!-------------------------------------------------------------------------------------------------- !> @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 !> @author Philip Eisenlohr, Michigan State University !-------------------------------------------------------------------------------------------------- module HDF5_utilities use IO use HDF5 #ifdef PETSC #include use PETScSys #if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY) use MPI_f08 use MPI, only: MPI_INFO_NULL_F90 => MPI_INFO_NULL #endif #endif use prec use parallelization use misc #if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY) implicit none(type,external) #else implicit none #endif private !-------------------------------------------------------------------------------------------------- !> @brief Read integer or real 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_int1 module procedure HDF5_read_int2 module procedure HDF5_read_int3 module procedure HDF5_read_int4 module procedure HDF5_read_int5 end interface HDF5_read !-------------------------------------------------------------------------------------------------- !> @brief Write 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 #if defined(__GFORTRAN__) ! https://gcc.gnu.org/bugzilla/show_bug.cgi?id=105674 ! https://gcc.gnu.org/bugzilla/show_bug.cgi?id=105687 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_int1 module procedure HDF5_write_int2 module procedure HDF5_write_int3 module procedure HDF5_write_int4 module procedure HDF5_write_int5 #else module procedure HDF5_write_real module procedure HDF5_write_int #endif end interface HDF5_write !-------------------------------------------------------------------------------------------------- !> @brief Attach attribute 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_str_array module procedure HDF5_addAttribute_int_array module procedure HDF5_addAttribute_real_array end interface HDF5_addAttribute #ifdef PETSC logical, parameter :: parallel_default = .true. #else logical, parameter :: parallel_default = .false. #endif logical :: compression_possible public :: & HDF5_utilities_init, & HDF5_chkerr, & HDF5_read, & HDF5_write, & HDF5_write_str, & HDF5_addAttribute, & HDF5_addGroup, & HDF5_openGroup, & HDF5_closeGroup, & HDF5_openFile, & HDF5_closeFile, & HDF5_objectExists, & HDF5_setLink contains !-------------------------------------------------------------------------------------------------- !> @brief Initialize HDF5 libary and perform sanity checks. !-------------------------------------------------------------------------------------------------- subroutine HDF5_utilities_init() integer :: hdferr, HDF5_major, HDF5_minor, HDF5_release, configFlags logical :: avail integer(SIZE_T) :: typeSize print'(/,1x,a)', '<<<+- HDF5_utilities init -+>>>' call H5Open_f(hdferr) call HDF5_chkerr(hdferr) call H5Tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr) call HDF5_chkerr(hdferr) 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) call HDF5_chkerr(hdferr) if (int(storage_size(0.0_pREAL),SIZE_T)/=typeSize*8) & error stop 'pREAL does not match H5T_NATIVE_DOUBLE' call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr) call HDF5_chkerr(hdferr) compression_possible = (HDF5_major == 1 .and. HDF5_minor >= 12) ! https://forum.hdfgroup.org/t/6186 call H5Zfilter_avail_f(H5Z_FILTER_DEFLATE_F,avail,hdferr) call HDF5_chkerr(hdferr) compression_possible = compression_possible .and. avail if (avail) then call H5Zget_filter_info_f(H5Z_FILTER_DEFLATE_F,configFlags,hdferr) call HDF5_chkerr(hdferr) compression_possible = compression_possible .and. iand(H5Z_FILTER_ENCODE_ENABLED_F,configFlags) > 0 end if call H5Zfilter_avail_f(H5Z_FILTER_SHUFFLE_F,avail,hdferr) call HDF5_chkerr(hdferr) compression_possible = compression_possible .and. avail if (avail) then call H5Zget_filter_info_f(H5Z_FILTER_SHUFFLE_F,configFlags,hdferr) call HDF5_chkerr(hdferr) compression_possible = compression_possible .and. iand(H5Z_FILTER_ENCODE_ENABLED_F,configFlags) > 0 end if end subroutine HDF5_utilities_init !-------------------------------------------------------------------------------------------------- !> @brief Check for HDF5 error. !-------------------------------------------------------------------------------------------------- subroutine HDF5_chkerr(e) integer, intent(in) :: e if (e<0) error stop 'HDF5 error' end subroutine HDF5_chkerr !-------------------------------------------------------------------------------------------------- !> @brief Open and initialize HDF5 file. !-------------------------------------------------------------------------------------------------- integer(HID_T) function HDF5_openFile(fileName,mode,parallel) character(len=*), intent(in) :: fileName character, intent(in), optional :: mode logical, intent(in), optional :: parallel character :: m integer(HID_T) :: plist_id integer :: hdferr logical :: exist m = misc_optional(mode,'r') call H5Pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr) call HDF5_chkerr(hdferr) #ifdef PETSC if (misc_optional(parallel,.true.)) & #if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY) call H5Pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL_F90, hdferr) #else call H5Pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr) #endif call HDF5_chkerr(hdferr) #endif if (m == 'w') then call H5Fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,access_prp = plist_id) call HDF5_chkerr(hdferr) elseif (m == 'a') then call H5Fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp = plist_id) call HDF5_chkerr(hdferr) elseif (m == 'r') then inquire(file=fileName,exist=exist) if (.not. exist) call IO_error(100,trim(fileName)) call H5Fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp = plist_id) call HDF5_chkerr(hdferr) else error stop 'unknown access mode' end if call H5Pclose_f(plist_id, hdferr) call HDF5_chkerr(hdferr) end function HDF5_openFile !-------------------------------------------------------------------------------------------------- !> @brief Close an open HDF5 file. !-------------------------------------------------------------------------------------------------- subroutine HDF5_closeFile(fileHandle) integer(HID_T), intent(in) :: fileHandle integer :: hdferr call H5Fclose_f(fileHandle,hdferr) call HDF5_chkerr(hdferr) end subroutine HDF5_closeFile !-------------------------------------------------------------------------------------------------- !> @brief Add a new group to the file. !-------------------------------------------------------------------------------------------------- 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) call HDF5_chkerr(hdferr) !------------------------------------------------------------------------------------------------- ! setting I/O mode to collective #ifdef PETSC call H5Pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) call HDF5_chkerr(hdferr) #endif !------------------------------------------------------------------------------------------------- ! Create group call H5Gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id) call HDF5_chkerr(hdferr) call H5Pclose_f(aplist_id,hdferr) end function HDF5_addGroup !-------------------------------------------------------------------------------------------------- !> @brief Open an existing group in 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) call HDF5_chkerr(hdferr) !------------------------------------------------------------------------------------------------- ! setting I/O mode to collective #ifdef PETSC call H5Pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr) call HDF5_chkerr(hdferr) #endif !------------------------------------------------------------------------------------------------- ! opening the group call H5Gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id) call HDF5_chkerr(hdferr) 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) call HDF5_chkerr(hdferr) 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 p = trim(misc_optional(path,'.')) call H5Lexists_f(loc_id, p, HDF5_objectExists, hdferr) call HDF5_chkerr(hdferr) if (HDF5_objectExists) then call H5Oexists_by_name_f(loc_id, p, HDF5_objectExists, hdferr) call HDF5_chkerr(hdferr) end if end function HDF5_objectExists !-------------------------------------------------------------------------------------------------- !> @brief Add 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 logical :: attrExists integer :: hdferr character(len=:), allocatable :: p character(len=len_trim(attrValue)+1,kind=C_CHAR), dimension(1), target :: attrValue_ type(C_PTR), target, dimension(1) :: ptr p = trim(misc_optional(path,'.')) attrValue_(1) = trim(attrValue)//C_NULL_CHAR ptr(1) = c_loc(attrValue_(1)) call H5Screate_f(H5S_SCALAR_F,space_id,hdferr) call HDF5_chkerr(hdferr) call H5Aexists_by_name_f(loc_id,p,attrLabel,attrExists,hdferr) call HDF5_chkerr(hdferr) if (attrExists) then call H5Adelete_by_name_f(loc_id,p,attrLabel,hdferr) call HDF5_chkerr(hdferr) end if call H5Acreate_by_name_f(loc_id,p,trim(attrLabel),H5T_STRING,space_id,attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Awrite_f(attr_id, H5T_STRING, c_loc(ptr), hdferr) ! ptr instead of c_loc(ptr) works on gfortran, not on ifort call HDF5_chkerr(hdferr) call H5Aclose_f(attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(space_id,hdferr) call HDF5_chkerr(hdferr) end subroutine HDF5_addAttribute_str !-------------------------------------------------------------------------------------------------- !> @brief Add an 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 p = trim(misc_optional(path,'.')) call H5Screate_f(H5S_SCALAR_F,space_id,hdferr) call HDF5_chkerr(hdferr) call H5Aexists_by_name_f(loc_id,p,attrLabel,attrExists,hdferr) call HDF5_chkerr(hdferr) if (attrExists) then call H5Adelete_by_name_f(loc_id,p,attrLabel,hdferr) call HDF5_chkerr(hdferr) end if call H5Acreate_by_name_f(loc_id,p,trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, int([1],HSIZE_T), hdferr) call HDF5_chkerr(hdferr) call H5Aclose_f(attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(space_id,hdferr) call HDF5_chkerr(hdferr) end subroutine HDF5_addAttribute_int !-------------------------------------------------------------------------------------------------- !> @brief Add a real 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 p = trim(misc_optional(path,'.')) call H5Screate_f(H5S_SCALAR_F,space_id,hdferr) call HDF5_chkerr(hdferr) call H5Aexists_by_name_f(loc_id,p,attrLabel,attrExists,hdferr) call HDF5_chkerr(hdferr) if (attrExists) then call H5Adelete_by_name_f(loc_id,p,attrLabel,hdferr) call HDF5_chkerr(hdferr) end if call H5Acreate_by_name_f(loc_id,p,trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, int([1],HSIZE_T), hdferr) call HDF5_chkerr(hdferr) call H5Aclose_f(attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(space_id,hdferr) call HDF5_chkerr(hdferr) end subroutine HDF5_addAttribute_real !-------------------------------------------------------------------------------------------------- !> @brief Add a string array attribute to the path given relative to the location. !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_str_array(loc_id,attrLabel,attrValue,path) integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: attrLabel character(len=*), intent(in), dimension(:) :: attrValue character(len=*), intent(in), optional :: path integer(HID_T) :: attr_id, space_id logical :: attrExists integer :: hdferr,i character(len=:), allocatable :: p character(len=len(attrValue)+1,kind=C_CHAR), dimension(size(attrValue)), target :: attrValue_ type(C_PTR), target, dimension(size(attrValue)) :: ptr p = trim(misc_optional(path,'.')) do i=1,size(attrValue) attrValue_(i) = attrValue(i)//C_NULL_CHAR ptr(i) = c_loc(attrValue_(i)) end do call H5Screate_simple_f(1,shape(attrValue_,kind=HSIZE_T),space_id,hdferr,shape(attrValue_,kind=HSIZE_T)) call HDF5_chkerr(hdferr) call H5Aexists_by_name_f(loc_id,p,attrLabel,attrExists,hdferr) call HDF5_chkerr(hdferr) if (attrExists) then call H5Adelete_by_name_f(loc_id,p,attrLabel,hdferr) call HDF5_chkerr(hdferr) end if call H5Acreate_by_name_f(loc_id,p,trim(attrLabel),H5T_STRING,space_id,attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Awrite_f(attr_id, H5T_STRING, c_loc(ptr), hdferr) ! ptr instead of c_loc(ptr) works on gfortran, not on ifort call HDF5_chkerr(hdferr) call H5Aclose_f(attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(space_id,hdferr) call HDF5_chkerr(hdferr) end subroutine HDF5_addAttribute_str_array !-------------------------------------------------------------------------------------------------- !> @brief Add an integer array 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 p = trim(misc_optional(path,'.')) array_size = size(attrValue,kind=HSIZE_T) call H5Screate_simple_f(1, array_size, space_id, hdferr, array_size) call HDF5_chkerr(hdferr) call H5Aexists_by_name_f(loc_id,p,attrLabel,attrExists,hdferr) call HDF5_chkerr(hdferr) if (attrExists) then call H5Adelete_by_name_f(loc_id,p,attrLabel,hdferr) call HDF5_chkerr(hdferr) end if call H5Acreate_by_name_f(loc_id,p,trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, array_size, hdferr) call HDF5_chkerr(hdferr) call H5Aclose_f(attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(space_id,hdferr) call HDF5_chkerr(hdferr) end subroutine HDF5_addAttribute_int_array !-------------------------------------------------------------------------------------------------- !> @brief Add a real array 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 p = trim(misc_optional(path,'.')) array_size = size(attrValue,kind=HSIZE_T) call H5Screate_simple_f(1, array_size, space_id, hdferr, array_size) call HDF5_chkerr(hdferr) call H5Aexists_by_name_f(loc_id,p,attrLabel,attrExists,hdferr) call HDF5_chkerr(hdferr) if (attrExists) then call H5Adelete_by_name_f(loc_id,p,attrLabel,hdferr) call HDF5_chkerr(hdferr) end if call H5Acreate_by_name_f(loc_id,p,trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, array_size, hdferr) call HDF5_chkerr(hdferr) call H5Aclose_f(attr_id,hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(space_id,hdferr) call HDF5_chkerr(hdferr) 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) call HDF5_chkerr(hdferr) if (linkExists) then call H5Ldelete_f(loc_id,link_name, hdferr) call HDF5_chkerr(hdferr) end if call H5Lcreate_soft_f(target_name, loc_id, link_name, hdferr) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) call initialize_read(dset_id,filespace_id,memspace_id,plist_id, aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_real5 !-------------------------------------------------------------------------------------------------- !> @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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) 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(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) integer :: hdferr myShape = int(shape(dataset),HSIZE_T) call initialize_read(dset_id,filespace_id,memspace_id,plist_id,aplist_id, & myStart,totalShape,loc_id,myShape,datasetName, & misc_optional(parallel,parallel_default)) if (any(totalShape == 0)) return 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) call HDF5_chkerr(hdferr) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) end subroutine HDF5_read_int5 #if defined(__GFORTRAN__) !-------------------------------------------------------------------------------------------------- !> @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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real5 #else !-------------------------------------------------------------------------------------------------- !> @brief write dataset of type real with 1-5 dimension !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_real(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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE, & misc_optional(parallel,parallel_default)) if (product(totalShape) /= 0) then select rank(dataset) rank (1) 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) rank (2) 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) rank (3) 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) rank (4) 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) rank (5) 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) end select call HDF5_chkerr(hdferr) end if call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_real #endif !-------------------------------------------------------------------------------------------------- !> @brief Write dataset of type string (scalar). !> @details Not collective, must be called by one process at at time. !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_str(dataset,loc_id,datasetName) character(len=*), intent(in) :: dataset integer(HID_T), intent(in) :: loc_id character(len=*), intent(in) :: datasetName !< name of the dataset in the file integer(HID_T) :: filetype_id, memtype_id, space_id, dataset_id, dcpl integer :: hdferr character(len=len_trim(dataset,pI64),kind=C_CHAR), target :: dataset_ dataset_ = trim(dataset) call H5Tcopy_f(H5T_C_S1, filetype_id, hdferr) call HDF5_chkerr(hdferr) call H5Tset_size_f(filetype_id, len(dataset_,SIZE_T)+1_SIZE_T, hdferr) ! +1 for NULL call HDF5_chkerr(hdferr) call H5Tcopy_f(H5T_FORTRAN_S1, memtype_id, hdferr) call HDF5_chkerr(hdferr) call H5Tset_size_f(memtype_id, len(dataset_,SIZE_T), hdferr) call HDF5_chkerr(hdferr) call H5Pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr) call HDF5_chkerr(hdferr) call H5Pset_chunk_f(dcpl, 1, [1_HSIZE_T], hdferr) call HDF5_chkerr(hdferr) call H5Pset_Fletcher32_f(dcpl,hdferr) call HDF5_chkerr(hdferr) if (compression_possible .and. len(dataset,pI64) > 1024_pI64*256_pI64) then call H5Pset_shuffle_f(dcpl, hdferr) call HDF5_chkerr(hdferr) call H5Pset_deflate_f(dcpl, 6, hdferr) call HDF5_chkerr(hdferr) end if call H5Screate_simple_f(1, [1_HSIZE_T], space_id, hdferr) call HDF5_chkerr(hdferr) CALL H5Dcreate_f(loc_id, datasetName, filetype_id, space_id, dataset_id, hdferr, dcpl) call HDF5_chkerr(hdferr) call H5Dwrite_f(dataset_id, memtype_id, c_loc(dataset_(1:1)), hdferr) call HDF5_chkerr(hdferr) call H5Pclose_f(dcpl, hdferr) call HDF5_chkerr(hdferr) call H5Dclose_f(dataset_id, hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(space_id, hdferr) call HDF5_chkerr(hdferr) call H5Tclose_f(memtype_id, hdferr) call HDF5_chkerr(hdferr) call H5Tclose_f(filetype_id, hdferr) call HDF5_chkerr(hdferr) end subroutine HDF5_write_str #if defined(__GFORTRAN__) !-------------------------------------------------------------------------------------------------- !> @brief Write dataset of type integer with 1 dimensions. !-------------------------------------------------------------------------------------------------- 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_INTEGER, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_INTEGER, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_INTEGER, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_INTEGER, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if 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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_INTEGER, & misc_optional(parallel,parallel_default)) 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) call HDF5_chkerr(hdferr) end if call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int5 #else !-------------------------------------------------------------------------------------------------- !> @brief Write dataset of type integer with 1-5 dimensions. !-------------------------------------------------------------------------------------------------- subroutine HDF5_write_int(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(rank(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) call initialize_write(dset_id,filespace_id,memspace_id,plist_id, & myStart,totalShape,loc_id,myShape,datasetName,H5T_NATIVE_INTEGER, & misc_optional(parallel,parallel_default)) if (product(totalShape) /= 0) then select rank(dataset) rank(1) 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) rank(2) 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) rank(3) 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) rank(4) 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) rank(5) 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) end select call HDF5_chkerr(hdferr) end if call finalize_write(plist_id, dset_id, filespace_id, memspace_id) end subroutine HDF5_write_int #endif !-------------------------------------------------------------------------------------------------- !> @brief Initialize read handles and determine global shape in case of parallel IO. !-------------------------------------------------------------------------------------------------- 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)) :: & myStart, & globalShape !< shape of the dataset (all processes) integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id integer(MPI_INTEGER_KIND), dimension(worldsize) :: readSize !< contribution of all processes integer :: hdferr integer(MPI_INTEGER_KIND) :: err_MPI !------------------------------------------------------------------------------------------------- ! creating a property list for transfer properties (is collective for MPI) call H5Pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call HDF5_chkerr(hdferr) !-------------------------------------------------------------------------------------------------- readSize = 0_MPI_INTEGER_KIND readSize(worldrank+1) = int(localShape(ubound(localShape,1)),MPI_INTEGER_KIND) #ifdef PETSC if (parallel) then call H5Pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call HDF5_chkerr(hdferr) call MPI_Allgather(int(localShape(ubound(localShape,1)),MPI_INTEGER_KIND),1_MPI_INTEGER_KIND,MPI_INTEGER,& readSize,1_MPI_INTEGER_KIND,MPI_INTEGER,MPI_COMM_WORLD,err_MPI) if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error' end if #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)] if (any(globalShape == 0)) then call H5Pclose_f(plist_id, hdferr) call HDF5_chkerr(hdferr) return end if !-------------------------------------------------------------------------------------------------- ! create dataspace in memory (local shape) call H5Screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape) call HDF5_chkerr(hdferr) !-------------------------------------------------------------------------------------------------- ! creating a property list for IO and set it to collective call H5Pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call HDF5_chkerr(hdferr) #ifdef PETSC call H5Pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) call HDF5_chkerr(hdferr) #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) call HDF5_chkerr(hdferr) call H5Dget_space_f(dset_id, filespace_id, hdferr) call HDF5_chkerr(hdferr) !-------------------------------------------------------------------------------------------------- ! 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) call HDF5_chkerr(hdferr) end subroutine initialize_read !-------------------------------------------------------------------------------------------------- !> @brief Close read 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) call HDF5_chkerr(hdferr) call H5Pclose_f(aplist_id, hdferr) call HDF5_chkerr(hdferr) call H5Dclose_f(dset_id, hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(filespace_id, hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(memspace_id, hdferr) call HDF5_chkerr(hdferr) end subroutine finalize_read !-------------------------------------------------------------------------------------------------- !> @brief Initialize write handles and determine global shape in case of parallel IO. !-------------------------------------------------------------------------------------------------- subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, & myStart, totalShape, & loc_id,localShape,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(:) :: localShape integer(HSIZE_T), intent(out), dimension(size(localShape)) :: & myStart, & totalShape !< shape of the dataset (all processes) integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id integer(MPI_INTEGER_KIND), dimension(worldsize) :: writeSize !< contribution of all processes integer(HID_T) :: dcpl integer :: hdferr integer(MPI_INTEGER_KIND) :: err_MPI integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T !------------------------------------------------------------------------------------------------- ! creating a property list for transfer properties (is collective when writing in parallel) call H5Pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call HDF5_chkerr(hdferr) #ifdef PETSC if (parallel) then call H5Pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call HDF5_chkerr(hdferr) end if #endif !-------------------------------------------------------------------------------------------------- ! determine the global data layout among all processes writeSize = 0_MPI_INTEGER_KIND writeSize(worldrank+1) = int(localShape(ubound(localShape,1)),MPI_INTEGER_KIND) #ifdef PETSC if (parallel) then call MPI_Allgather(int(localShape(ubound(localShape,1)),MPI_INTEGER_KIND),1_MPI_INTEGER_KIND,MPI_INTEGER,& writeSize,1_MPI_INTEGER_KIND,MPI_INTEGER,MPI_COMM_WORLD,err_MPI) if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error' end if #endif myStart = int(0,HSIZE_T) myStart(ubound(myStart)) = int(sum(writeSize(1:worldrank)),HSIZE_T) totalShape = [localShape(1:ubound(localShape,1)-1),int(sum(writeSize),HSIZE_T)] !-------------------------------------------------------------------------------------------------- ! chunk dataset, enable compression for larger datasets call H5Pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr) call HDF5_chkerr(hdferr) if (product(totalShape) > 0) then call H5Pset_Fletcher32_f(dcpl,hdferr) call HDF5_chkerr(hdferr) if (product(totalShape) >= chunkSize*2_HSIZE_T) then call H5Pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr) call HDF5_chkerr(hdferr) if (compression_possible) then call H5Pset_shuffle_f(dcpl, hdferr) call HDF5_chkerr(hdferr) call H5Pset_deflate_f(dcpl, 6, hdferr) call HDF5_chkerr(hdferr) end if else call H5Pset_chunk_f(dcpl, size(totalShape), totalShape, hdferr) call HDF5_chkerr(hdferr) end if end if !-------------------------------------------------------------------------------------------------- ! create dataspace in memory (local shape) and in file (global shape) call H5Screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape) call HDF5_chkerr(hdferr) call H5Screate_simple_f(size(totalShape), totalShape, filespace_id, hdferr, totalShape) call HDF5_chkerr(hdferr) !-------------------------------------------------------------------------------------------------- ! 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) call HDF5_chkerr(hdferr) call H5Sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr) call HDF5_chkerr(hdferr) call H5Pclose_f(dcpl , hdferr) call HDF5_chkerr(hdferr) 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 write 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) call HDF5_chkerr(hdferr) call H5Dclose_f(dset_id, hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(filespace_id, hdferr) call HDF5_chkerr(hdferr) call H5Sclose_f(memspace_id, hdferr) call HDF5_chkerr(hdferr) end subroutine finalize_write end module HDF5_Utilities