm(rodrigues)) c = math.cos(halfangle) w = c - x,y,z = rodrigues/c + x,y,z = c*rodrigues return cls([w,x,y,z]) @@ -411,19 +431,24 @@ class Quaternion: @classmethod def fromEulers(cls, eulers, + type = 'Bunge', degrees = False): if not isinstance(eulers, np.ndarray): eulers = np.array(eulers,dtype='d') eulers = np.radians(eulers) if degrees else eulers - sigma = 0.5*(eulers[0]+eulers[2]) - delta = 0.5*(eulers[0]-eulers[2]) - c = np.cos(0.5*eulers[1]) - s = np.sin(0.5*eulers[1]) + c = np.cos(0.5 * eulers) + s = np.sin(0.5 * eulers) - w = c * np.cos(sigma) - x = -s * np.cos(delta) - y = -s * np.sin(delta) - z = -c * np.sin(sigma) + if type.lower() == 'bunge' or type.lower() == 'zxz': + w = c[0] * c[1] * c[2] - s[0] * c[1] * s[2] + x = c[0] * s[1] * c[2] + s[0] * s[1] * s[2] + y = - c[0] * s[1] * s[2] + s[0] * s[1] * c[2] + z = c[0] * c[1] * s[2] + s[0] * c[1] * c[2] + else: + w = c[0] * c[1] * c[2] - s[0] * s[1] * s[2] + x = s[0] * s[1] * c[2] + c[0] * c[1] * s[2] + y = s[0] * c[1] * c[2] + c[0] * s[1] * s[2] + z = c[0] * s[1] * c[2] - s[0] * c[1] * s[2] return cls([w,x,y,z]) @@ -435,16 +460,49 @@ class Quaternion: if m.shape != (3,3) and np.prod(m.shape) == 9: m = m.reshape(3,3) - w = 0.5*math.sqrt(1.+m[0,0]+m[1,1]+m[2,2]) - x = 0.5*math.sqrt(1.+m[0,0]-m[1,1]-m[2,2]) - y = 0.5*math.sqrt(1.-m[0,0]+m[1,1]-m[2,2]) - z = 0.5*math.sqrt(1.-m[0,0]-m[1,1]+m[2,2]) + tr = np.trace(m) + if tr > 1e-8: + s = math.sqrt(tr + 1.0)*2.0 - x *= -1 if m[2,1] < m[1,2] else 1 - y *= -1 if m[0,2] < m[2,0] else 1 - z *= -1 if m[1,0] < m[0,1] else 1 + return cls( + [ s*0.25, + (m[2,1] - m[1,2])/s, + (m[0,2] - m[2,0])/s, + (m[1,0] - m[0,1])/s, + ]) - return cls( np.array([w,x,y,z])/math.sqrt(w**2 + x**2 + y**2 + z**2)) + elif m[0,0] > m[1,1] and m[0,0] > m[2,2]: + t = m[0,0] - m[1,1] - m[2,2] + 1.0 + s = 2.0*math.sqrt(t) + + return cls( + [ (m[2,1] - m[1,2])/s, + s*0.25, + (m[0,1] + m[1,0])/s, + (m[2,0] + m[0,2])/s, + ]) + + elif m[1,1] > m[2,2]: + t = -m[0,0] + m[1,1] - m[2,2] + 1.0 + s = 2.0*math.sqrt(t) + + return cls( + [ (m[0,2] - m[2,0])/s, + (m[0,1] + m[1,0])/s, + s*0.25, + (m[1,2] + m[2,1])/s, + ]) + + else: + t = -m[0,0] - m[1,1] + m[2,2] + 1.0 + s = 2.0*math.sqrt(t) + + return cls( + [ (m[1,0] - m[0,1])/s, + (m[2,0] + m[0,2])/s, + (m[1,2] + m[2,1])/s, + s*0.25, + ]) @classmethod @@ -771,7 +829,7 @@ class Orientation: else: self.quaternion = Quaternion.fromRandom(randomSeed=random) elif isinstance(Eulers, np.ndarray) and Eulers.shape == (3,): # based on given Euler angles - self.quaternion = Quaternion.fromEulers(Eulers,degrees=degrees) + self.quaternion = Quaternion.fromEulers(Eulers,type='bunge',degrees=degrees) elif isinstance(matrix, np.ndarray) : # based on given rotation matrix self.quaternion = Quaternion.fromMatrix(matrix) elif isinstance(angleAxis, np.ndarray) and angleAxis.shape == (4,): # based on given angle and rotation axis @@ -797,15 +855,16 @@ class Orientation: return 'Symmetry: %s\n' % (self.symmetry) + \ 'Quaternion: %s\n' % (self.quaternion) + \ 'Matrix:\n%s\n' % ( '\n'.join(['\t'.join(map(str,self.asMatrix()[i,:])) for i in range(3)]) ) + \ - 'Bunge Eulers / deg: %s' % ('\t'.join(map(str,self.asEulers(degrees=True))) ) + 'Bunge Eulers / deg: %s' % ('\t'.join(map(str,self.asEulers('bunge',degrees=True))) ) def asQuaternion(self): return self.quaternion.asList() def asEulers(self, + type = 'bunge', degrees = False, - ): - return self.quaternion.asEulers(degrees) + standardRange = False): + return self.quaternion.asEulers(type, degrees, standardRange) eulers = property(asEulers) def asRodrigues(self): From ce6e6679d53ef712d8f66235c577f133d35fb67e Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 11 Sep 2018 12:20:05 +0200 Subject: [PATCH 66/67] causes array access out of bounds, needs further checks --- src/crystallite.f90 | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/crystallite.f90 b/src/crystallite.f90 index 66ee395aa..4cce2fd88 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -440,18 +440,18 @@ subroutine crystallite_init enddo !$OMP END PARALLEL DO - do ph = 1_pInt,material_Nphase !-------------------------------------------------------------------------------------------------- ! propagate dependent states to materialpoint and boundary value problem level - plasticState(ph)%partionedState0(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & - plasticState(ph)%sizeState,:) & - = plasticState(ph)%state(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & - plasticState(ph)%sizeState,:) - plasticState(ph)%state0 (plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & - plasticState(ph)%sizeState,:) & - = plasticState(ph)%state(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & - plasticState(ph)%sizeState,:) - enddo +! do ph = 1_pInt,material_Nphase +! plasticState(ph)%partionedState0(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & +! plasticState(ph)%sizeState,:) & +! = plasticState(ph)%state(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & +! plasticState(ph)%sizeState,:) +! plasticState(ph)%state0 (plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & +! plasticState(ph)%sizeState,:) & +! = plasticState(ph)%state(plasticState(ph)%offsetDeltaState+plasticState(ph)%sizeDeltaState: & +! plasticState(ph)%sizeState,:) +! enddo call crystallite_stressAndItsTangent(.true.) ! request elastic answers crystallite_fallbackdPdF = crystallite_dPdF ! use initial elastic stiffness as fallback From 42fdf4702787a707aea24e2f59d193d42013141e Mon Sep 17 00:00:00 2001 From: Test User Date: Tue, 11 Sep 2018 16:16:41 +0200 Subject: [PATCH 67/67] [skip ci] updated version information after successful test of v2.0.2-540-gce6e6679 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 069730c70..119546fa7 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.2-514-gbfa56e9b +v2.0.2-540-gce6e6679