!-------------------------------------------------------------------------------------------------- !> @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 HDF5 #ifdef PETSC #include use PETScSys #if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY) use MPI #endif #endif use prec use parallelization implicit none private !-------------------------------------------------------------------------------------------------- !> @brief reads integer or float data of defined shape from file !> @details for parallel IO, all dimension except for the last need to match !-------------------------------------------------------------------------------------------------- interface HDF5_read module procedure HDF5_read_real1 module procedure HDF5_read_real2 module procedure HDF5_read_real3 module procedure HDF5_read_real4 module procedure HDF5_read_real5 module procedure HDF5_read_real6 module procedure HDF5_read_real7 module procedure HDF5_read_int1 module procedure HDF5_read_int2 module procedure HDF5_read_int3 module procedure HDF5_read_int4 module procedure HDF5_read_int5 module procedure HDF5_read_int6 module procedure HDF5_read_int7 end interface HDF5_read !-------------------------------------------------------------------------------------------------- !> @brief writes integer or real data of defined shape to file !> @details for parallel IO, all dimension except for the last need to match !-------------------------------------------------------------------------------------------------- interface HDF5_write module procedure HDF5_write_real1 module procedure HDF5_write_real2 module procedure HDF5_write_real3 module procedure HDF5_write_real4 module procedure HDF5_write_real5 module procedure HDF5_write_real6 module procedure HDF5_write_real7 module procedure HDF5_write_int1 module procedure HDF5_write_int2 module procedure HDF5_write_int3 module procedure HDF5_write_int4 module procedure HDF5_write_int5 module procedure HDF5_write_int6 module procedure HDF5_write_int7 end interface HDF5_write !-------------------------------------------------------------------------------------------------- !> @brief attached attributes of type char, integer or real to a file/dataset/group !-------------------------------------------------------------------------------------------------- interface HDF5_addAttribute module procedure HDF5_addAttribute_str module procedure HDF5_addAttribute_int module procedure HDF5_addAttribute_real module procedure HDF5_addAttribute_int_array module procedure HDF5_addAttribute_real_array end interface HDF5_addAttribute #ifdef PETSC logical, parameter, private :: parallel_default = .true. #else logical, parameter, private :: parallel_default = .false. #endif public :: & HDF5_utilities_init, & HDF5_read, & HDF5_write, & HDF5_addAttribute, & HDF5_addGroup, & HDF5_openGroup, & HDF5_closeGroup, & HDF5_openFile, & HDF5_closeFile, & HDF5_objectExists, & HDF5_setLink contains !-------------------------------------------------------------------------------------------------- !> @brief initialize HDF5 libary and do sanity checks !-------------------------------------------------------------------------------------------------- subroutine HDF5_utilities_init integer :: hdferr integer(SIZE_T) :: typeSize print'(/,a)', ' <<<+- HDF5_Utilities init -+>>>' !-------------------------------------------------------------------------------------------------- !initialize HDF5 library and check if integer and float type size match call h5open_f(hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr) if(hdferr < 0) error stop 'HDF5 error' if (int(bit_size(0),SIZE_T)/=typeSize*8) & error stop 'Default integer size does not match H5T_NATIVE_INTEGER' call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr) if(hdferr < 0) error stop 'HDF5 error' if (int(storage_size(0.0_pReal),SIZE_T)/=typeSize*8) & error stop '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) character(len=*), intent(in) :: fileName character, intent(in), optional :: mode character :: m integer(HID_T) :: plist_id integer :: hdferr if (present(mode)) then m = mode else m = 'r' endif call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' #ifdef PETSC call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr) if(hdferr < 0) error stop 'HDF5 error' #endif if (m == 'w') then call h5fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,access_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' elseif(m == 'a') then call h5fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' elseif(m == 'r') then call h5fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' else error stop 'unknown access mode' endif call h5pclose_f(plist_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' end function HDF5_openFile !-------------------------------------------------------------------------------------------------- !> @brief close the opened HDF5 output file !-------------------------------------------------------------------------------------------------- subroutine HDF5_closeFile(fileHandle) integer(HID_T), intent(in) :: fileHandle integer :: hdferr call h5fclose_f(fileHandle,hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_closeFile !-------------------------------------------------------------------------------------------------- !> @brief adds a new group to the fileHandle !-------------------------------------------------------------------------------------------------- integer(HID_T) function HDF5_addGroup(fileHandle,groupName) integer(HID_T), intent(in) :: fileHandle character(len=*), intent(in) :: groupName integer :: 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) error stop 'HDF5 error' !------------------------------------------------------------------------------------------------- ! setting I/O mode to collective #ifdef PETSC call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) if(hdferr < 0) error stop 'HDF5 error' #endif !------------------------------------------------------------------------------------------------- ! Create group call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id) if(hdferr < 0) error stop 'HDF5 error' call h5pclose_f(aplist_id,hdferr) end function HDF5_addGroup !-------------------------------------------------------------------------------------------------- !> @brief open an existing group of a file !-------------------------------------------------------------------------------------------------- integer(HID_T) function HDF5_openGroup(fileHandle,groupName) integer(HID_T), intent(in) :: fileHandle character(len=*), intent(in) :: groupName integer :: 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) error stop 'HDF5 error' !------------------------------------------------------------------------------------------------- ! setting I/O mode to collective #ifdef PETSC call h5pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr) if(hdferr < 0) error stop 'HDF5 error' #endif !------------------------------------------------------------------------------------------------- ! opening the group call h5gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id) if(hdferr < 0) error stop 'HDF5 error' call h5pclose_f(aplist_id,hdferr) end function HDF5_openGroup !-------------------------------------------------------------------------------------------------- !> @brief close a group !-------------------------------------------------------------------------------------------------- subroutine HDF5_closeGroup(group_id) integer(HID_T), intent(in) :: group_id integer :: hdferr call h5gclose_f(group_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_closeGroup !-------------------------------------------------------------------------------------------------- !> @brief check whether a group or a dataset exists !-------------------------------------------------------------------------------------------------- logical function HDF5_objectExists(loc_id,path) integer(HID_T), intent(in) :: loc_id character(len=*), intent(in), optional :: path integer :: hdferr character(len=:), allocatable :: p if (present(path)) then p = trim(path) else p = '.' endif call h5lexists_f(loc_id, p, HDF5_objectExists, hdferr) if(hdferr < 0) error stop 'HDF5 error' if(HDF5_objectExists) then call h5oexists_by_name_f(loc_id, p, HDF5_objectExists, hdferr) if(hdferr < 0) error stop 'HDF5 error' 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) integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel, attrValue character(len=*), intent(in), optional :: path integer(HID_T) :: attr_id, space_id, type_id logical :: attrExists integer :: hdferr character(len=:), allocatable :: p character(len=:,kind=C_CHAR), allocatable,target :: attrValue_ type(c_ptr), target, dimension(1) :: ptr if (present(path)) then p = trim(path) else p = '.' endif attrValue_ = trim(attrValue)//C_NULL_CHAR ptr(1) = c_loc(attrValue_) call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5tcopy_f(H5T_STRING, type_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if(hdferr < 0) error stop 'HDF5 error' endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, type_id, c_loc(ptr(1)), hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5tclose_f(type_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_addAttribute_str !-------------------------------------------------------------------------------------------------- !> @brief adds a integer attribute to the path given relative to the location !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path) integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel integer, intent(in) :: attrValue character(len=*), intent(in), optional :: path integer(HID_T) :: attr_id, space_id integer :: hdferr logical :: attrExists character(len=:), allocatable :: p if (present(path)) then p = trim(path) else p = '.' endif call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if(hdferr < 0) error stop 'HDF5 error' endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, int([1],HSIZE_T), hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_addAttribute_int !-------------------------------------------------------------------------------------------------- !> @brief adds a integer attribute to the path given relative to the location !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel real(pReal), intent(in) :: attrValue character(len=*), intent(in), optional :: path integer(HID_T) :: attr_id, space_id integer :: hdferr logical :: attrExists character(len=:), allocatable :: p if (present(path)) then p = trim(path) else p = '.' endif call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if(hdferr < 0) error stop 'HDF5 error' endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, int([1],HSIZE_T), hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_addAttribute_real !-------------------------------------------------------------------------------------------------- !> @brief adds a integer attribute to the path given relative to the location !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path) integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel integer, intent(in), dimension(:) :: attrValue character(len=*), intent(in), optional :: path integer(HSIZE_T),dimension(1) :: array_size integer(HID_T) :: attr_id, space_id integer :: hdferr logical :: attrExists character(len=:), allocatable :: p if (present(path)) then p = trim(path) else p = '.' endif array_size = size(attrValue,kind=HSIZE_T) call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) if(hdferr < 0) error stop 'HDF5 error' call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if(hdferr < 0) error stop 'HDF5 error' endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, array_size, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_addAttribute_int_array !-------------------------------------------------------------------------------------------------- !> @brief adds a real attribute to the path given relative to the location !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path) integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel real(pReal), intent(in), dimension(:) :: attrValue character(len=*), intent(in), optional :: path integer(HSIZE_T),dimension(1) :: array_size integer(HID_T) :: attr_id, space_id integer :: hdferr logical :: attrExists character(len=:), allocatable :: p if (present(path)) then p = trim(path) else p = '.' endif array_size = size(attrValue,kind=HSIZE_T) call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) if(hdferr < 0) error stop 'HDF5 error' call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) if(hdferr < 0) error stop 'HDF5 error' endif call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, array_size, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_addAttribute_real_array !-------------------------------------------------------------------------------------------------- !> @brief set link to object in results file !-------------------------------------------------------------------------------------------------- subroutine HDF5_setLink(loc_id,target_name,link_name) character(len=*), intent(in) :: target_name, link_name integer(HID_T), intent(in) :: loc_id integer :: hdferr logical :: linkExists call h5lexists_f(loc_id, link_name,linkExists, hdferr) if(hdferr < 0) error stop 'HDF5 error' if (linkExists) then call h5ldelete_f(loc_id,link_name, hdferr) if(hdferr < 0) error stop 'HDF5 error' endif call h5lcreate_soft_f(target_name, loc_id, link_name, hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine HDF5_setLink !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type real with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_real1(dataset,loc_id,datasetName,parallel) real(pReal), intent(out), dimension(:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & ! ToDo: Fortran 2018 size(shape(A)) = rank(A) myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real1 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type real with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_real2(dataset,loc_id,datasetName,parallel) real(pReal), intent(out), dimension(:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real2 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type real with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_real3(dataset,loc_id,datasetName,parallel) real(pReal), intent(out), dimension(:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real3 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type real with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_real4(dataset,loc_id,datasetName,parallel) real(pReal), intent(out), dimension(:,:,:,:) :: dataset !< read data 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real4 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type real with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_real5(dataset,loc_id,datasetName,parallel) real(pReal), intent(out), dimension(:,:,:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real5 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type real with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_real6(dataset,loc_id,datasetName,parallel) real(pReal), intent(out), dimension(:,:,:,:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real6 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type real with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_real7(dataset,loc_id,datasetName,parallel) real(pReal), intent(out), dimension(:,:,:,:,:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real7 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type integer with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_int1(dataset,loc_id,datasetName,parallel) integer, intent(out), dimension(:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int1 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type integer with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_int2(dataset,loc_id,datasetName,parallel) integer, intent(out), dimension(:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int2 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type integer with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_int3(dataset,loc_id,datasetName,parallel) integer, intent(out), dimension(:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int3 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type integer withh 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_int4(dataset,loc_id,datasetName,parallel) integer, intent(out), dimension(:,:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int4 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type integer with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_int5(dataset,loc_id,datasetName,parallel) integer, intent(out), dimension(:,:,:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int5 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type integer with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_int6(dataset,loc_id,datasetName,parallel) integer, intent(out), dimension(:,:,:,:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int6 !-------------------------------------------------------------------------------------------------- !> @brief read dataset of type integer with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_read_int7(dataset,loc_id,datasetName,parallel) integer, intent(out), dimension(:,:,:,:,:,:,:) :: dataset !< data read from file 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 !< dataset is distributed over multiple processes integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,parallel) else call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, & myStart, totalShape, loc_id,myShape,datasetName,parallel_default) endif call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) if(hdferr < 0) error stop 'HDF5 error' call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int7 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real1(dataset,loc_id,datasetName,parallel) real(pReal), intent(in), dimension(:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real1 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real2(dataset,loc_id,datasetName,parallel) real(pReal), intent(in), dimension(:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real2 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real3(dataset,loc_id,datasetName,parallel) real(pReal), intent(in), dimension(:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real3 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real4(dataset,loc_id,datasetName,parallel) real(pReal), intent(in), dimension(:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real4 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real5(dataset,loc_id,datasetName,parallel) real(pReal), intent(in), dimension(:,:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real5 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real6(dataset,loc_id,datasetName,parallel) real(pReal), intent(in), dimension(:,:,:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real6 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real7(dataset,loc_id,datasetName,parallel) real(pReal), intent(in), dimension(:,:,:,:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real7 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type integer with 1 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int1(dataset,loc_id,datasetName,parallel) integer, intent(in), dimension(:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int1 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type integer with 2 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int2(dataset,loc_id,datasetName,parallel) integer, intent(in), dimension(:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int2 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type integer with 3 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int3(dataset,loc_id,datasetName,parallel) integer, intent(in), dimension(:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int3 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type integer with 4 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int4(dataset,loc_id,datasetName,parallel) integer, intent(in), dimension(:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int4 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type integer with 5 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int5(dataset,loc_id,datasetName,parallel) integer, intent(in), dimension(:,:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int5 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type integer with 6 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int6(dataset,loc_id,datasetName,parallel) integer, intent(in), dimension(:,:,:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int6 !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type integer with 7 dimensions !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int7(dataset,loc_id,datasetName,parallel) integer, intent(in), dimension(:,:,:,:,:,:,:) :: dataset !< data written to file 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 !< dataset is distributed over multiple processes integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id integer(HSIZE_T), dimension(size(shape(dataset))) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) !--------------------------------------------------------------------------------------------------- ! determine shape of dataset myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-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, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel) else call initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default) endif if (product(totalShape) /= 0) then call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) if(hdferr < 0) error stop 'HDF5 error' endif call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int7 !-------------------------------------------------------------------------------------------------- !> @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) 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, dimension(worldsize) :: & readSize !< contribution of all processes integer :: ierr integer :: 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) error stop 'HDF5 error' !-------------------------------------------------------------------------------------------------- readSize = 0 readSize(worldrank+1) = int(localShape(ubound(localShape,1))) #ifdef PETSC if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if(hdferr < 0) error stop 'HDF5 error' 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) error stop 'MPI error' 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) error stop 'HDF5 error' !-------------------------------------------------------------------------------------------------- ! creating a property list for IO and set it to collective call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' #ifdef PETSC call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) if(hdferr < 0) error stop 'HDF5 error' #endif !-------------------------------------------------------------------------------------------------- ! 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) error stop 'HDF5 error' call h5dget_space_f(dset_id, filespace_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' !-------------------------------------------------------------------------------------------------- ! 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) error stop 'HDF5 error' end subroutine initialize_read !-------------------------------------------------------------------------------------------------- !> @brief closes HDF5 handles !-------------------------------------------------------------------------------------------------- subroutine finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer :: hdferr call h5pclose_f(plist_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5pclose_f(aplist_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5dclose_f(dset_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(filespace_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(memspace_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' 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, totalShape, & loc_id,myShape,datasetName,datatype,parallel) 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(:) :: & myShape integer(HSIZE_T), intent(out), dimension(size(myShape,1)):: & myStart, & totalShape !< shape of the dataset (all processes) integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id integer, dimension(worldsize) :: writeSize !< contribution of all processes integer(HID_T) :: dcpl integer :: ierr, hdferr, HDF5_major, HDF5_minor, HDF5_release integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T !------------------------------------------------------------------------------------------------- ! creating a property list for transfer properties (is collective when reading in parallel) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' #ifdef PETSC if (parallel) then call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) if(hdferr < 0) error stop 'HDF5 error' endif #endif !-------------------------------------------------------------------------------------------------- ! determine the global data layout among all processes writeSize = 0 writeSize(worldrank+1) = int(myShape(ubound(myShape,1))) #ifdef PETSC if (parallel) then 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) error stop 'MPI error' endif #endif myStart = int(0,HSIZE_T) myStart(ubound(myStart)) = int(sum(writeSize(1:worldrank)),HSIZE_T) totalShape = [myShape(1:ubound(myShape,1)-1),int(sum(writeSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! compress (and chunk) larger datasets call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr) if(hdferr < 0) error stop 'HDF5 error' if(product(totalShape) >= chunkSize*2_HSIZE_T) then call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr) if (hdferr < 0) error stop 'HDF5 error' if (HDF5_major == 1 .and. HDF5_minor >= 12) then ! https://forum.hdfgroup.org/t/6186 call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr) if (hdferr < 0) error stop 'HDF5 error' call h5pset_shuffle_f(dcpl, hdferr) if (hdferr < 0) error stop 'HDF5 error' call h5pset_deflate_f(dcpl, 6, hdferr) if (hdferr < 0) error stop 'HDF5 error' call h5pset_Fletcher32_f(dcpl,hdferr) if (hdferr < 0) error stop 'HDF5 error' endif endif !-------------------------------------------------------------------------------------------------- ! create dataspace in memory (local shape) and in file (global shape) call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape) if(hdferr < 0) error stop 'HDF5 error' call h5screate_simple_f(size(totalShape), totalShape, filespace_id, hdferr, totalShape) if(hdferr < 0) error stop 'HDF5 error' !-------------------------------------------------------------------------------------------------- ! create dataset in the file and select a hyperslab from it (the portion of the current process) call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr, dcpl) if(hdferr < 0) error stop 'HDF5 error' call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, myShape, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5pclose_f(dcpl , hdferr) if(hdferr < 0) error stop 'HDF5 error' contains !------------------------------------------------------------------------------------------------ !> @brief determine chunk layout !------------------------------------------------------------------------------------------------ pure function getChunks(totalShape,chunkSize) integer(HSIZE_T), dimension(:), intent(in) :: totalShape integer(HSIZE_T), intent(in) :: chunkSize integer(HSIZE_T), dimension(size(totalShape)) :: getChunks getChunks = [totalShape(1:size(totalShape)-1),& chunkSize/product(totalShape(1:size(totalShape)-1))] end function getChunks end subroutine initialize_write !-------------------------------------------------------------------------------------------------- !> @brief closes HDF5 handles !-------------------------------------------------------------------------------------------------- subroutine finalize_write(plist_id, dset_id, filespace_id, memspace_id) integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id integer :: hdferr call h5pclose_f(plist_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5dclose_f(dset_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(filespace_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(memspace_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' end subroutine finalize_write end module HDF5_Utilities