From c668260c37bfeb0407c85bff3a47d5e284651d44 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 9 Feb 2019 08:05:29 +0100 Subject: [PATCH] avoiding code duplication --- src/HDF5_utilities.f90 | 1030 ++++++++++------------------------------ 1 file changed, 259 insertions(+), 771 deletions(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index 2a302d6ed..39cca9502 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -449,9 +449,6 @@ end subroutine HDF5_setLink !> @brief subroutine for reading dataset of type pReal with 1 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none real(pReal), intent(inout), dimension(:) :: dataset @@ -459,9 +456,7 @@ 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(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(size(shape(dataset))) :: & @@ -469,65 +464,28 @@ subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_all_coll_metadata_ops_f') -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dread_f') -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- !close types, dataspaces call h5pclose_f(plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: plist_id') @@ -545,9 +503,6 @@ end subroutine HDF5_read_pReal1 !> @brief subroutine for reading dataset of type pReal with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal2(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none real(pReal), intent(inout), dimension(:,:) :: dataset @@ -555,9 +510,7 @@ 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(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(size(shape(dataset))) :: & @@ -565,59 +518,22 @@ subroutine HDF5_read_pReal2(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5pset_all_coll_metadata_ops_f') -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal2: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -641,9 +557,6 @@ end subroutine HDF5_read_pReal2 !> @brief subroutine for reading dataset of type pReal with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal3(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none real(pReal), intent(inout), dimension(:,:,:) :: dataset @@ -651,9 +564,7 @@ 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(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(size(shape(dataset))) :: & @@ -661,59 +572,22 @@ subroutine HDF5_read_pReal3(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5pset_all_coll_metadata_ops_f') -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal3: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -737,9 +611,6 @@ end subroutine HDF5_read_pReal3 !> @brief subroutine for reading dataset of type pReal with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal4(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none real(pReal), intent(inout), dimension(:,:,:,:) :: dataset @@ -747,9 +618,7 @@ 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(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(size(shape(dataset))) :: & @@ -757,59 +626,22 @@ subroutine HDF5_read_pReal4(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5pset_all_coll_metadata_ops_f') -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal4: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -833,9 +665,6 @@ end subroutine HDF5_read_pReal4 !> @brief subroutine for reading dataset of type pReal with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal5(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset @@ -843,9 +672,7 @@ 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(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(size(shape(dataset))) :: & @@ -853,59 +680,22 @@ subroutine HDF5_read_pReal5(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5pset_all_coll_metadata_ops_f') -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal5: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -929,9 +719,6 @@ end subroutine HDF5_read_pReal5 !> @brief subroutine for reading dataset of type pReal with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal6(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset @@ -939,9 +726,7 @@ 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(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(size(shape(dataset))) :: & @@ -949,59 +734,22 @@ subroutine HDF5_read_pReal6(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5pset_all_coll_metadata_ops_f') -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal6: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1025,9 +773,6 @@ end subroutine HDF5_read_pReal6 !> @brief subroutine for reading dataset of type pReal with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal7(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset @@ -1035,9 +780,7 @@ 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(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(size(shape(dataset))) :: & @@ -1045,59 +788,22 @@ subroutine HDF5_read_pReal7(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5pset_all_coll_metadata_ops_f') -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal7: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1121,9 +827,6 @@ end subroutine HDF5_read_pReal7 !> @brief subroutine for reading dataset of type pInt with 1 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt1(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none integer(pInt), intent(inout), dimension(:) :: dataset @@ -1131,9 +834,7 @@ 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(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(size(shape(dataset))) :: & @@ -1141,59 +842,22 @@ subroutine HDF5_read_pInt1(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5pset_all_coll_metadata_ops_f') - -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt1: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, & file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1217,9 +881,6 @@ end subroutine HDF5_read_pInt1 !> @brief subroutine for reading dataset of type pInt with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt2(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none integer(pInt), intent(inout), dimension(:,:) :: dataset @@ -1227,9 +888,7 @@ 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(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(size(shape(dataset))) :: & @@ -1237,59 +896,22 @@ subroutine HDF5_read_pInt2(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5pset_all_coll_metadata_ops_f') - -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt2: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, & file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1313,9 +935,6 @@ end subroutine HDF5_read_pInt2 !> @brief subroutine for reading dataset of type pInt with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt3(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none integer(pInt), intent(inout), dimension(:,:,:) :: dataset @@ -1323,9 +942,7 @@ 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(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(size(shape(dataset))) :: & @@ -1333,59 +950,22 @@ subroutine HDF5_read_pInt3(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5pset_all_coll_metadata_ops_f') - -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt3: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, & file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1409,9 +989,6 @@ end subroutine HDF5_read_pInt3 !> @brief subroutine for reading dataset of type pInt with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt4(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none integer(pInt), intent(inout), dimension(:,:,:,:) :: dataset @@ -1419,9 +996,7 @@ 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(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(size(shape(dataset))) :: & @@ -1429,59 +1004,22 @@ subroutine HDF5_read_pInt4(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5pset_all_coll_metadata_ops_f') - -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt4: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, & file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1505,9 +1043,6 @@ end subroutine HDF5_read_pInt4 !> @brief subroutine for reading dataset of type pInt with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt5(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:) :: dataset @@ -1515,9 +1050,7 @@ 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(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(size(shape(dataset))) :: & @@ -1525,59 +1058,22 @@ subroutine HDF5_read_pInt5(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5pset_all_coll_metadata_ops_f') - -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt5: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, & file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1601,9 +1097,6 @@ end subroutine HDF5_read_pInt5 !> @brief subroutine for reading dataset of type pInt with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt6(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:,:) :: dataset @@ -1611,9 +1104,7 @@ 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(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(size(shape(dataset))) :: & @@ -1621,59 +1112,22 @@ subroutine HDF5_read_pInt6(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5pset_all_coll_metadata_ops_f') - -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt6: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, & file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -1697,9 +1151,6 @@ end subroutine HDF5_read_pInt6 !> @brief subroutine for reading dataset of type pInt with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt7(loc_id,dataset,datasetName,parallel) - use numerics, only: & - worldrank, & - worldsize implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset @@ -1707,9 +1158,7 @@ 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(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(size(shape(dataset))) :: & @@ -1717,59 +1166,22 @@ subroutine HDF5_read_pInt7(loc_id,dataset,datasetName,parallel) localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) -!------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! determine shape of dataset 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 + if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) -!------------------------------------------------------------------------------------------------- -! creating a property list for transfer properties - call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) + if (present(parallel)) then + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + else + call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,.false.) + endif -!------------------------------------------------------------------------------------------------- -! creating a property list for data access properties - call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) -!-------------------------------------------------------------------------------------------------- - 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_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,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) - call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & - int(localShape,HSIZE_T)) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt{}: h5screate_simple_f/memspace_id') -!-------------------------------------------------------------------------------------------------- -! set I/O mode for read operations to collective - call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5pset_all_coll_metadata_ops_f') - -!-------------------------------------------------------------------------------------------------- -! open the dataset in the file - call h5dopen_f(loc_id,datasetName,dset_id,hdferr,dapl_id = aplist_id) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5dopen_f') - -!-------------------------------------------------------------------------------------------------- -! get the space_id of dataset in the file - call h5dget_space_f(dset_id, filespace_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5dget_space_f') - -!-------------------------------------------------------------------------------------------------- -! select a hyperslab (the portion of the current process) in the file - call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, int(localShape,HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pInt7: h5sselect_hyperslab_f') - -!-------------------------------------------------------------------------------------------------- +!--------------------------------------------------------------------------------------------------- ! read call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr, & file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) @@ -3050,6 +2462,82 @@ subroutine HDF5_write_pInt7(loc_id,dataset,datasetName,parallel) end subroutine HDF5_write_pInt7 +!-------------------------------------------------------------------------------------------------- +!> @brief subroutine for reading dataset of type pReal with 1 dimensions +!-------------------------------------------------------------------------------------------------- +subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & + myStart, globalShape, & + loc_id,localShape,datasetName,parallel) + use numerics, only: & + worldrank, & + worldsize + + implicit none + integer(HID_T), intent(in) :: loc_id !< file or group handle + character(len=*), intent(in) :: datasetName !< name of the dataset in the file + logical, intent(in), optional :: parallel + + integer(pInt), dimension(worldsize) :: & + readSize !< contribution of all processes + integer :: ierr + integer(HDF5_ERR_TYPE) :: hdferr + integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id + integer(HSIZE_T), intent(in), dimension(:) :: & + localShape + integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: & + myStart, & + globalShape !< shape of the dataset (all processes) + +!------------------------------------------------------------------------------------------------- +! 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) +!-------------------------------------------------------------------------------------------------- + readSize = 0_pInt + readSize(worldrank+1) = int(localShape(ubound(localShape,1)),pInt) +#ifdef PETSc + if (parallel) then + call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_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 + 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) + call h5screate_simple_f(size(localShape), int(localShape,HSIZE_T), memspace_id, hdferr, & + int(localShape,HSIZE_T)) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal{}: h5screate_simple_f/memspace_id') +!-------------------------------------------------------------------------------------------------- +! set I/O mode for read operations to collective + call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5pset_all_coll_metadata_ops_f') +!-------------------------------------------------------------------------------------------------- +! open the dataset in the file + call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dopen_f') + +!-------------------------------------------------------------------------------------------------- +! get the space_id of dataset in the file + call h5dget_space_f(dset_id, filespace_id, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5dget_space_f') + +!-------------------------------------------------------------------------------------------------- +! select a hyperslab (the portion of the current process) in the file + call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_read_pReal1: h5sselect_hyperslab_f') + + +end subroutine initialize_read + end module HDF5_Utilities