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writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer

This commit is contained in:
Vitesh Shah 2018-09-25 16:42:43 +02:00
parent 8e63cb3897
commit b71896d4b6
4 changed files with 268 additions and 9 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit aeae4513b1ffb43b949399c12bae27fc6abb6f29
Subproject commit 50eb21714e2f501b111bb62096ebb6a5bfc6708a

3
examples/SpectralMethod/Polycrystal/tensionX.load
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@ -1,2 +1 @@
fdot 1.0e-3 0 0 0 * 0 0 0 * stress * * * * 0 * * * 0 time 10 incs 40 freq 4
fdot 1.0e-3 0 0 0 * 0 0 0 * stress * * * * 0 * * * 0 time 60 incs 60
fdot 1.0e-3 0 0 0 * 0 0 0 * stress * * * * 0 * * * 0 time 0.001 incs 2 restart 1

26
src/CPFEM2.f90 Normal file → Executable file
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@ -247,8 +247,13 @@ subroutine CPFEM_age()
HDF5_createFile, &
HDF5_closeFile, &
HDF5_closeGroup, &
HDF5_addGroup2
use HDF5
HDF5_addGroup2, &
HDF5_writeScalarDataset3, &
HDF5_writeScalarDataset4, &
HDF5_writeScalarDataset5, &
HDF5_writeScalarDataset7, &
HDF5_addScalarDataset2
use hdf5
use DAMASK_interface, only: &
getSolverJobName
@ -257,6 +262,8 @@ subroutine CPFEM_age()
integer(pInt) :: i, k, l, m, ph, homog, mySource
character(len=32) :: rankStr
integer(HID_T) :: fileHandle
integer :: hdferr
integer(HSIZE_T) :: hdfsize
if (iand(debug_level(debug_CPFEM), debug_levelBasic) /= 0_pInt) &
write(6,'(a)') '<< CPFEM >> aging states'
@ -291,8 +298,19 @@ if (restartWrite) then
write(rankStr,'(a1,i0)')'_',worldrank
fileHandle = HDF5_createFile(trim(getSolverJobName())//trim(rankStr)//'.hdf5_restart')
call HDF5_closeGroup(HDF5_addGroup2(fileHandle,'HelloWorld'))
!call HDF5_closeGroup(HDF5_addGroup2(fileHandle,'recordedPhase'))
!hdfsize = size(material_phase)
!call h5dwrite_f(HDF5_addGroup2(fileHandle,'recordedPhase'), H5T_NATIVE_INTEGER, material_phase, hdfsize, hdferr)
call HDF5_addScalarDataset2(fileHandle,shape(material_phase),'recordedPhase')
call HDF5_writeScalarDataset3(fileHandle,real(material_phase,pReal),'recordedPhase',shape(material_phase))
call HDF5_addScalarDataset2(fileHandle,shape(crystallite_F0),'convergedF')
call HDF5_writeScalarDataset5(fileHandle,real(crystallite_F0,pReal),'convergedF',shape(crystallite_F0))
call HDF5_addScalarDataset2(fileHandle,shape(crystallite_Fp0),'convergedFp')
call HDF5_writeScalarDataset5(fileHandle,real(crystallite_Fp0,pReal),'convergedFp',shape(crystallite_Fp0))
!call HDF5_closeGroup(HDF5_addGroup2(fileHandle,'recordedPhase'))
call HDF5_closeFile(fileHandle)
call IO_write_jobRealFile(777,'recordedPhase'//trim(rankStr),size(material_phase))

246
src/HDF5_utilities.f90 Normal file → Executable file
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@ -30,7 +30,9 @@ module HDF5_Utilities
HDF5_removeLink, &
HDF5_createFile, &
HDF5_closeFile, &
HDF5_addGroup2
HDF5_addGroup2, HDF5_addScalarDataset2, HDF5_writeScalarDataset3, HDF5_writeScalarDataset4, HDF5_writeScalarDataset5, &
HDF5_writeScalarDataset7
contains
subroutine HDF5_Utilities_init
@ -1047,6 +1049,7 @@ subroutine HDF5_backwardMappingCrystallite(crystalliteAt,crystmemberAt,crystalli
end subroutine HDF5_backwardMappingCrystallite
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique cell to node mapping
!--------------------------------------------------------------------------------------------------
@ -1090,7 +1093,6 @@ end subroutine HDF5_mappingCells
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
@ -1340,6 +1342,213 @@ subroutine HDF5_writeScalarDataset(group,dataset,label,SIunit,dataspace_size,mpi
end subroutine HDF5_writeScalarDataset
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_writeScalarDataset3(group,dataset,label,dataspace_size)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
character(len=*), intent(in) :: label
integer(pInt), intent(in),dimension(:) :: dataspace_size
real(pReal), intent(in), dimension(:,:,:) :: dataset
integer :: hdferr
integer(HID_T) :: dset_id, space_id, memspace, plist_id
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
call h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dopen_f')
! Define and select hyperslabs
counter = size(dataset) ! how big i am
fileOffset = 0 ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dget_space_f')
!call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
!if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5sselect_hyperslab_f')
! Create property list for collective dataset write
#ifdef PETSc
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f')
#endif
! Write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int(dataspace_size,HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace)!, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dwrite_f')
call h5sclose_f(space_id, hdferr)
call h5sclose_f(memspace, hdferr)
call h5dclose_f(dset_id, hdferr)
call h5pclose_f(plist_id, hdferr)
end subroutine HDF5_writeScalarDataset3
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_writeScalarDataset4(group,dataset,label,dataspace_size)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
character(len=*), intent(in) :: label
integer(pInt), intent(in),dimension(:) :: dataspace_size
real(pReal), intent(in), dimension(:,:,:,:) :: dataset
integer :: hdferr
integer(HID_T) :: dset_id, space_id, memspace, plist_id
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
call h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dopen_f')
! Define and select hyperslabs
counter = size(dataset) ! how big i am
fileOffset = 0 ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dget_space_f')
!call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
!if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5sselect_hyperslab_f')
! Create property list for collective dataset write
#ifdef PETSc
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f')
#endif
! Write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int(dataspace_size,HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace)!, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dwrite_f')
call h5sclose_f(space_id, hdferr)
call h5sclose_f(memspace, hdferr)
call h5dclose_f(dset_id, hdferr)
call h5pclose_f(plist_id, hdferr)
end subroutine HDF5_writeScalarDataset4
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_writeScalarDataset5(group,dataset,label,dataspace_size)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
character(len=*), intent(in) :: label
integer(pInt), intent(in),dimension(:) :: dataspace_size
real(pReal), intent(in), dimension(:,:,:,:,:) :: dataset
integer :: hdferr
integer(HID_T) :: dset_id, space_id, memspace, plist_id
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
call h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dopen_f')
! Define and select hyperslabs
counter = size(dataset) ! how big i am
fileOffset = 0 ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dget_space_f')
!call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
!if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5sselect_hyperslab_f')
! Create property list for collective dataset write
#ifdef PETSc
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f')
#endif
! Write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int(dataspace_size,HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace)!, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dwrite_f')
call h5sclose_f(space_id, hdferr)
call h5sclose_f(memspace, hdferr)
call h5dclose_f(dset_id, hdferr)
call h5pclose_f(plist_id, hdferr)
end subroutine HDF5_writeScalarDataset5
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_writeScalarDataset7(group,dataset,label,dataspace_size)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
character(len=*), intent(in) :: label
integer(pInt), intent(in),dimension(:) :: dataspace_size
real(pReal), intent(in), dimension(:,:,:,:,:,:,:) :: dataset
integer :: hdferr
integer(HID_T) :: dset_id, space_id, memspace, plist_id
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
call h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dopen_f')
! Define and select hyperslabs
counter = size(dataset) ! how big i am
fileOffset = 0 ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dget_space_f')
!call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
!if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5sselect_hyperslab_f')
! Create property list for collective dataset write
#ifdef PETSc
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f')
#endif
! Write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int(dataspace_size,HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace)!, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dwrite_f')
call h5sclose_f(space_id, hdferr)
call h5sclose_f(memspace, hdferr)
call h5dclose_f(dset_id, hdferr)
call h5pclose_f(plist_id, hdferr)
end subroutine HDF5_writeScalarDataset7
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
@ -1375,6 +1584,39 @@ subroutine HDF5_addScalarDataset(group,nnodes,label,SIunit)
end subroutine HDF5_addScalarDataset
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addScalarDataset2(fileHandle,dataShape,label)
use hdf5
implicit none
integer(HID_T), intent(in) :: fileHandle
integer(pInt), dimension(:), intent(in) :: dataShape
character(len=*), intent(in) :: label
integer :: hdferr
integer(HID_T) :: space_id, dset_id
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(size(dataShape), int(dataShape,HSIZE_T), space_id, hdferr, &
int(dataShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(fileHandle, trim(label),H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dclose_f')
call h5sclose_f(space_id, hdferr)
end subroutine HDF5_addScalarDataset2
!--------------------------------------------------------------------------------------------------