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DAMASK_EICMD/src/HDF5_utilities.f90

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adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
!> @author Vitesh Shah, Max-Planck-Institut für Eisenforschung GmbH
!> @author Yi-Chin Yang, Max-Planck-Institut für Eisenforschung GmbH
!> @author Jennifer Nastola, Max-Planck-Institut für Eisenforschung GmbH
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!--------------------------------------------------------------------------------------------------
MPI file access needed for output
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module HDF5_utilities
Parallel writing and reading of integer datasets working
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use prec
use IO
use HDF5
MPI write only in case that PETSc is used
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#ifdef PETSc
Parallel writing and reading of integer datasets working
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use PETSC
MPI write only in case that PETSc is used
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#endif
number of helper functions for HDF5
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adjusted variable names and added comments
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implicit none
cleaned + suggested structure to write data
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public
hdferr needs to be integer type during compile time of HDF5 library
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integer(pInt), parameter, private :: &
HDF5_ERR_TYPE = 4_pInt !< kind of the integer return in the HDF5 library
number of helper functions for HDF5
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adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
reading and writing of subroutines of datasets of different ranks
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!> @brief reads pInt or pReal data of defined shape from file
adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
preprocessor statements are case sensitive.. ... and the PETSc variable is PETSc, not PETSC
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interface HDF5_read
Parallel writing and reading of integer datasets working
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module procedure HDF5_read_pReal1
module procedure HDF5_read_pReal2
module procedure HDF5_read_pReal3
module procedure HDF5_read_pReal4
module procedure HDF5_read_pReal5
module procedure HDF5_read_pReal6
module procedure HDF5_read_pReal7
module procedure HDF5_read_pInt1
module procedure HDF5_read_pInt2
module procedure HDF5_read_pInt3
module procedure HDF5_read_pInt4
module procedure HDF5_read_pInt5
module procedure HDF5_read_pInt6
module procedure HDF5_read_pInt7 !ABOVE 8 DIMENSIONS IT GIVES ERROR: THE CALL TO H5DREAD_F DOESNT WORK
close all objects of type integer(HID_T) created by native hdf5 routines
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preprocessor statements are case sensitive.. ... and the PETSc variable is PETSc, not PETSC
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end interface HDF5_read
Interfacing for subroutines to identify real and integer data
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adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
reading and writing of subroutines of datasets of different ranks
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!> @brief writes pInt or pReal data of defined shape to file
adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
preprocessor statements are case sensitive.. ... and the PETSc variable is PETSc, not PETSC
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interface HDF5_write
reading and writing of subroutines of datasets of different ranks
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module procedure HDF5_write_pReal1
module procedure HDF5_write_pReal2
module procedure HDF5_write_pReal3
module procedure HDF5_write_pReal4
module procedure HDF5_write_pReal5
module procedure HDF5_write_pReal6
module procedure HDF5_write_pReal7
close all objects of type integer(HID_T) created by native hdf5 routines
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reading and writing of subroutines of datasets of different ranks
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module procedure HDF5_write_pInt1
module procedure HDF5_write_pInt2
module procedure HDF5_write_pInt3
module procedure HDF5_write_pInt4
module procedure HDF5_write_pInt5
module procedure HDF5_write_pInt6
cleaning up the codes
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module procedure HDF5_write_pInt7 !ABOVE 8 DIMENSIONS IT GIVES ERROR: THE CALL TO H5DREAD_F DOESNT WORK
close all objects of type integer(HID_T) created by native hdf5 routines
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preprocessor statements are case sensitive.. ... and the PETSc variable is PETSc, not PETSC
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end interface HDF5_write
The attribute interface works for single processor output and single valued attribute
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!--------------------------------------------------------------------------------------------------
!> @brief attached attributes of type char,pInt or pReal to a file/dataset/group
!--------------------------------------------------------------------------------------------------
interface HDF5_attributes
module procedure HDF5_addStringAttribute
module procedure HDF5_addIntegerAttribute
module procedure HDF5_addRealAttribute
end interface HDF5_attributes
!--------------------------------------------------------------------------------------------------
number of helper functions for HDF5
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public :: &
keep only general functionality in HDF5_results
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HDF5_utilities_init, &
planning the forwarding of the results
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HDF5_openFile, &
HDF5_closeFile, &
HDF5_addStringAttribute, &
HDF5_addIntegerAttribute, &
The attribute interface works for single processor output and single valued attribute
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HDF5_addRealAttribute, &
number of helper functions for HDF5
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HDF5_closeGroup ,&
cleaning and separating functions
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HDF5_openGroup, &
HDF5_addGroup, &
preprocessor statements are case sensitive.. ... and the PETSc variable is PETSc, not PETSC
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HDF5_read, &
cleaned + suggested structure to write data
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HDF5_write, &
HDF5_setLink
number of helper functions for HDF5
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contains
MPI file access needed for output
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subroutine HDF5_utilities_init
number of helper functions for HDF5
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use, intrinsic :: &
cleaning up the codes
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iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
number of helper functions for HDF5
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implicit none
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
integer(SIZE_T) :: typeSize
number of helper functions for HDF5
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write(6,'(/,a)') ' <<<+- HDF5_Utilities init -+>>>'
#include "compilation_info.f90"
initializing and closing the HDF5 library
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!--------------------------------------------------------------------------------------------------
!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')
close all objects of type integer(HID_T) created by native hdf5 routines
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MPI file access needed for output
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end subroutine HDF5_utilities_init
number of helper functions for HDF5
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Reading and writing not very efficient method
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!--------------------------------------------------------------------------------------------------
!> @brief open and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
MPI file access needed for output
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integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
close all objects of type integer(HID_T) created by native hdf5 routines
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Reading and writing not very efficient method
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implicit none
avoid errors by consistently closing objects general bugfixes, works now
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character(len=*), intent(in) :: fileName
more flexible file open routine
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character, intent(in), optional :: mode
MPI file access needed for output
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logical, intent(in), optional :: parallel
more flexible file open routine
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character :: m
MPI file access needed for output
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integer(HID_T) :: plist_id
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
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more flexible file open routine
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if (present(mode)) then
m = mode
else
m = 'r'
endif
close all objects of type integer(HID_T) created by native hdf5 routines
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setting the property when opening the file
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call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5pcreate_f')
setting the property when opening the file
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MPI file access needed for output
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5pset_fapl_mpio_f')
MPI file access needed for output
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endif; endif
#endif
setting the property when opening the file
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if (m == 'w') then
call h5fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,access_prp = plist_id)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fcreate_f')
avoid errors by consistently closing objects general bugfixes, works now
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elseif(m == 'a') then
setting the property when opening the file
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call h5fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp = plist_id)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fopen_f (a)')
more flexible file open routine
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elseif(m == 'r') then
setting the property when opening the file
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call h5fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp = plist_id)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fopen_f (r)')
more flexible file open routine
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else
setting the property when opening the file
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call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fopen_f unknown access mode')
more flexible file open routine
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endif
Reading and writing not very efficient method
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setting the property when opening the file
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call h5pclose_f(plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5pclose_f')
setting the property when opening the file
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Reading and writing not very efficient method
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end function HDF5_openFile
number of helper functions for HDF5
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keep only general functionality in HDF5_results
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creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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!--------------------------------------------------------------------------------------------------
Interfacing for subroutines to identify real and integer data
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!> @brief close the opened HDF5 output file
creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeFile(fileHandle)
close all objects of type integer(HID_T) created by native hdf5 routines
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creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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implicit none
integer(HID_T), intent(in) :: fileHandle
hdferr needs to be integer type during compile time of HDF5 library
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cleaning and separating functions
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integer(HDF5_ERR_TYPE) :: hdferr
creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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call h5fclose_f(fileHandle,hdferr)
hdferr needs to be integer type during compile time of HDF5 library
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_closeFile: h5fclose_f')
creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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end subroutine HDF5_closeFile
number of helper functions for HDF5
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creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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!--------------------------------------------------------------------------------------------------
cleaning and separating functions
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!> @brief adds a new group to the fileHandle
creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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!--------------------------------------------------------------------------------------------------
cleaning and separating functions
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integer(HID_T) function HDF5_addGroup(fileHandle,groupName)
creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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implicit none
cleaning up the codes
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integer(HID_T), intent(in) :: fileHandle
cleaning and separating functions
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character(len=*), intent(in) :: groupName
Parallel works for groups and included write function for integer data
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cleaning and separating functions
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integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: aplist_id
Parallel works for groups and included write function for integer data
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Read and write works for all types of data in parallel with test module passed
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!-------------------------------------------------------------------------------------------------
cleaning and separating functions
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! creating a property list for data access properties
Read and write works for all types of data in parallel with test module passed
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call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
cleaning and separating functions
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if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5pcreate_f ('//trim(groupName)//')')
Read and write works for all types of data in parallel with test module passed
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!-------------------------------------------------------------------------------------------------
cleaning and separating functions
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! setting I/O mode to collective
Read and write works for all types of data in parallel with test module passed
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call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
cleaning and separating functions
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if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')')
Read and write works for all types of data in parallel with test module passed
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!-------------------------------------------------------------------------------------------------
cleaning and separating functions
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! Create group
call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5gcreate_f ('//trim(groupName)//')')
close all objects of type integer(HID_T) created by native hdf5 routines
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cleaning and separating functions
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end function HDF5_addGroup
creating hdf5 file to contain restart information first quick and dirty implementation to get started. needs polishing and renaming
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number of helper functions for HDF5
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Reading and writing not very efficient method
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!--------------------------------------------------------------------------------------------------
close all objects of type integer(HID_T) created by native hdf5 routines
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!> @brief open an existing group of a file
Reading and writing not very efficient method
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!--------------------------------------------------------------------------------------------------
cleaning and separating functions
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integer(HID_T) function HDF5_openGroup(fileHandle,groupName)
Reading and writing not very efficient method
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implicit none
cleaning and separating functions
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integer(HID_T), intent(in) :: fileHandle
close all objects of type integer(HID_T) created by native hdf5 routines
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character(len=*), intent(in) :: groupName
cleaning and separating functions
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integer(HDF5_ERR_TYPE) :: hdferr
Able to read the independent datasets (outside the groups) in parallel
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integer(HID_T) :: aplist_id
Read and write works for all types of data in parallel with test module passed
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logical :: is_collective
Able to read the independent datasets (outside the groups) in parallel
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!-------------------------------------------------------------------------------------------------
cleaning and separating functions
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! creating a property list for data access properties
Able to read the independent datasets (outside the groups) in parallel
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call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
cleaning and separating functions
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if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5pcreate_f ('//trim(groupName)//')')
Able to read the independent datasets (outside the groups) in parallel
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!-------------------------------------------------------------------------------------------------
cleaning and separating functions
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! setting I/O mode to collective
Read and write works for all types of data in parallel with test module passed
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call h5pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr)
cleaning and separating functions
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if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')')
!-------------------------------------------------------------------------------------------------
! opening the group
call h5gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5gopen_f ('//trim(groupName)//')')
Reading and writing not very efficient method
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cleaning and separating functions
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end function HDF5_openGroup
Reading and writing not very efficient method
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number of helper functions for HDF5
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!--------------------------------------------------------------------------------------------------
close all objects of type integer(HID_T) created by native hdf5 routines
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!> @brief close a group
number of helper functions for HDF5
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!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeGroup(ID)
implicit none
integer(HID_T), intent(in) :: ID
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
number of helper functions for HDF5
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call h5gclose_f(ID, hdferr)
type mismatch
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if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = int(ID,pInt))
number of helper functions for HDF5
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end subroutine HDF5_closeGroup
planning the forwarding of the results
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!--------------------------------------------------------------------------------------------------
!> @brief adds a StringAttribute to the results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addStringAttribute(entity,attrLabel,attrValue)
implicit none
integer(HID_T), intent(in) :: entity
character(len=*), intent(in) :: attrLabel, attrValue
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
planning the forwarding of the results
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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='HDF5_addStringAttribute: h5screate_f')
call h5tcopy_f(H5T_NATIVE_CHARACTER, type_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_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='HDF5_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='HDF5_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='HDF5_addStringAttribute: h5awrite_f')
call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addStringAttribute: h5aclose_f')
call h5tclose_f(type_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addStringAttribute: h5tclose_f')
call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addStringAttribute: h5sclose_f')
end subroutine HDF5_addStringAttribute
!--------------------------------------------------------------------------------------------------
The attribute interface works for single processor output and single valued attribute
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!> @brief adds a IntegerAttribute to the results file
planning the forwarding of the results
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!--------------------------------------------------------------------------------------------------
subroutine HDF5_addIntegerAttribute(entity,attrLabel,attrValue)
implicit none
integer(HID_T), intent(in) :: entity
character(len=*), intent(in) :: attrLabel
integer(pInt), intent(in) :: attrValue
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
planning the forwarding of the results
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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='HDF5_addIntegerAttribute: h5screate_f')
The attribute interface works for single processor output and single valued attribute
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call h5tcopy_f(H5T_NATIVE_INTEGER, type_id, hdferr)
planning the forwarding of the results
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addIntegerAttribute: h5tcopy_f')
call h5tset_size_f(type_id, 1_HSIZE_T, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addIntegerAttribute: 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='HDF5_addIntegerAttribute: h5acreate_f')
call h5awrite_f(attr_id, type_id, attrValue, int([1],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addIntegerAttribute: h5awrite_f')
call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addIntegerAttribute: h5aclose_f')
call h5tclose_f(type_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addIntegerAttribute: h5tclose_f')
call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addIntegerAttribute: h5sclose_f')
end subroutine HDF5_addIntegerAttribute
The attribute interface works for single processor output and single valued attribute
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!--------------------------------------------------------------------------------------------------
!> @brief adds a Real number Attribute to the results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addRealAttribute(entity,attrLabel,attrValue)
implicit none
integer(HID_T), intent(in) :: entity
character(len=*), intent(in) :: attrLabel
real(pReal), intent(in) :: attrValue
integer(HDF5_ERR_TYPE) :: 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='HDF5_addRealAttribute: h5screate_f')
call h5tcopy_f(H5T_NATIVE_DOUBLE, type_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addRealAttribute: h5tcopy_f')
call h5tset_size_f(type_id, 8_HSIZE_T, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addRealAttribute: 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='HDF5_addRealAttribute: h5acreate_f')
call h5awrite_f(attr_id, type_id, attrValue, int([1],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addRealAttribute: h5awrite_f')
call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addRealAttribute: h5aclose_f')
call h5tclose_f(type_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addRealAttribute: h5tclose_f')
call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addRealAttribute: h5sclose_f')
end subroutine HDF5_addRealAttribute
cleaned + suggested structure to write data
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!--------------------------------------------------------------------------------------------------
!> @brief set link to object in results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_setLink(fileHandle,path,link)
use hdf5
implicit none
character(len=*), intent(in) :: path, link
integer(HID_T), intent(in) :: fileHandle
integer(HDF5_ERR_TYPE) :: hdferr
logical :: linkExists
call h5lexists_f(fileHandle, 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(fileHandle,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, fileHandle, link, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5lcreate_soft_f ('//trim(path)//' '//trim(link)//')')
planning the forwarding of the results
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cleaned + suggested structure to write data
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end subroutine HDF5_setLink
Parallel writing and reading of integer datasets working
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writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pReal with 1 dimensions
adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel)
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use numerics, only: &
worldrank, &
worldsize
adjusted variable names and added comments
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reading and writing of subroutines of datasets of different ranks
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implicit none
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real(pReal), intent(inout), dimension(:) :: dataset
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
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logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
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adjusted variable names and added comments
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(1) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(1)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
Able to read the independent datasets (outside the groups) in parallel
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call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif
#endif
myStart = int([sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:0),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
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! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
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int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_all_coll_metadata_ops_f')
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
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! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dread_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5sclose_f/memspace_id')
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end subroutine HDF5_read_pReal1
adjusted variable names and added comments
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pReal with 2 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pReal2(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
Interfacing for subroutines to identify real and integer data
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reading and writing of subroutines of datasets of different ranks
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implicit none
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real(pReal), intent(inout), dimension(:,:) :: dataset
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
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logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
Parallel writing and reading of integer datasets working
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(2) :: myStart
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
Interfacing for subroutines to identify real and integer data
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Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(2)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5pset_dxpl_mpio_f')
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal2: MPI_allreduce')
endif; endif
#endif
myStart = int([0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:1),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
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! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
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int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
Interfacing for subroutines to identify real and integer data
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5pset_all_coll_metadata_ops_f')
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5dopen_f')
Interfacing for subroutines to identify real and integer data
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5dget_space_f')
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Read and write works for all types of data in parallel with test module passed
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5sselect_hyperslab_f')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5dread_f')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
Read and write works for all types of data in parallel with test module passed
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: plist_id')
Parallel writing and reading of integer datasets working
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call h5dclose_f(dset_id, hdferr)
Read and write works for all types of data in parallel with test module passed
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5dclose_f')
Parallel writing and reading of integer datasets working
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call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
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Read and write works for all types of data in parallel with test module passed
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end subroutine HDF5_read_pReal2
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pReal with 3 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pReal3(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
adjusted variable names and added comments
2018-10-09 18:16:57 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Parallel writing and reading of integer datasets working
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real(pReal), intent(inout), dimension(:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
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logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(3) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
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Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(3)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5pset_dxpl_mpio_f')
Able to read the independent datasets (outside the groups) in parallel
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call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal3: MPI_allreduce')
endif; endif
#endif
myStart = int([0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:2),sum(readSize)]
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
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int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5pset_all_coll_metadata_ops_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5dopen_f')
adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5dread_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
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end subroutine HDF5_read_pReal3
!--------------------------------------------------------------------------------------------------
!> @brief subroutine for reading dataset of type pReal with 4 dimensions
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pReal4(loc_id,dataset,datasetName,parallel)
started read parallelization but getting errors
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use numerics, only: &
worldrank, &
worldsize
adjusted variable names and added comments
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reading and writing of subroutines of datasets of different ranks
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implicit none
Parallel writing and reading of integer datasets working
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real(pReal), intent(inout), dimension(:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
started read parallelization but getting errors
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logical, intent(in), optional :: parallel
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
started read parallelization but getting errors
2018-11-23 20:19:43 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
Parallel writing and reading of integer datasets working
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readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(4) :: myStart
started read parallelization but getting errors
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Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! determine shape of dataset
started read parallelization but getting errors
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localShape = shape(dataset)
Parallel writing and reading of integer datasets working
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if (any(localShape(1:size(localShape)) == 0)) return
started read parallelization but getting errors
2018-11-23 20:19:43 +05:30
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
started read parallelization but getting errors
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(4)
started read parallelization but getting errors
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5pset_dxpl_mpio_f')
Able to read the independent datasets (outside the groups) in parallel
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call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal4: MPI_allreduce')
started read parallelization but getting errors
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endif; endif
#endif
Parallel writing and reading of integer datasets working
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myStart = int([0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:3),sum(readSize)]
started read parallelization but getting errors
2018-11-23 20:19:43 +05:30
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5pset_all_coll_metadata_ops_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5dopen_f')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
started read parallelization but getting errors
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call h5dget_space_f(dset_id, filespace_id, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5dread_f')
started read parallelization but getting errors
2018-11-23 20:19:43 +05:30
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
started read parallelization but getting errors
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!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: plist_id')
started read parallelization but getting errors
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call h5dclose_f(dset_id, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
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end subroutine HDF5_read_pReal4
adjusted variable names and added comments
2018-10-09 18:16:57 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pReal with 5 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pReal5(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
Interfacing for subroutines to identify real and integer data
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reading and writing of subroutines of datasets of different ranks
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implicit none
Parallel writing and reading of integer datasets working
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real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(5) :: myStart
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(5)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5pset_dxpl_mpio_f')
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal5: MPI_allreduce')
endif; endif
#endif
myStart = int([0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:4),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5pset_all_coll_metadata_ops_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5dread_f')
writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
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end subroutine HDF5_read_pReal5
adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pReal with 6 dimensions
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pReal6(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
adjusted variable names and added comments
2018-10-09 18:16:57 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Parallel writing and reading of integer datasets working
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real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
logical, intent(in), optional :: parallel
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(6) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(6)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5pset_dxpl_mpio_f')
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal6: MPI_allreduce')
endif; endif
#endif
myStart = int([0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:5),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5pset_all_coll_metadata_ops_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5dread_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
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end subroutine HDF5_read_pReal6
!--------------------------------------------------------------------------------------------------
!> @brief subroutine for reading dataset of type pReal with 7 dimensions
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pReal7(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(7) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(7)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5pset_dxpl_mpio_f')
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal7: MPI_allreduce')
endif; endif
#endif
myStart = int([0,0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:6),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5pset_all_coll_metadata_ops_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5dread_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
end subroutine HDF5_read_pReal7
!--------------------------------------------------------------------------------------------------
!> @brief subroutine for reading dataset of type pInt with 1 dimensions
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_read_pInt1(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
use numerics, only: &
worldrank, &
worldsize
implicit none
integer(pInt), intent(inout), dimension(:) :: dataset
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(1) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!--------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(1)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt1: MPI_allreduce')
endif; endif
#endif
myStart = int([sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:0),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5pset_all_coll_metadata_ops_f')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, &
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5dread_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
end subroutine HDF5_read_pInt1
!--------------------------------------------------------------------------------------------------
!> @brief subroutine for reading dataset of type pInt with 2 dimensions
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_read_pInt2(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
use numerics, only: &
worldrank, &
worldsize
implicit none
integer(pInt), intent(inout), dimension(:,:) :: dataset
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(2) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!--------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(2)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt2: MPI_allreduce')
endif; endif
#endif
myStart = int([0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:1),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5pset_all_coll_metadata_ops_f')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, &
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5dread_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5sclose_f/memspace_id')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
end subroutine HDF5_read_pInt2
adjusted variable names and added comments
2018-10-09 18:16:57 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!> @brief subroutine for reading dataset of type pInt with 3 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_read_pInt3(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
Interfacing for subroutines to identify real and integer data
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reading and writing of subroutines of datasets of different ranks
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implicit none
Parallel writing and reading of integer datasets working
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integer(pInt), intent(inout), dimension(:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
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logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
Parallel writing and reading of integer datasets working
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(3) :: myStart
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Interfacing for subroutines to identify real and integer data
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Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
Interfacing for subroutines to identify real and integer data
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
Interfacing for subroutines to identify real and integer data
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(3)
Interfacing for subroutines to identify real and integer data
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Parallel writing and reading of integer datasets working
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
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call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt3: MPI_allreduce')
endif; endif
#endif
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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myStart = int([0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:2),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
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! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
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int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
Able to read the independent datasets (outside the groups) in parallel
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5pset_all_coll_metadata_ops_f')
reading and writing of subroutines of datasets of different ranks
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5dopen_f')
Interfacing for subroutines to identify real and integer data
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5dget_space_f')
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5sselect_hyperslab_f')
adjusted variable names and added comments
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, &
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5dread_f')
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5sclose_f/memspace_id')
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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end subroutine HDF5_read_pInt3
reading and writing of subroutines of datasets of different ranks
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adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pInt with 4 dimensions
adjusted variable names and added comments
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pInt4(loc_id,dataset,datasetName,parallel)
Functionality to avoid creating datasets in HDF5 of zero dimensions
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use numerics, only: &
worldrank, &
worldsize
adjusted variable names and added comments
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reading and writing of subroutines of datasets of different ranks
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implicit none
Parallel writing and reading of integer datasets working
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integer(pInt), intent(inout), dimension(:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Functionality to avoid creating datasets in HDF5 of zero dimensions
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logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
Functionality to avoid creating datasets in HDF5 of zero dimensions
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
Parallel writing and reading of integer datasets working
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integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(4) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
Fixed error with parallel write
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
Functionality to avoid creating datasets in HDF5 of zero dimensions
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!--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt)
Parallel writing and reading of integer datasets working
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readSize(worldrank+1) = localShape(4)
Functionality to avoid creating datasets in HDF5 of zero dimensions
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
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call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt4: MPI_allreduce')
Functionality to avoid creating datasets in HDF5 of zero dimensions
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endif; endif
#endif
Parallel writing and reading of integer datasets working
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myStart = int([0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:3),sum(readSize)]
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5pset_all_coll_metadata_ops_f')
Functionality to avoid creating datasets in HDF5 of zero dimensions
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!--------------------------------------------------------------------------------------------------
! open the dataset in the file
Parallel writing and reading of integer datasets working
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call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5dopen_f')
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! get the space_id of dataset in the file
Functionality to avoid creating datasets in HDF5 of zero dimensions
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call h5dget_space_f(dset_id, filespace_id, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5dget_space_f')
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5sselect_hyperslab_f')
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!--------------------------------------------------------------------------------------------------
! read
Parallel writing and reading of integer datasets working
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call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, &
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5dread_f')
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!close types, dataspaces
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
call h5pclose_f(plist_id, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: plist_id')
Functionality to avoid creating datasets in HDF5 of zero dimensions
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call h5dclose_f(dset_id, hdferr)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5sclose_f/memspace_id')
Parallel writing and reading of integer datasets working
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end subroutine HDF5_read_pInt4
adjusted variable names and added comments
2018-10-09 18:16:57 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pInt with 5 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pInt5(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Parallel writing and reading of integer datasets working
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integer(pInt), intent(inout), dimension(:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(5) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(5)
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
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call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt5: MPI_allreduce')
endif; endif
#endif
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
myStart = int([0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:4),sum(readSize)]
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5pset_all_coll_metadata_ops_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5dopen_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5dget_space_f')
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5sselect_hyperslab_f')
reading and writing of subroutines of datasets of different ranks
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, &
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5dread_f')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5sclose_f/memspace_id')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
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end subroutine HDF5_read_pInt5
reading and writing of subroutines of datasets of different ranks
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writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer
2018-09-25 20:12:43 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pInt with 6 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_read_pInt6(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer
2018-09-25 20:12:43 +05:30
reading and writing of subroutines of datasets of different ranks
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implicit none
Parallel writing and reading of integer datasets working
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integer(pInt), intent(inout), dimension(:,:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
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logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
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Parallel writing and reading of integer datasets working
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(6) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
reading and writing of subroutines of datasets of different ranks
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Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
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Combined the dataset creation and writing dataset in single subroutine. Created group for looped writing.
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(6)
reading and writing of subroutines of datasets of different ranks
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Parallel writing and reading of integer datasets working
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
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call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt6: MPI_allreduce')
endif; endif
#endif
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
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myStart = int([0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:5),sum(readSize)]
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Read and write works for all types of data in parallel with test module passed
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!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
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! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id')
Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
Able to read the independent datasets (outside the groups) in parallel
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5pset_all_coll_metadata_ops_f')
reading and writing of subroutines of datasets of different ranks
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5dopen_f')
writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5dget_space_f')
writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer
2018-09-25 20:12:43 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5sselect_hyperslab_f')
reading and writing of subroutines of datasets of different ranks
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Parallel writing and reading of integer datasets working
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!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, &
Read and write works for all types of data in parallel with test module passed
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file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5dread_f')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5sclose_f/memspace_id')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
end subroutine HDF5_read_pInt6
[skip ci] [skip sc] generic interfaces for HDF5 operations most existing HDF5 functions are only designed for writing output files and more general functionality is needed for storing the restart data
2018-10-05 12:26:06 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
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!> @brief subroutine for reading dataset of type pInt with 7 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_read_pInt7(loc_id,dataset,datasetName,parallel)
Parallel writing and reading of integer datasets working
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use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
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implicit none
Parallel writing and reading of integer datasets working
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integer(pInt), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
logical, intent(in), optional :: parallel
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(7) :: myStart
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Parallel writing and reading of integer datasets working
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
allocate(readSize(worldsize), source = 0_pInt)
readSize(worldrank+1) = localShape(7)
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt7: MPI_allreduce')
endif; endif
#endif
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
myStart = int([0,0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:6),sum(readSize)]
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
!--------------------------------------------------------------------------------------------------
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
int(localShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! set I/O mode for read operations to collective
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
Able to read the independent datasets (outside the groups) in parallel
2018-11-30 14:46:04 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5pset_all_coll_metadata_ops_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! open the dataset in the file
call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5dopen_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
! get the space_id of dataset in the file
call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5dget_space_f')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5sselect_hyperslab_f')
close all objects of type integer(HID_T) created by native hdf5 routines
2018-11-09 20:41:19 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
! read
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, &
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: plist_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5dclose_f')
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5sclose_f/filespace_id')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Parallel writing and reading of integer datasets working
2018-11-27 23:20:51 +05:30
end subroutine HDF5_read_pInt7
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
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!> @brief subroutine for writing dataset of type pReal with 1 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pReal1(loc_id,dataset,datasetName,parallel)
parallel writing for pReal
2018-11-18 14:17:50 +05:30
use numerics, only: &
worldrank, &
worldsize
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
real(pReal), intent(inout), dimension(:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
parallel writing for pReal
2018-11-18 14:17:50 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
parallel writing for pReal
2018-11-18 14:17:50 +05:30
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(1) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
parallel writing for pReal
2018-11-18 14:17:50 +05:30
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(1)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
parallel writing for pReal
2018-11-18 14:17:50 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal1: MPI_allreduce')
endif; endif
#endif
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
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myStart = int([sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:0),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dopen_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
parallel writing for pReal
2018-11-18 14:17:50 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dget_space_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
parallel writing for pReal
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call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dcreate_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5sselect_hyperslab_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dread_f')
[skip ci] [skip sc] generic interfaces for HDF5 operations most existing HDF5 functions are only designed for writing output files and more general functionality is needed for storing the restart data
2018-10-05 12:26:06 +05:30
!--------------------------------------------------------------------------------------------------
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!close types, dataspaces
parallel writing for pReal
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call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dclose_f')
parallel writing for pReal
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call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5sclose_f/filespace_id')
parallel writing for pReal
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
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Made changes with the calling signature
2018-12-14 16:05:41 +05:30
end subroutine HDF5_write_pReal1
reading and writing of subroutines of datasets of different ranks
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parallel writing for pReal
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
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!> @brief subroutine for writing dataset of type pReal with 2 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pReal2(loc_id,dataset,datasetName,parallel)
parallel writing for pReal
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use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
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implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
real(pReal), intent(inout), dimension(:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
parallel writing for pReal
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logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
parallel writing for pReal
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
parallel writing for pReal
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(2) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
2018-11-18 14:17:50 +05:30
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(2)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
parallel writing for pReal
2018-11-18 14:17:50 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal2: MPI_allreduce')
endif; endif
#endif
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
myStart = int([0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:1),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dopen_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
parallel writing for pReal
2018-11-18 14:17:50 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dget_space_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dcreate_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5sselect_hyperslab_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dread_f')
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
[skip ci] [skip sc] generic interfaces for HDF5 operations most existing HDF5 functions are only designed for writing output files and more general functionality is needed for storing the restart data
2018-10-05 12:26:06 +05:30
!--------------------------------------------------------------------------------------------------
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
!close types, dataspaces
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5pclose_f(plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: plist_id')
Interfacing for subroutines to identify real and integer data
2018-10-09 14:27:06 +05:30
call h5dclose_f(dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dclose_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5sclose_f/filespace_id')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
end subroutine HDF5_write_pReal2
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!> @brief subroutine for writing dataset of type pReal with 3 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pReal3(loc_id,dataset,datasetName,parallel)
parallel writing for pReal
2018-11-18 14:17:50 +05:30
use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
real(pReal), intent(inout), dimension(:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
parallel writing for pReal
2018-11-18 14:17:50 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
parallel writing for pReal
2018-11-18 14:17:50 +05:30
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(3) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
parallel writing for pReal
2018-11-18 14:17:50 +05:30
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(3)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
parallel writing for pReal
2018-11-18 14:17:50 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal3: MPI_allreduce')
endif; endif
#endif
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
myStart = int([0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:2),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dopen_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
parallel writing for pReal
2018-11-18 14:17:50 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dget_space_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dcreate_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5sselect_hyperslab_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5pclose_f(plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dclose_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5sclose_f/filespace_id')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
end subroutine HDF5_write_pReal3
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!> @brief subroutine for writing dataset of type pReal with 4 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pReal4(loc_id,dataset,datasetName,parallel)
parallel writing for pReal
2018-11-18 14:17:50 +05:30
use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
real(pReal), intent(inout), dimension(:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
parallel writing for pReal
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logical, intent(in), optional :: parallel
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
parallel writing for pReal
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(4) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Made changes with the calling signature
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
hdferr needs to be integer type during compile time of HDF5 library
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(4)
Made changes with the calling signature
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parallel writing for pReal
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
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call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
parallel writing for pReal
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal4: MPI_allreduce')
endif; endif
#endif
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
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myStart = int([0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:3),sum(outputSize)]
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
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! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dopen_f')
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
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call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
parallel writing for pReal
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int(globalShape,HSIZE_T))
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dget_space_f')
parallel writing for pReal
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
! create dataset
parallel writing for pReal
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call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dcreate_f')
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5sselect_hyperslab_f')
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dread_f')
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
!close types, dataspaces
parallel writing for pReal
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call h5pclose_f(plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: plist_id')
reading and writing of subroutines of datasets of different ranks
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call h5dclose_f(dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dclose_f')
parallel writing for pReal
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call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5sclose_f/filespace_id')
parallel writing for pReal
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
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end subroutine HDF5_write_pReal4
parallel writing for pReal
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
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!> @brief subroutine for writing dataset of type pReal with 5 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_write_pReal5(loc_id,dataset,datasetName,parallel)
parallel writing for pReal
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use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
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implicit none
Changed the intent of input argument of dataset to inout
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real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
parallel writing for pReal
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logical, intent(in), optional :: parallel
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
parallel writing for pReal
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(5) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
hdferr needs to be integer type during compile time of HDF5 library
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(5)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
parallel writing for pReal
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal5: MPI_allreduce')
endif; endif
#endif
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
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myStart = int([0,0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:4),sum(outputSize)]
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
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! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dopen_f')
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
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call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
parallel writing for pReal
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int(globalShape,HSIZE_T))
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dget_space_f')
parallel writing for pReal
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
! create dataset
parallel writing for pReal
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call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dcreate_f')
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5sselect_hyperslab_f')
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
parallel writing for pReal
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call h5pclose_f(plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: plist_id')
reading and writing of subroutines of datasets of different ranks
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call h5dclose_f(dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dclose_f')
parallel writing for pReal
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call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5sclose_f/filespace_id')
parallel writing for pReal
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call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
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end subroutine HDF5_write_pReal5
parallel writing for pReal
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
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!> @brief subroutine for writing dataset of type pReal with 6 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_write_pReal6(loc_id,dataset,datasetName,parallel)
parallel writing for pReal
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use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
parallel writing for pReal
2018-11-18 14:17:50 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
parallel writing for pReal
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(6) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
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allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(6)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
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#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
parallel writing for pReal
2018-11-18 14:17:50 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal6: MPI_allreduce')
endif; endif
#endif
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
myStart = int([0,0,0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:5),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dopen_f')
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
parallel writing for pReal
2018-11-18 14:17:50 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dget_space_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
parallel writing for pReal
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call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dcreate_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5sselect_hyperslab_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5pclose_f(plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dclose_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5sclose_f/filespace_id')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
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end subroutine HDF5_write_pReal6
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!> @brief subroutine for writing dataset of type pReal with 7 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pReal7(loc_id,dataset,datasetName,parallel)
parallel writing for pReal
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use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
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implicit none
Changed the intent of input argument of dataset to inout
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real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
parallel writing for pReal
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logical, intent(in), optional :: parallel
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
parallel writing for pReal
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(7) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
if (any(localShape(1:size(localShape)) == 0)) return
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(7)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
parallel writing for pReal
2018-11-18 14:17:50 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal7: MPI_allreduce')
endif; endif
#endif
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
parallel writing for pReal
2018-11-18 14:17:50 +05:30
myStart = int([0,0,0,0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:6),sum(outputSize)]
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
parallel writing for pReal
2018-11-18 14:17:50 +05:30
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dopen_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
parallel writing for pReal
2018-11-18 14:17:50 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dget_space_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
! create dataset
parallel writing for pReal
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call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dcreate_f')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5sselect_hyperslab_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
parallel writing for pReal
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!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
parallel writing for pReal
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call h5pclose_f(plist_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made hdferr < 0 and removed the unnecessary call to h5getspace in hyperslab
2018-11-21 20:40:17 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dclose_f')
parallel writing for pReal
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call h5sclose_f(filespace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5sclose_f/filespace_id')
parallel writing for pReal
2018-11-18 14:17:50 +05:30
call h5sclose_f(memspace_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
end subroutine HDF5_write_pReal7
parallel writing for pReal
2018-11-18 14:17:50 +05:30
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!> @brief subroutine for writing dataset of type pInt with 1 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pInt1(loc_id,dataset,datasetName,parallel)
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
integer(pInt), intent(inout), dimension(:) :: dataset
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(1) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
if (any(localShape(1:size(localShape)) == 0)) return
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!--------------------------------------------------------------------------------------------------
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(1)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt1: MPI_allreduce')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
endif; endif
#endif
myStart = int([sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:0),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5dopen_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5dget_space_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_INTEGER, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5dclose_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
end subroutine HDF5_write_pInt1
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!> @brief subroutine for writing dataset of type pInt with 2 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pInt2(loc_id,dataset,datasetName,parallel)
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
integer(pInt), intent(inout), dimension(:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(2) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
if (any(localShape(1:size(localShape)) == 0)) return
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(2)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt2: MPI_allreduce')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
endif; endif
#endif
myStart = int([0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:1),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5dopen_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5dget_space_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_INTEGER, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5dclose_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
end subroutine HDF5_write_pInt2
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!> @brief subroutine for writing dataset of type pInt with 3 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pInt3(loc_id,dataset,datasetName,parallel)
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
integer(pInt), intent(inout), dimension(:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(3) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
if (any(localShape(1:size(localShape)) == 0)) return
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(3)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt3: MPI_allreduce')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
endif; endif
#endif
myStart = int([0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:2),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5dopen_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5dget_space_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_INTEGER, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5dclose_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
end subroutine HDF5_write_pInt3
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!> @brief subroutine for writing dataset of type pInt with 4 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pInt4(loc_id,dataset,datasetName,parallel)
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
integer(pInt), intent(inout), dimension(:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(4) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
if (any(localShape(1:size(localShape)) == 0)) return
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(4)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt4: MPI_allreduce')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
endif; endif
#endif
myStart = int([0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:3),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5dopen_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5dget_space_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_INTEGER, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5dclose_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
end subroutine HDF5_write_pInt4
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!> @brief subroutine for writing dataset of type pInt with 5 dimensions
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
subroutine HDF5_write_pInt5(loc_id,dataset,datasetName,parallel)
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
implicit none
Changed the intent of input argument of dataset to inout
2018-11-20 16:24:51 +05:30
integer(pInt), intent(inout), dimension(:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(5) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
if (any(localShape(1:size(localShape)) == 0)) return
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(5)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
2018-11-30 22:03:30 +05:30
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt5: MPI_allreduce')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
endif; endif
#endif
myStart = int([0,0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:4),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5dopen_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5dget_space_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
! create dataset
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_INTEGER, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: plist_id')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5dclose_f')
Added the parallelized functionality for integer datatypes (works for groups?)
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call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
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end subroutine HDF5_write_pInt5
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reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
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!> @brief subroutine for writing dataset of type pInt with 6 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_write_pInt6(loc_id,dataset,datasetName,parallel)
Added the parallelized functionality for integer datatypes (works for groups?)
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use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
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implicit none
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integer(pInt), intent(inout), dimension(:,:,:,:,:,:) :: dataset
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
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logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
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integer(HDF5_ERR_TYPE) :: hdferr
Added the parallelized functionality for integer datatypes (works for groups?)
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(6) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
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!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
The attribute interface works for single processor output and single valued attribute
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if (any(localShape(1:size(localShape)) == 0)) return
Functionality to avoid creating datasets in HDF5 of zero dimensions
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Made changes with the calling signature
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
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!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
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allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(6)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5pset_dxpl_mpio_f')
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call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Made changes with the calling signature
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if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt6: MPI_allreduce')
Added the parallelized functionality for integer datatypes (works for groups?)
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endif; endif
#endif
myStart = int([0,0,0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:5),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5dopen_f')
Added the parallelized functionality for integer datatypes (works for groups?)
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!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
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call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
Added the parallelized functionality for integer datatypes (works for groups?)
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int(globalShape,HSIZE_T))
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5dget_space_f')
Added the parallelized functionality for integer datatypes (works for groups?)
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!--------------------------------------------------------------------------------------------------
! create dataset
Added the parallelized functionality for integer datatypes (works for groups?)
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call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_INTEGER, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5dread_f')
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
!close types, dataspaces
Added the parallelized functionality for integer datatypes (works for groups?)
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call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: plist_id')
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call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5dclose_f')
Added the parallelized functionality for integer datatypes (works for groups?)
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call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
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end subroutine HDF5_write_pInt6
Added the parallelized functionality for integer datatypes (works for groups?)
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!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
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!> @brief subroutine for writing dataset of type pInt with 7 dimensions
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Made changes with the calling signature
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subroutine HDF5_write_pInt7(loc_id,dataset,datasetName,parallel)
Added the parallelized functionality for integer datatypes (works for groups?)
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use numerics, only: &
worldrank, &
worldsize
reading and writing of subroutines of datasets of different ranks
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implicit none
Changed the intent of input argument of dataset to inout
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integer(pInt), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
reading and writing of subroutines of datasets of different ranks
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integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
Added the parallelized functionality for integer datatypes (works for groups?)
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logical, intent(in), optional :: parallel
reading and writing of subroutines of datasets of different ranks
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Added the parallelized functionality for integer datatypes (works for groups?)
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integer(pInt), dimension(:), allocatable :: &
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
outputSize !< contribution of all processes
integer :: ierr
hdferr needs to be integer type during compile time of HDF5 library
2018-11-20 19:56:49 +05:30
integer(HDF5_ERR_TYPE) :: hdferr
Added the parallelized functionality for integer datatypes (works for groups?)
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(7) :: myStart
Functionality to avoid creating datasets in HDF5 of zero dimensions
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!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
The attribute interface works for single processor output and single valued attribute
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if (any(localShape(1:size(localShape)) == 0)) return
Functionality to avoid creating datasets in HDF5 of zero dimensions
2018-11-26 20:08:31 +05:30
Made changes with the calling signature
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!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
Added the parallelized functionality for integer datatypes (works for groups?)
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allocate(outputSize(worldsize), source = 0_pInt)
outputSize(worldrank+1) = localShape(7)
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5pset_dxpl_mpio_f')
Read and write works for all types of data in parallel with test module passed
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call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt7: MPI_allreduce')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
endif; endif
#endif
myStart = int([0,0,0,0,0,0,sum(outputSize(1:worldrank))],HSIZE_T)
globalShape = [localShape(1:6),sum(outputSize)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5dopen_f')
Added the parallelized functionality for integer datatypes (works for groups?)
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!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
int(globalShape,HSIZE_T))
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5dget_space_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
reading and writing of subroutines of datasets of different ranks
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!--------------------------------------------------------------------------------------------------
! create dataset
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_INTEGER, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! write
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5dread_f')
reading and writing of subroutines of datasets of different ranks
2018-10-10 21:24:55 +05:30
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5pclose_f(plist_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: plist_id')
reading and writing of subroutines of datasets of different ranks
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call h5dclose_f(dset_id, hdferr)
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5dclose_f')
Added the parallelized functionality for integer datatypes (works for groups?)
2018-11-21 21:27:36 +05:30
call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5sclose_f/filespace_id')
call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5sclose_f/memspace_id')
reading and writing of subroutines of datasets of different ranks
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end subroutine HDF5_write_pInt7
number of helper functions for HDF5
2018-08-03 12:23:37 +05:30
keep only general functionality in HDF5_results
2018-11-15 11:37:59 +05:30
end module HDF5_Utilities
Made changes with the calling signature
2018-12-14 16:05:41 +05:30
The attribute interface works for single processor output and single valued attribute
2018-12-15 21:51:03 +05:30
Made changes with the calling signature
2018-12-14 16:05:41 +05:30