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DAMASK_EICMD
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more generic formulation (works for all dimensions)

This commit is contained in:
Martin Diehl 2019-02-09 05:38:24 +01:00
parent d13b0f1164
commit 36662f8419
1 changed files with 223 additions and 223 deletions
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src/HDF5_utilities.f90
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@ -459,20 +459,20 @@ subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
@ -482,8 +482,8 @@ subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel)
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(1) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
@ -492,8 +492,9 @@ subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel)
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int([sum(readSize(1:worldrank))],HSIZE_T) myStart = int(0,HSIZE_T)
globalShape = [localShape(1:0),sum(readSize)] myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -517,7 +518,7 @@ subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file ! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5sselect_hyperslab_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5sselect_hyperslab_f')
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -554,20 +555,20 @@ subroutine HDF5_read_pReal2(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
@ -577,18 +578,19 @@ subroutine HDF5_read_pReal2(loc_id,dataset,datasetName,parallel)
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(2) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal2: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int([0,sum(readSize(1:worldrank))],HSIZE_T) myStart = int(0,HSIZE_T)
globalShape = [localShape(1:1),sum(readSize)] myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -649,20 +651,20 @@ subroutine HDF5_read_pReal3(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
@ -672,18 +674,19 @@ subroutine HDF5_read_pReal3(loc_id,dataset,datasetName,parallel)
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(3) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal3: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int([0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart = int(0,HSIZE_T)
globalShape = [localShape(1:2),sum(readSize)] myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -744,20 +747,20 @@ subroutine HDF5_read_pReal4(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
@ -767,18 +770,19 @@ subroutine HDF5_read_pReal4(loc_id,dataset,datasetName,parallel)
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(4) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal4: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int([0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart = int(0,HSIZE_T)
globalShape = [localShape(1:3),sum(readSize)] myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -839,20 +843,20 @@ subroutine HDF5_read_pReal5(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
@ -862,18 +866,19 @@ subroutine HDF5_read_pReal5(loc_id,dataset,datasetName,parallel)
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(5) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal5: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int([0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart = int(0,HSIZE_T)
globalShape = [localShape(1:4),sum(readSize)] myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -934,20 +939,20 @@ subroutine HDF5_read_pReal6(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
@ -957,18 +962,19 @@ subroutine HDF5_read_pReal6(loc_id,dataset,datasetName,parallel)
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(6) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal6: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int([0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart = int(0,HSIZE_T)
globalShape = [localShape(1:5),sum(readSize)] myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -1029,20 +1035,20 @@ subroutine HDF5_read_pReal7(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
@ -1052,18 +1058,19 @@ subroutine HDF5_read_pReal7(loc_id,dataset,datasetName,parallel)
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(7) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal7: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int([0,0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart = int(0,HSIZE_T)
globalShape = [localShape(1:6),sum(readSize)] myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -1124,43 +1131,42 @@ subroutine HDF5_read_pInt1(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(1) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt1: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int(0,HSIZE_T)
myStart = int([sum(readSize(1:worldrank))],HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:0),sum(readSize)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
@ -1221,43 +1227,42 @@ subroutine HDF5_read_pInt2(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(2) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt2: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int(0,HSIZE_T)
myStart = int([0,sum(readSize(1:worldrank))],HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:1),sum(readSize)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
@ -1318,43 +1323,42 @@ subroutine HDF5_read_pInt3(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(3) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt3: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int(0,HSIZE_T)
myStart = int([0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:2),sum(readSize)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
@ -1415,43 +1419,42 @@ subroutine HDF5_read_pInt4(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(4) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt4: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int(0,HSIZE_T)
myStart = int([0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:3),sum(readSize)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
@ -1512,43 +1515,42 @@ subroutine HDF5_read_pInt5(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(5) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt5: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int(0,HSIZE_T)
myStart = int([0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:4),sum(readSize)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
@ -1609,43 +1611,42 @@ subroutine HDF5_read_pInt6(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(6) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt6: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int(0,HSIZE_T)
myStart = int([0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:5),sum(readSize)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
@ -1706,43 +1707,42 @@ subroutine HDF5_read_pInt7(loc_id,dataset,datasetName,parallel)
character(len=*), intent(in) :: datasetName !< name of the dataset in the file character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel logical, intent(in), optional :: parallel
integer(pInt), dimension(worldsize) :: &
integer(pInt), dimension(:), allocatable :: & readSize !< contribution of all processes
globalShape, & !< shape of the dataset (all processes)
localShape, & !< shape of the dataset (this process)
readSize !< contribution of all processes
integer :: ierr integer :: ierr
integer(HDF5_ERR_TYPE) :: hdferr integer(HDF5_ERR_TYPE) :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_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 ! determine shape of dataset
localShape = shape(dataset) localShape = int(shape(dataset),HSIZE_T)
if (any(localShape(1:size(localShape)) == 0)) return if (any(localShape(1:size(localShape)) == 0)) return ! ToDo: Correct? Seems to result in a deadlock for MPI if my processor has nothing to read
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties ! creating a property list for transfer properties
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
allocate(readSize(worldsize), source = 0_pInt) readSize = 0_pInt
readSize(worldrank+1) = localShape(7) readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt)
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5pset_dxpl_mpio_f') if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_dxpl_mpio_f')
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt7: MPI_allreduce') if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce')
endif; endif endif; endif
#endif #endif
myStart = int(0,HSIZE_T)
myStart = int([0,0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:6),sum(readSize)] globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)