From 36662f84192ec8a6131b6d09d6d582c2326d8f98 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 9 Feb 2019 05:38:24 +0100 Subject: [PATCH] more generic formulation (works for all dimensions) --- src/HDF5_utilities.f90 | 446 ++++++++++++++++++++--------------------- 1 file changed, 223 insertions(+), 223 deletions(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index 2a05f101c..2a302d6ed 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(1) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 @@ -482,8 +482,8 @@ subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel) ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(1) + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then 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') endif; endif #endif - myStart = int([sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:0),sum(readSize)] + myStart = int(0,HSIZE_T) + 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 - 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') !-------------------------------------------------------------------------------------------------- @@ -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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(2) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 @@ -577,18 +578,19 @@ subroutine HDF5_read_pReal2(loc_id,dataset,datasetName,parallel) ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(2) + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5pset_dxpl_mpio_f') + 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 - 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 - myStart = int([0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:1),sum(readSize)] + myStart = int(0,HSIZE_T) + 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(3) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 @@ -672,18 +674,19 @@ subroutine HDF5_read_pReal3(loc_id,dataset,datasetName,parallel) ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(3) + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5pset_dxpl_mpio_f') + 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 - 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 - myStart = int([0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:2),sum(readSize)] + myStart = int(0,HSIZE_T) + 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(4) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 @@ -767,18 +770,19 @@ subroutine HDF5_read_pReal4(loc_id,dataset,datasetName,parallel) ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(4) + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_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 - 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 - myStart = int([0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:3),sum(readSize)] + myStart = int(0,HSIZE_T) + 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(5) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 @@ -862,18 +866,19 @@ subroutine HDF5_read_pReal5(loc_id,dataset,datasetName,parallel) ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(5) + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5pset_dxpl_mpio_f') + 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 - 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 - myStart = int([0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:4),sum(readSize)] + myStart = int(0,HSIZE_T) + 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(6) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 @@ -957,18 +962,19 @@ subroutine HDF5_read_pReal6(loc_id,dataset,datasetName,parallel) ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(6) + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5pset_dxpl_mpio_f') + 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 - 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 - myStart = int([0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:5),sum(readSize)] + myStart = int(0,HSIZE_T) + 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(7) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 @@ -1052,18 +1058,19 @@ subroutine HDF5_read_pReal7(loc_id,dataset,datasetName,parallel) ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(7) + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5pset_dxpl_mpio_f') + 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 - 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 - myStart = int([0,0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:6),sum(readSize)] + myStart = int(0,HSIZE_T) + 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(1) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) -!-------------------------------------------------------------------------------------------------- +!------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(1) - + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5pset_dxpl_mpio_f') - call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,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 (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 + if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') endif; endif #endif - - myStart = int([sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:0),sum(readSize)] + myStart = int(0,HSIZE_T) + myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) + globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(2) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) -!-------------------------------------------------------------------------------------------------- +!------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(2) - + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5pset_dxpl_mpio_f') - call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,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 (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 + if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') endif; endif #endif - - myStart = int([0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:1),sum(readSize)] + myStart = int(0,HSIZE_T) + myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) + globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(3) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) -!-------------------------------------------------------------------------------------------------- +!------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(3) - + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5pset_dxpl_mpio_f') - call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,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 (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 + if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') endif; endif #endif - - myStart = int([0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:2),sum(readSize)] + myStart = int(0,HSIZE_T) + myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) + globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(4) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) -!-------------------------------------------------------------------------------------------------- +!------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(4) - + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: 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 - if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pInt4: MPI_allreduce') + 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 + if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') endif; endif #endif - - myStart = int([0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:3),sum(readSize)] + myStart = int(0,HSIZE_T) + myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) + globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(5) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) -!-------------------------------------------------------------------------------------------------- +!------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(5) - + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5pset_dxpl_mpio_f') - call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,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 (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 + if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') endif; endif #endif - - myStart = int([0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:4),sum(readSize)] + myStart = int(0,HSIZE_T) + myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) + globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(6) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) -!-------------------------------------------------------------------------------------------------- +!------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(6) - + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5pset_dxpl_mpio_f') - call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,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 (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 + if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') endif; endif #endif - - myStart = int([0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:5),sum(readSize)] + myStart = int(0,HSIZE_T) + myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) + globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! 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 logical, intent(in), optional :: parallel - - integer(pInt), dimension(:), allocatable :: & - globalShape, & !< shape of the dataset (all processes) - localShape, & !< shape of the dataset (this process) - readSize !< contribution of all processes + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(7) :: myStart + 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) - if (any(localShape(1:size(localShape)) == 0)) return + localShape = int(shape(dataset),HSIZE_T) + 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 call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) -!-------------------------------------------------------------------------------------------------- +!------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) !-------------------------------------------------------------------------------------------------- - allocate(readSize(worldsize), source = 0_pInt) - readSize(worldrank+1) = localShape(7) - + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5pset_dxpl_mpio_f') - call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_LONG,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 (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 + if (ierr /= 0) call IO_error(894_pInt,ext_msg='HDF5_read_pReal1: MPI_allreduce') endif; endif #endif - - myStart = int([0,0,0,0,0,0,sum(readSize(1:worldrank))],HSIZE_T) - globalShape = [localShape(1:6),sum(readSize)] + myStart = int(0,HSIZE_T) + myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T) + globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! create dataspace in memory (local shape)