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also modularize write

This commit is contained in:
Martin Diehl 2019-02-09 09:01:37 +01:00
parent c668260c37
commit d934f2b141
1 changed files with 172 additions and 359 deletions
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531
src/HDF5_utilities.f90
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@ -1204,9 +1204,6 @@ end subroutine HDF5_read_pInt7
!> @brief subroutine for writing dataset of type pReal with 1 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_pReal1(loc_id,dataset,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:) :: dataset
@ -1215,61 +1212,27 @@ subroutine HDF5_write_pReal1(loc_id,dataset,datasetName,parallel)
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
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(1) :: myStart
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
localShape, & !< shape of the dataset (this process)
globalShape !< shape of the dataset (all processes)
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
localShape = int(shape(dataset),HSIZE_T)
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)
!--------------------------------------------------------------------------------------------------
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)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal1: MPI_allreduce')
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))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
int(globalShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: 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_pReal1: h5sselect_hyperslab_f')
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,.false.)
endif
!--------------------------------------------------------------------------------------------------
! write
@ -1295,9 +1258,6 @@ end subroutine HDF5_write_pReal1
!> @brief subroutine for writing dataset of type pReal with 2 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_pReal2(loc_id,dataset,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:,:) :: dataset
@ -1306,61 +1266,27 @@ subroutine HDF5_write_pReal2(loc_id,dataset,datasetName,parallel)
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
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(2) :: myStart
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
localShape, & !< shape of the dataset (this process)
globalShape !< shape of the dataset (all processes)
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
localShape = int(shape(dataset),HSIZE_T)
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)
!--------------------------------------------------------------------------------------------------
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)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal2: MPI_allreduce')
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))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
int(globalShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: 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_pReal2: h5sselect_hyperslab_f')
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,.false.)
endif
!--------------------------------------------------------------------------------------------------
! write
@ -1386,9 +1312,6 @@ end subroutine HDF5_write_pReal2
!> @brief subroutine for writing dataset of type pReal with 3 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_pReal3(loc_id,dataset,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:,:,:) :: dataset
@ -1397,61 +1320,27 @@ subroutine HDF5_write_pReal3(loc_id,dataset,datasetName,parallel)
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
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(3) :: myStart
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
localShape, & !< shape of the dataset (this process)
globalShape !< shape of the dataset (all processes)
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
localShape = int(shape(dataset),HSIZE_T)
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)
!--------------------------------------------------------------------------------------------------
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)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal3: MPI_allreduce')
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))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
int(globalShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: 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_pReal3: h5sselect_hyperslab_f')
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,.false.)
endif
!--------------------------------------------------------------------------------------------------
! write
@ -1477,9 +1366,6 @@ end subroutine HDF5_write_pReal3
!> @brief subroutine for writing dataset of type pReal with 4 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_pReal4(loc_id,dataset,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:,:,:,:) :: dataset
@ -1488,61 +1374,27 @@ subroutine HDF5_write_pReal4(loc_id,dataset,datasetName,parallel)
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
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(4) :: myStart
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
localShape, & !< shape of the dataset (this process)
globalShape !< shape of the dataset (all processes)
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
localShape = int(shape(dataset),HSIZE_T)
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)
!--------------------------------------------------------------------------------------------------
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)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal4: MPI_allreduce')
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))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
int(globalShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: 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_pReal4: h5sselect_hyperslab_f')
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,.false.)
endif
!--------------------------------------------------------------------------------------------------
! write
@ -1568,9 +1420,6 @@ end subroutine HDF5_write_pReal4
!> @brief subroutine for writing dataset of type pReal with 5 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_pReal5(loc_id,dataset,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset
@ -1579,61 +1428,27 @@ subroutine HDF5_write_pReal5(loc_id,dataset,datasetName,parallel)
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
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(5) :: myStart
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
localShape, & !< shape of the dataset (this process)
globalShape !< shape of the dataset (all processes)
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
localShape = int(shape(dataset),HSIZE_T)
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)
!--------------------------------------------------------------------------------------------------
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)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal5: MPI_allreduce')
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))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
int(globalShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: 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_pReal5: h5sselect_hyperslab_f')
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,.false.)
endif
!--------------------------------------------------------------------------------------------------
! write
@ -1659,9 +1474,6 @@ end subroutine HDF5_write_pReal5
!> @brief subroutine for writing dataset of type pReal with 6 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_pReal6(loc_id,dataset,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset
@ -1670,61 +1482,27 @@ subroutine HDF5_write_pReal6(loc_id,dataset,datasetName,parallel)
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
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(6) :: myStart
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
localShape, & !< shape of the dataset (this process)
globalShape !< shape of the dataset (all processes)
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
localShape = int(shape(dataset),HSIZE_T)
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)
!--------------------------------------------------------------------------------------------------
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)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal6: MPI_allreduce')
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))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
int(globalShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: 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_pReal6: h5sselect_hyperslab_f')
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,.false.)
endif
!--------------------------------------------------------------------------------------------------
! write
@ -1750,9 +1528,6 @@ end subroutine HDF5_write_pReal6
!> @brief subroutine for writing dataset of type pReal with 7 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_pReal7(loc_id,dataset,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
@ -1761,61 +1536,27 @@ subroutine HDF5_write_pReal7(loc_id,dataset,datasetName,parallel)
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
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(7) :: myStart
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
localShape, & !< shape of the dataset (this process)
globalShape !< shape of the dataset (all processes)
!-------------------------------------------------------------------------------------------------
! determine shape of dataset
localShape = shape(dataset)
localShape = int(shape(dataset),HSIZE_T)
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)
!--------------------------------------------------------------------------------------------------
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)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal7: MPI_allreduce')
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))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), int(globalShape,HSIZE_T), filespace_id, hdferr, &
int(globalShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: 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_pReal7: h5sselect_hyperslab_f')
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,.false.)
endif
!--------------------------------------------------------------------------------------------------
! write
@ -2513,8 +2254,7 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, &
int(localShape,HSIZE_T))
call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id')
!--------------------------------------------------------------------------------------------------
! set I/O mode for read operations to collective
@ -2538,6 +2278,79 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
end subroutine initialize_read
!--------------------------------------------------------------------------------------------------
!> @brief subroutine for writing dataset of type pReal with 1 dimensions
!--------------------------------------------------------------------------------------------------
subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
use numerics, only: &
worldrank, &
worldsize
implicit none
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(HSIZE_T), intent(in), dimension(:) :: &
localShape
integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: &
myStart, &
globalShape !< shape of the dataset (all processes)
integer(pInt), dimension(worldsize) :: &
outputSize !< contribution of all processes
integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!--------------------------------------------------------------------------------------------------
outputSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc
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_write_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_write_pReal1: MPI_allreduce')
endif
#endif
myStart = int(0,HSIZE_T)
myStart(ubound(myStart)) = int(sum(outputSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(outputSize),HSIZE_T)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dopen_f')
!--------------------------------------------------------------------------------------------------
! create dataspace in file (global shape)
call h5screate_simple_f(size(globalShape), globalShape, filespace_id, hdferr, globalShape)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dget_space_f')
!--------------------------------------------------------------------------------------------------
! create dataset
call h5dcreate_f(loc_id, trim(datasetName), H5T_NATIVE_DOUBLE, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: 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, localShape, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5sselect_hyperslab_f')
end subroutine initialize_write
end module HDF5_Utilities