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DAMASK_EICMD/src/HDF5_utilities.f90

2061 lines
98 KiB
Fortran
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!--------------------------------------------------------------------------------------------------
!> @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 <petsc/finclude/petscsys.h>
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_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 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__)
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
#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 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(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_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(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_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(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
!--------------------------------------------------------------------------------------------------
!> @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(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_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(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_int7
#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
!--------------------------------------------------------------------------------------------------
!> @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(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_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(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_real7
#else
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 1-7 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)
rank (6)
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 (7)
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
!--------------------------------------------------------------------------------------------------
!> @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(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_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(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_int7
#else
!--------------------------------------------------------------------------------------------------
!> @brief Write dataset of type integer with 1-7 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)
rank(6)
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(7)
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
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