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white space adjustments

This commit is contained in:
Martin Diehl 2019-06-15 16:42:16 +02:00
parent 4256f67919
commit f54a6cdc3b
2 changed files with 611 additions and 615 deletions
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204
src/HDF5_utilities.f90
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@ -22,7 +22,7 @@ module HDF5_utilities
#if defined(PETSc) || defined(DAMASK_HDF5) #if defined(PETSc) || defined(DAMASK_HDF5)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief reads integer or float data of defined shape from file ! ToDo: order of arguments wrong !> @brief reads integer or float data of defined shape from file ! ToDo: order of arguments wrong
!> @details for parallel IO, all dimension except for the last need to match !> @details for parallel IO, all dimension except for the last need to match
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
interface HDF5_read interface HDF5_read
@ -45,7 +45,7 @@ module HDF5_utilities
end interface HDF5_read end interface HDF5_read
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief writes integer or real data of defined shape to file ! ToDo: order of arguments wrong !> @brief writes integer or real data of defined shape to file ! ToDo: order of arguments wrong
!> @details for parallel IO, all dimension except for the last need to match !> @details for parallel IO, all dimension except for the last need to match
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
interface HDF5_write interface HDF5_write
@ -1759,66 +1759,66 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
myStart, globalShape, & myStart, globalShape, &
loc_id,localShape,datasetName,parallel) loc_id,localShape,datasetName,parallel)
integer(HID_T), intent(in) :: loc_id !< file or group handle integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in) :: parallel logical, intent(in) :: parallel
integer(HSIZE_T), intent(in), dimension(:) :: & integer(HSIZE_T), intent(in), dimension(:) :: &
localShape localShape
integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: & integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: &
myStart, & myStart, &
globalShape !< shape of the dataset (all processes) globalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer, dimension(worldsize) :: & integer, dimension(worldsize) :: &
readSize !< contribution of all processes readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer :: hdferr integer :: hdferr
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective for MPI) ! creating a property list for transfer properties (is collective for MPI)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pcreate_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pcreate_f')
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
readSize = 0 readSize = 0
readSize(worldrank+1) = int(localShape(ubound(localShape,1))) readSize(worldrank+1) = int(localShape(ubound(localShape,1)))
#ifdef PETSc #ifdef PETSc
if (parallel) then if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894,ext_msg='initialize_read: MPI_allreduce') if (ierr /= 0) call IO_error(894,ext_msg='initialize_read: MPI_allreduce')
endif endif
#endif #endif
myStart = int(0,HSIZE_T) myStart = int(0,HSIZE_T)
myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape) call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5screate_simple_f/memspace_id') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5screate_simple_f/memspace_id')
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! creating a property list for IO and set it to collective ! creating a property list for IO and set it to collective
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pcreate_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pcreate_f')
#ifdef PETSc #ifdef PETSc
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pset_all_coll_metadata_ops_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pset_all_coll_metadata_ops_f')
#endif #endif
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! open the dataset in the file and get the space ID ! open the dataset in the file and get the space ID
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5dopen_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5dopen_f')
call h5dget_space_f(dset_id, filespace_id, hdferr) call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5dget_space_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5dget_space_f')
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file ! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr) call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5sselect_hyperslab_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5sselect_hyperslab_f')
end subroutine initialize_read end subroutine initialize_read
@ -1828,19 +1828,19 @@ end subroutine initialize_read
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
subroutine finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) subroutine finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer :: hdferr integer :: hdferr
call h5pclose_f(plist_id, hdferr) call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: plist_id') if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: plist_id')
call h5pclose_f(aplist_id, hdferr) call h5pclose_f(aplist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: aplist_id') if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: aplist_id')
call h5dclose_f(dset_id, hdferr) call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5dclose_f') if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5dclose_f')
call h5sclose_f(filespace_id, hdferr) call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5sclose_f/filespace_id') if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr) call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5sclose_f/memspace_id') if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5sclose_f/memspace_id')
end subroutine finalize_read end subroutine finalize_read
@ -1852,60 +1852,60 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, & myStart, totalShape, &
loc_id,myShape,datasetName,datatype,parallel) loc_id,myShape,datasetName,datatype,parallel)
integer(HID_T), intent(in) :: loc_id !< file or group handle integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in) :: parallel logical, intent(in) :: parallel
integer(HID_T), intent(in) :: datatype integer(HID_T), intent(in) :: datatype
integer(HSIZE_T), intent(in), dimension(:) :: & integer(HSIZE_T), intent(in), dimension(:) :: &
myShape myShape
integer(HSIZE_T), intent(out), dimension(size(myShape,1)):: & integer(HSIZE_T), intent(out), dimension(size(myShape,1)):: &
myStart, & myStart, &
totalShape !< shape of the dataset (all processes) totalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id
integer, dimension(worldsize) :: & integer, dimension(worldsize) :: &
writeSize !< contribution of all processes writeSize !< contribution of all processes
integer :: ierr integer :: ierr
integer :: hdferr integer :: hdferr
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective when reading in parallel) ! creating a property list for transfer properties (is collective when reading in parallel)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5pcreate_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5pcreate_f')
#ifdef PETSc #ifdef PETSc
if (parallel) then if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5pset_dxpl_mpio_f')
endif endif
#endif #endif
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! determine the global data layout among all processes ! determine the global data layout among all processes
writeSize = 0 writeSize = 0
writeSize(worldrank+1) = int(myShape(ubound(myShape,1))) writeSize(worldrank+1) = int(myShape(ubound(myShape,1)))
#ifdef PETSc #ifdef PETSc
if (parallel) then if (parallel) then
call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894,ext_msg='initialize_write: MPI_allreduce') if (ierr /= 0) call IO_error(894,ext_msg='initialize_write: MPI_allreduce')
endif endif
#endif #endif
myStart = int(0,HSIZE_T) myStart = int(0,HSIZE_T)
myStart(ubound(myStart)) = int(sum(writeSize(1:worldrank)),HSIZE_T) myStart(ubound(myStart)) = int(sum(writeSize(1:worldrank)),HSIZE_T)
totalShape = [myShape(1:ubound(myShape,1)-1),int(sum(writeSize),HSIZE_T)] totalShape = [myShape(1:ubound(myShape,1)-1),int(sum(writeSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) and in file (global shape) ! create dataspace in memory (local shape) and in file (global shape)
call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape) call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dopen_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dopen_f')
call h5screate_simple_f(size(totalShape), totalShape, filespace_id, hdferr, totalShape) call h5screate_simple_f(size(totalShape), totalShape, filespace_id, hdferr, totalShape)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dget_space_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dget_space_f')
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataset in the file and select a hyperslab from it (the portion of the current process) ! create dataset in the file and select a hyperslab from it (the portion of the current process)
call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr) call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dcreate_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dcreate_f')
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, myShape, hdferr) call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, myShape, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5sselect_hyperslab_f') if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5sselect_hyperslab_f')
end subroutine initialize_write end subroutine initialize_write
@ -1915,19 +1915,19 @@ end subroutine initialize_write
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
subroutine finalize_write(plist_id, dset_id, filespace_id, memspace_id) subroutine finalize_write(plist_id, dset_id, filespace_id, memspace_id)
integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id
integer :: hdferr integer :: hdferr
call h5pclose_f(plist_id, hdferr) call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: plist_id') if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: plist_id')
call h5dclose_f(dset_id, hdferr) call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5dclose_f') if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5dclose_f')
call h5sclose_f(filespace_id, hdferr) call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5sclose_f/filespace_id') if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr) call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5sclose_f/memspace_id') if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5sclose_f/memspace_id')
end subroutine finalize_write end subroutine finalize_write
#endif #endif
end module HDF5_Utilities end module HDF5_Utilities

1022
src/homogenization.f90
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