!-------------------------------------------------------------------------------------------------- !> @author Vitesh Shah, Max-Planck-Institut für Eisenforschung GmbH !> @author Yi-Chin Yang, Max-Planck-Institut für Eisenforschung GmbH !> @author Jennifer Nastola, Max-Planck-Institut für Eisenforschung GmbH !> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH !-------------------------------------------------------------------------------------------------- module HDF5_utilities use prec use IO use HDF5 #ifdef PETSc use PETSC #endif implicit none public integer(pInt), parameter, private :: & HDF5_ERR_TYPE = 4_pInt !< kind of the integer return in the HDF5 library !-------------------------------------------------------------------------------------------------- !> @brief reads pInt or pReal data of defined shape from file ! ToDo: order of arguments wrong !> @details for parallel IO, all dimension except for the last need to match !-------------------------------------------------------------------------------------------------- interface HDF5_read module procedure HDF5_read_pReal1 module procedure HDF5_read_pReal2 module procedure HDF5_read_pReal3 module procedure HDF5_read_pReal4 module procedure HDF5_read_pReal5 module procedure HDF5_read_pReal6 module procedure HDF5_read_pReal7 module procedure HDF5_read_pInt1 module procedure HDF5_read_pInt2 module procedure HDF5_read_pInt3 module procedure HDF5_read_pInt4 module procedure HDF5_read_pInt5 module procedure HDF5_read_pInt6 module procedure HDF5_read_pInt7 end interface HDF5_read !-------------------------------------------------------------------------------------------------- !> @brief writes pInt or pReal data of defined shape to file ! ToDo: order of arguments wrong !> @details for parallel IO, all dimension except for the last need to match !-------------------------------------------------------------------------------------------------- interface HDF5_write module procedure HDF5_write_pReal1 module procedure HDF5_write_pReal2 module procedure HDF5_write_pReal3 module procedure HDF5_write_pReal4 module procedure HDF5_write_pReal5 module procedure HDF5_write_pReal6 module procedure HDF5_write_pReal7 module procedure HDF5_write_pInt1 module procedure HDF5_write_pInt2 module procedure HDF5_write_pInt3 module procedure HDF5_write_pInt4 module procedure HDF5_write_pInt5 module procedure HDF5_write_pInt6 module procedure HDF5_write_pInt7 end interface HDF5_write !-------------------------------------------------------------------------------------------------- !> @brief attached attributes of type char,pInt or pReal to a file/dataset/group !-------------------------------------------------------------------------------------------------- interface HDF5_addAttribute module procedure HDF5_addAttribute_str module procedure HDF5_addAttribute_pInt module procedure HDF5_addAttribute_pReal end interface HDF5_addAttribute !-------------------------------------------------------------------------------------------------- public :: & HDF5_utilities_init, & HDF5_openFile, & HDF5_closeFile, & HDF5_addAttribute, & HDF5_closeGroup ,& HDF5_openGroup, & HDF5_addGroup, & HDF5_read, & HDF5_write, & HDF5_setLink, & HDF5_objectExists contains subroutine HDF5_utilities_init implicit none integer(HDF5_ERR_TYPE) :: hdferr integer(SIZE_T) :: typeSize write(6,'(/,a)') ' <<<+- HDF5_Utilities init -+>>>' !-------------------------------------------------------------------------------------------------- !initialize HDF5 library and check if integer and float type size match call h5open_f(hdferr) if (hdferr < 0) call IO_error(1,ext_msg='HDF5_Utilities_init: h5open_f') call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr) if (hdferr < 0) call IO_error(1,ext_msg='HDF5_Utilities_init: h5tget_size_f (int)') if (int(bit_size(0),SIZE_T)/=typeSize*8) & call IO_error(0_pInt,ext_msg='Default integer size does not match H5T_NATIVE_INTEGER') call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr) if (hdferr < 0) call IO_error(1,ext_msg='HDF5_Utilities_init: h5tget_size_f (double)') if (int(storage_size(0.0_pReal),SIZE_T)/=typeSize*8) & call IO_error(0,ext_msg='pReal does not match H5T_NATIVE_DOUBLE') end subroutine HDF5_utilities_init !-------------------------------------------------------------------------------------------------- !> @brief open and initializes HDF5 output file !-------------------------------------------------------------------------------------------------- integer(HID_T) function HDF5_openFile(fileName,mode,parallel) implicit none character(len=*), intent(in) :: fileName character, intent(in), optional :: mode logical, intent(in), optional :: parallel character :: m integer(HID_T) :: plist_id integer(HDF5_ERR_TYPE) :: hdferr if (present(mode)) then m = mode else m = 'r' endif call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5pcreate_f') #ifdef PETSc if (present(parallel)) then; if (parallel) then call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5pset_fapl_mpio_f') endif; endif #endif if (m == 'w') then call h5fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,access_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fcreate_f') elseif(m == 'a') then call h5fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fopen_f (a)') elseif(m == 'r') then call h5fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fopen_f (r)') else call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fopen_f unknown access mode') endif call h5pclose_f(plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5pclose_f') end function HDF5_openFile !-------------------------------------------------------------------------------------------------- !> @brief close the opened HDF5 output file !-------------------------------------------------------------------------------------------------- subroutine HDF5_closeFile(fileHandle) implicit none integer(HID_T), intent(in) :: fileHandle integer(HDF5_ERR_TYPE) :: hdferr call h5fclose_f(fileHandle,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_closeFile: h5fclose_f') end subroutine HDF5_closeFile !-------------------------------------------------------------------------------------------------- !> @brief adds a new group to the fileHandle !-------------------------------------------------------------------------------------------------- integer(HID_T) function HDF5_addGroup(fileHandle,groupName) implicit none integer(HID_T), intent(in) :: fileHandle character(len=*), intent(in) :: groupName integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: aplist_id !------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5pcreate_f ('//trim(groupName)//')') !------------------------------------------------------------------------------------------------- ! setting I/O mode to collective call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')') !------------------------------------------------------------------------------------------------- ! Create group call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5gcreate_f ('//trim(groupName)//')') end function HDF5_addGroup !-------------------------------------------------------------------------------------------------- !> @brief open an existing group of a file !-------------------------------------------------------------------------------------------------- integer(HID_T) function HDF5_openGroup(fileHandle,groupName) implicit none integer(HID_T), intent(in) :: fileHandle character(len=*), intent(in) :: groupName integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: aplist_id logical :: is_collective !------------------------------------------------------------------------------------------------- ! creating a property list for data access properties call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5pcreate_f ('//trim(groupName)//')') !------------------------------------------------------------------------------------------------- ! setting I/O mode to collective call h5pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')') !------------------------------------------------------------------------------------------------- ! opening the group call h5gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5gopen_f ('//trim(groupName)//')') end function HDF5_openGroup !-------------------------------------------------------------------------------------------------- !> @brief close a group !-------------------------------------------------------------------------------------------------- subroutine HDF5_closeGroup(group_id) implicit none integer(HID_T), intent(in) :: group_id integer(HDF5_ERR_TYPE) :: hdferr call h5gclose_f(group_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = int(group_id,pInt)) end subroutine HDF5_closeGroup !-------------------------------------------------------------------------------------------------- !> @brief check whether a group or a dataset exists !-------------------------------------------------------------------------------------------------- logical function HDF5_objectExists(loc_id,path) implicit none integer(HID_T), intent(in) :: loc_id character(len=*), intent(in), optional :: path integer(HDF5_ERR_TYPE) :: hdferr character(len=256) :: p if (present(path)) then p = trim(path) else p = '.' endif call h5lexists_f(loc_id, p, HDF5_objectExists, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_objectExists: h5oexists_by_name_f') if(HDF5_objectExists) then call h5oexists_by_name_f(loc_id, p, HDF5_objectExists, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_objectExists: h5oexists_by_name_f') endif end function HDF5_objectExists !-------------------------------------------------------------------------------------------------- !> @brief adds a string attribute to the path given relative to the location !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path) implicit none integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel, attrValue character(len=*), intent(in), optional :: path integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: attr_id, space_id, type_id logical :: attrExists character(len=256) :: p if (present(path)) then p = trim(path) else p = '.' endif call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5screate_f') call h5tcopy_f(H5T_NATIVE_CHARACTER, type_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5tcopy_f') call h5tset_size_f(type_id, int(len(trim(attrValue)),HSIZE_T), hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5tset_size_f') call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5aexists_by_name_f') if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5adelete_by_name_f') endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5acreate_f') call h5awrite_f(attr_id, type_id, trim(attrValue), int([1],HSIZE_T), hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5awrite_f') call h5aclose_f(attr_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5aclose_f') call h5tclose_f(type_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5tclose_f') call h5sclose_f(space_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_str: h5sclose_f') end subroutine HDF5_addAttribute_str !-------------------------------------------------------------------------------------------------- !> @brief adds a integer attribute to the path given relative to the location !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_pInt(loc_id,attrLabel,attrValue,path) implicit none integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel integer(pInt), intent(in) :: attrValue character(len=*), intent(in), optional :: path integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: attr_id, space_id, type_id logical :: attrExists character(len=256) :: p if (present(path)) then p = trim(path) else p = '.' endif call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5screate_f') call h5tcopy_f(H5T_NATIVE_INTEGER, type_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5tcopy_f') call h5tset_size_f(type_id, 1_HSIZE_T, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5tset_size_f') call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5aexists_by_name_f') if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5adelete_by_name_f') endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5acreate_f') call h5awrite_f(attr_id, type_id, attrValue, int([1],HSIZE_T), hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5awrite_f') call h5aclose_f(attr_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5aclose_f') call h5tclose_f(type_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5tclose_f') call h5sclose_f(space_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5sclose_f') end subroutine HDF5_addAttribute_pInt !-------------------------------------------------------------------------------------------------- !> @brief adds a integer attribute to the path given relative to the location !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_pReal(loc_id,attrLabel,attrValue,path) implicit none integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel real(pReal), intent(in) :: attrValue character(len=*), intent(in), optional :: path integer(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: attr_id, space_id, type_id logical :: attrExists character(len=256) :: p if (present(path)) then p = trim(path) else p = '.' endif call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5screate_f') call h5tcopy_f(H5T_NATIVE_DOUBLE, type_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5tcopy_f') call h5tset_size_f(type_id, 8_HSIZE_T, hdferr) ! ToDo if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5tset_size_f') call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5aexists_by_name_f') if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5adelete_by_name_f') endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5acreate_f') call h5awrite_f(attr_id, type_id, attrValue, int([1],HSIZE_T), hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5awrite_f') call h5aclose_f(attr_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5aclose_f') call h5tclose_f(type_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5tclose_f') call h5sclose_f(space_id,hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5sclose_f') end subroutine HDF5_addAttribute_pReal !-------------------------------------------------------------------------------------------------- !> @brief set link to object in results file !-------------------------------------------------------------------------------------------------- subroutine HDF5_setLink(loc_id,target_name,link_name) use hdf5 implicit none character(len=*), intent(in) :: target_name, link_name integer(HID_T), intent(in) :: loc_id integer(HDF5_ERR_TYPE) :: hdferr logical :: linkExists call h5lexists_f(loc_id, link_name,linkExists, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5lexists_soft_f ('//trim(link_name)//')') if (linkExists) then call h5ldelete_f(loc_id,link_name, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5ldelete_soft_f ('//trim(link_name)//')') endif call h5lcreate_soft_f(target_name, loc_id, link_name, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5lcreate_soft_f ('//trim(target_name)//' '//trim(link_name)//')') end subroutine HDF5_setLink !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pReal with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal1(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,globalShape, 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_pReal2: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pReal1 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pReal with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal2(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,globalShape, 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') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pReal2 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pReal with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal3(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,globalShape, 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_pReal3: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pReal3 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pReal with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal4(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,globalShape, 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_pReal4: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pReal4 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pReal with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal5(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,globalShape, 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_pReal5: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pReal5 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pReal with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal6(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,globalShape, 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_pReal6: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pReal6 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pReal with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pReal7(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,globalShape, 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_pReal7: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pReal7 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pInt with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt1(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,globalShape, 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_pInt1: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pInt1 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pInt with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt2(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,globalShape, 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_pInt2: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pInt2 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pInt with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt3(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,globalShape, 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_pInt3: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pInt3 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pInt withh 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt4(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,globalShape, 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_pInt4: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pInt4 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pInt with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt5(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,globalShape, 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_pInt5: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pInt5 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pInt with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt6(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,globalShape, 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_pInt6: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pInt6 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type pInt with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_pInt7(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset 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(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & localShape, & !< shape of the dataset (this process) globalShape !< shape of the dataset (all processes) integer(HDF5_ERR_TYPE) :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset localShape = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) !--------------------------------------------------------------------------------------------------- ! initialize HDF5 data structures 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 call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,globalShape, 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_pInt7: h5dread_f') call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_pInt7 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pReal with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pReal1(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape,loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape,loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal1: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pReal1 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pReal with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pReal2(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal2: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pReal2 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pReal with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pReal3(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal3: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pReal3 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pReal with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pReal4(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal4: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pReal4 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pReal with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pReal5(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal5: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pReal5 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pReal with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pReal6(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal6: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pReal6 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pReal with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pReal7(loc_id,dataset,datasetName,parallel) implicit none real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_DOUBLE,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pReal7: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pReal7 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pInt with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pInt1(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt1: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pInt1 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pInt with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pInt2(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt2: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pInt2 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pInt with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pInt3(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt3: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pInt3 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pInt with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pInt4(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt4: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pInt4 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pInt with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pInt5(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt5: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pInt5 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pInt with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pInt6(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt6: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pInt6 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type pInt with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_pInt7(loc_id,dataset,datasetName,parallel) implicit none integer(pInt), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset 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(HDF5_ERR_TYPE) :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id 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 = int(shape(dataset),HSIZE_T) if (any(localShape(1:size(localShape)-1) == 0)) return !< empty dataset (last dimension can be empty) if (present(parallel)) then call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, loc_id,localShape,datasetName,H5T_NATIVE_INTEGER,.false.) endif call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(globalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_write_pInt7: h5dread_f') call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_pInt7 !-------------------------------------------------------------------------------------------------- !> @brief initialize HDF5 handles, determines global shape and start for parallel read !-------------------------------------------------------------------------------------------------- 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) :: parallel integer(HSIZE_T), intent(in), dimension(:) :: & localShape integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: & myStart, & globalShape !< shape of the dataset (all processes) integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(pInt), dimension(worldsize) :: & readSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr !------------------------------------------------------------------------------------------------- ! creating a property list for transfer properties (is collective for MPI) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_read: h5pcreate_f') !-------------------------------------------------------------------------------------------------- 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='initialize_read: 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='initialize_read: 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), localShape, memspace_id, hdferr, localShape) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_read: h5screate_simple_f/memspace_id') !-------------------------------------------------------------------------------------------------- ! creating a property list for IO and set it to collective call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_read: h5pcreate_f') call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_read: h5pset_all_coll_metadata_ops_f') !-------------------------------------------------------------------------------------------------- ! open the dataset in the file and get the space ID call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_read: h5dopen_f') call h5dget_space_f(dset_id, filespace_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_read: 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='initialize_read: h5sselect_hyperslab_f') end subroutine initialize_read !-------------------------------------------------------------------------------------------------- !> @brief closes HDF5 handles !-------------------------------------------------------------------------------------------------- subroutine finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) implicit none integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HDF5_ERR_TYPE) :: hdferr call h5pclose_f(plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_read: plist_id') call h5dclose_f(dset_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_read: h5dclose_f') call h5sclose_f(filespace_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_read: h5sclose_f/filespace_id') call h5sclose_f(memspace_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_read: h5sclose_f/memspace_id') end subroutine finalize_read !-------------------------------------------------------------------------------------------------- !> @brief initialize HDF5 handles, determines global shape and start for parallel write !-------------------------------------------------------------------------------------------------- subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, globalShape, & loc_id,localShape,datasetName,datatype,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) :: parallel integer(HID_T), intent(in) :: datatype integer(HSIZE_T), intent(in), dimension(:) :: & localShape integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: & myStart, & globalShape !< shape of the dataset (all processes) integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id integer(pInt), dimension(worldsize) :: & writeSize !< contribution of all processes integer :: ierr integer(HDF5_ERR_TYPE) :: hdferr !------------------------------------------------------------------------------------------------- ! creating a property list for transfer properties call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_write: h5pcreate_f') !-------------------------------------------------------------------------------------------------- writeSize = 0_pInt writeSize(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='initialize_write: h5pset_dxpl_mpio_f') call MPI_allreduce(MPI_IN_PLACE,writeSize,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='initialize_write: MPI_allreduce') endif #endif myStart = int(0,HSIZE_T) myStart(ubound(myStart)) = int(sum(writeSize(1:worldrank)),HSIZE_T) globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(writeSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! create dataspace in memory (local shape) and in file (global shape) call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_write: h5dopen_f') call h5screate_simple_f(size(globalShape), globalShape, filespace_id, hdferr, globalShape) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_write: h5dget_space_f') !-------------------------------------------------------------------------------------------------- ! create dataset call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_write: h5dcreate_f') !-------------------------------------------------------------------------------------------------- ! select a hyperslab (the portion of the current process) in the file call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='initialize_write: h5sselect_hyperslab_f') end subroutine initialize_write !-------------------------------------------------------------------------------------------------- !> @brief closes HDF5 handles !-------------------------------------------------------------------------------------------------- subroutine finalize_write(plist_id, dset_id, filespace_id, memspace_id) implicit none integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id integer(HDF5_ERR_TYPE) :: hdferr call h5pclose_f(plist_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_write: plist_id') call h5dclose_f(dset_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_write: h5dclose_f') call h5sclose_f(filespace_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_write: h5sclose_f/filespace_id') call h5sclose_f(memspace_id, hdferr) if (hdferr < 0) call IO_error(1_pInt,ext_msg='finalize_write: h5sclose_f/memspace_id') end subroutine finalize_write end module HDF5_Utilities