223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity
DAMASK_EICMD/src/HDF5_utilities.f90

1897 lines
96 KiB
Fortran
Raw Blame History

!--------------------------------------------------------------------------------------------------
!> @author Vitesh Shah, Max-Planck-Institut für Eisenforschung GmbH
!> @author Yi-Chin Yang, Max-Planck-Institut für Eisenforschung GmbH
!> @author Jennifer Nastola, Max-Planck-Institut für Eisenforschung GmbH
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!--------------------------------------------------------------------------------------------------
module HDF5_utilities
use HDF5
#ifdef PETSC
#include <petsc/finclude/petscsys.h>
use PETScSys
#if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY)
use MPI
#endif
#endif
use prec
use parallelization
implicit none
private
!--------------------------------------------------------------------------------------------------
!> @brief reads integer or float data of defined shape from file
!> @details for parallel IO, all dimension except for the last need to match
!--------------------------------------------------------------------------------------------------
interface HDF5_read
module procedure HDF5_read_real1
module procedure HDF5_read_real2
module procedure HDF5_read_real3
module procedure HDF5_read_real4
module procedure HDF5_read_real5
module procedure HDF5_read_real6
module procedure HDF5_read_real7
module procedure HDF5_read_int1
module procedure HDF5_read_int2
module procedure HDF5_read_int3
module procedure HDF5_read_int4
module procedure HDF5_read_int5
module procedure HDF5_read_int6
module procedure HDF5_read_int7
end interface HDF5_read
!--------------------------------------------------------------------------------------------------
!> @brief writes integer or real data of defined shape to file
!> @details for parallel IO, all dimension except for the last need to match
!--------------------------------------------------------------------------------------------------
interface HDF5_write
module procedure HDF5_write_real1
module procedure HDF5_write_real2
module procedure HDF5_write_real3
module procedure HDF5_write_real4
module procedure HDF5_write_real5
module procedure HDF5_write_real6
module procedure HDF5_write_real7
module procedure HDF5_write_int1
module procedure HDF5_write_int2
module procedure HDF5_write_int3
module procedure HDF5_write_int4
module procedure HDF5_write_int5
module procedure HDF5_write_int6
module procedure HDF5_write_int7
end interface HDF5_write
!--------------------------------------------------------------------------------------------------
!> @brief attached attributes of type char, integer or real to a file/dataset/group
!--------------------------------------------------------------------------------------------------
interface HDF5_addAttribute
module procedure HDF5_addAttribute_str
module procedure HDF5_addAttribute_int
module procedure HDF5_addAttribute_real
module procedure HDF5_addAttribute_int_array
module procedure HDF5_addAttribute_real_array
end interface HDF5_addAttribute
#ifdef PETSC
logical, parameter, private :: parallel_default = .true.
#else
logical, parameter, private :: parallel_default = .false.
#endif
public :: &
HDF5_utilities_init, &
HDF5_read, &
HDF5_write, &
HDF5_addAttribute, &
HDF5_addGroup, &
HDF5_openGroup, &
HDF5_closeGroup, &
HDF5_openFile, &
HDF5_closeFile, &
HDF5_objectExists, &
HDF5_setLink
contains
!--------------------------------------------------------------------------------------------------
!> @brief initialize HDF5 libary and do sanity checks
!--------------------------------------------------------------------------------------------------
subroutine HDF5_utilities_init
integer :: hdferr
integer(SIZE_T) :: typeSize
print'(/,a)', ' <<<+- HDF5_Utilities init -+>>>'
!--------------------------------------------------------------------------------------------------
!initialize HDF5 library and check if integer and float type size match
call h5open_f(hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (int(bit_size(0),SIZE_T)/=typeSize*8) &
error stop 'Default integer size does not match H5T_NATIVE_INTEGER'
call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (int(storage_size(0.0_pReal),SIZE_T)/=typeSize*8) &
error stop 'pReal does not match H5T_NATIVE_DOUBLE'
end subroutine HDF5_utilities_init
!--------------------------------------------------------------------------------------------------
!> @brief open and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openFile(fileName,mode)
character(len=*), intent(in) :: fileName
character, intent(in), optional :: mode
character :: m
integer(HID_T) :: plist_id
integer :: hdferr
if (present(mode)) then
m = mode
else
m = 'r'
endif
call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSC
call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
#endif
if (m == 'w') then
call h5fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,access_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
elseif(m == 'a') then
call h5fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
elseif(m == 'r') then
call h5fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
else
error stop 'unknown access mode'
endif
call h5pclose_f(plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end function HDF5_openFile
!--------------------------------------------------------------------------------------------------
!> @brief close the opened HDF5 output file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeFile(fileHandle)
integer(HID_T), intent(in) :: fileHandle
integer :: hdferr
call h5fclose_f(fileHandle,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_closeFile
!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the fileHandle
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_addGroup(fileHandle,groupName)
integer(HID_T), intent(in) :: fileHandle
character(len=*), intent(in) :: groupName
integer :: hdferr
integer(HID_T) :: aplist_id
!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------
! setting I/O mode to collective
#ifdef PETSC
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
#endif
!-------------------------------------------------------------------------------------------------
! Create group
call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id)
if(hdferr < 0) error stop 'HDF5 error'
call h5pclose_f(aplist_id,hdferr)
end function HDF5_addGroup
!--------------------------------------------------------------------------------------------------
!> @brief open an existing group of a file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openGroup(fileHandle,groupName)
integer(HID_T), intent(in) :: fileHandle
character(len=*), intent(in) :: groupName
integer :: hdferr
integer(HID_T) :: aplist_id
logical :: is_collective
!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------
! setting I/O mode to collective
#ifdef PETSC
call h5pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
#endif
!-------------------------------------------------------------------------------------------------
! opening the group
call h5gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id)
if(hdferr < 0) error stop 'HDF5 error'
call h5pclose_f(aplist_id,hdferr)
end function HDF5_openGroup
!--------------------------------------------------------------------------------------------------
!> @brief close a group
!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeGroup(group_id)
integer(HID_T), intent(in) :: group_id
integer :: hdferr
call h5gclose_f(group_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_closeGroup
!--------------------------------------------------------------------------------------------------
!> @brief check whether a group or a dataset exists
!--------------------------------------------------------------------------------------------------
logical function HDF5_objectExists(loc_id,path)
integer(HID_T), intent(in) :: loc_id
character(len=*), intent(in), optional :: path
integer :: hdferr
character(len=:), allocatable :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
call h5lexists_f(loc_id, p, HDF5_objectExists, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if(HDF5_objectExists) then
call h5oexists_by_name_f(loc_id, p, HDF5_objectExists, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
end function HDF5_objectExists
!--------------------------------------------------------------------------------------------------
!> @brief adds a string attribute to the path given relative to the location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path)
integer(HID_T), intent(in) :: loc_id
character(len=*), intent(in) :: attrLabel, attrValue
character(len=*), intent(in), optional :: path
integer(HID_T) :: attr_id, space_id, type_id
logical :: attrExists
integer :: hdferr
character(len=:), allocatable :: p
character(len=:,kind=C_CHAR), allocatable,target :: attrValue_
type(c_ptr), target, dimension(1) :: ptr
if (present(path)) then
p = trim(path)
else
p = '.'
endif
attrValue_ = trim(attrValue)//C_NULL_CHAR
ptr(1) = c_loc(attrValue_)
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tcopy_f(H5T_STRING, type_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, type_id, c_loc(ptr(1)), hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(type_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_str
!--------------------------------------------------------------------------------------------------
!> @brief adds a integer attribute to the path given relative to the location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path)
integer(HID_T), intent(in) :: loc_id
character(len=*), intent(in) :: attrLabel
integer, intent(in) :: attrValue
character(len=*), intent(in), optional :: path
integer(HID_T) :: attr_id, space_id
integer :: hdferr
logical :: attrExists
character(len=:), allocatable :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, int([1],HSIZE_T), hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_int
!--------------------------------------------------------------------------------------------------
!> @brief adds a integer attribute to the path given relative to the location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path)
integer(HID_T), intent(in) :: loc_id
character(len=*), intent(in) :: attrLabel
real(pReal), intent(in) :: attrValue
character(len=*), intent(in), optional :: path
integer(HID_T) :: attr_id, space_id
integer :: hdferr
logical :: attrExists
character(len=:), allocatable :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, int([1],HSIZE_T), hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_real
!--------------------------------------------------------------------------------------------------
!> @brief adds a integer attribute to the path given relative to the location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path)
integer(HID_T), intent(in) :: loc_id
character(len=*), intent(in) :: attrLabel
integer, intent(in), dimension(:) :: attrValue
character(len=*), intent(in), optional :: path
integer(HSIZE_T),dimension(1) :: array_size
integer(HID_T) :: attr_id, space_id
integer :: hdferr
logical :: attrExists
character(len=:), allocatable :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
array_size = size(attrValue,kind=HSIZE_T)
call h5screate_simple_f(1, array_size, space_id, hdferr, array_size)
if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, array_size, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_int_array
!--------------------------------------------------------------------------------------------------
!> @brief adds a real attribute to the path given relative to the location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path)
integer(HID_T), intent(in) :: loc_id
character(len=*), intent(in) :: attrLabel
real(pReal), intent(in), dimension(:) :: attrValue
character(len=*), intent(in), optional :: path
integer(HSIZE_T),dimension(1) :: array_size
integer(HID_T) :: attr_id, space_id
integer :: hdferr
logical :: attrExists
character(len=:), allocatable :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
array_size = size(attrValue,kind=HSIZE_T)
call h5screate_simple_f(1, array_size, space_id, hdferr, array_size)
if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, array_size, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_real_array
!--------------------------------------------------------------------------------------------------
!> @brief set link to object in results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_setLink(loc_id,target_name,link_name)
character(len=*), intent(in) :: target_name, link_name
integer(HID_T), intent(in) :: loc_id
integer :: hdferr
logical :: linkExists
call h5lexists_f(loc_id, link_name,linkExists, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if (linkExists) then
call h5ldelete_f(loc_id,link_name, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
call h5lcreate_soft_f(target_name, loc_id, link_name, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_setLink
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type real with 1 dimension
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real1(dataset,loc_id,datasetName,parallel)
real(pReal), intent(out), dimension(:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: & ! ToDo: Fortran 2018 size(shape(A)) = rank(A)
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real1
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type real with 2 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real2(dataset,loc_id,datasetName,parallel)
real(pReal), intent(out), dimension(:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real2
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type real with 2 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real3(dataset,loc_id,datasetName,parallel)
real(pReal), intent(out), dimension(:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real3
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type real with 4 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real4(dataset,loc_id,datasetName,parallel)
real(pReal), intent(out), dimension(:,:,:,:) :: dataset !< read data
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real4
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type real with 5 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real5(dataset,loc_id,datasetName,parallel)
real(pReal), intent(out), dimension(:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real5
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type real with 6 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real6(dataset,loc_id,datasetName,parallel)
real(pReal), intent(out), dimension(:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real6
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type real with 7 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real7(dataset,loc_id,datasetName,parallel)
real(pReal), intent(out), dimension(:,:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real7
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type integer with 1 dimension
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int1(dataset,loc_id,datasetName,parallel)
integer, intent(out), dimension(:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int1
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type integer with 2 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int2(dataset,loc_id,datasetName,parallel)
integer, intent(out), dimension(:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int2
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type integer with 3 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int3(dataset,loc_id,datasetName,parallel)
integer, intent(out), dimension(:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int3
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type integer withh 4 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int4(dataset,loc_id,datasetName,parallel)
integer, intent(out), dimension(:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int4
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type integer with 5 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int5(dataset,loc_id,datasetName,parallel)
integer, intent(out), dimension(:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int5
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type integer with 6 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int6(dataset,loc_id,datasetName,parallel)
integer, intent(out), dimension(:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int6
!--------------------------------------------------------------------------------------------------
!> @brief read dataset of type integer with 7 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int7(dataset,loc_id,datasetName,parallel)
integer, intent(out), dimension(:,:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
integer :: hdferr
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
!---------------------------------------------------------------------------------------------------
! initialize HDF5 data structures
if (present(parallel)) then
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int7
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 1 dimension
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real1(dataset,loc_id,datasetName,parallel)
real(pReal), intent(in), dimension(:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real1
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 2 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real2(dataset,loc_id,datasetName,parallel)
real(pReal), intent(in), dimension(:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real2
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 3 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real3(dataset,loc_id,datasetName,parallel)
real(pReal), intent(in), dimension(:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real3
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 4 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real4(dataset,loc_id,datasetName,parallel)
real(pReal), intent(in), dimension(:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real4
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 5 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real5(dataset,loc_id,datasetName,parallel)
real(pReal), intent(in), dimension(:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real5
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 6 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real6(dataset,loc_id,datasetName,parallel)
real(pReal), intent(in), dimension(:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real6
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type real with 7 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real7(dataset,loc_id,datasetName,parallel)
real(pReal), intent(in), dimension(:,:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real7
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type integer with 1 dimension
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int1(dataset,loc_id,datasetName,parallel)
integer, intent(in), dimension(:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int1
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type integer with 2 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int2(dataset,loc_id,datasetName,parallel)
integer, intent(in), dimension(:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int2
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type integer with 3 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int3(dataset,loc_id,datasetName,parallel)
integer, intent(in), dimension(:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int3
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type integer with 4 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int4(dataset,loc_id,datasetName,parallel)
integer, intent(in), dimension(:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int4
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type integer with 5 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int5(dataset,loc_id,datasetName,parallel)
integer, intent(in), dimension(:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int5
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type integer with 6 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int6(dataset,loc_id,datasetName,parallel)
integer, intent(in), dimension(:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int6
!--------------------------------------------------------------------------------------------------
!> @brief write dataset of type integer with 7 dimensions
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int7(dataset,loc_id,datasetName,parallel)
integer, intent(in), dimension(:,:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
myShape, & !< shape of the dataset (this process)
totalShape !< shape of the dataset (all processes)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int7
!--------------------------------------------------------------------------------------------------
!> @brief initialize HDF5 handles, determines global shape and start for parallel read
!--------------------------------------------------------------------------------------------------
subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, globalShape, &
loc_id,localShape,datasetName,parallel)
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in) :: parallel
integer(HSIZE_T), intent(in), dimension(:) :: &
localShape
integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: &
myStart, &
globalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer, dimension(worldsize) :: &
readSize !< contribution of all processes
integer :: ierr
integer :: hdferr
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective for MPI)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
readSize = 0
readSize(worldrank+1) = int(localShape(ubound(localShape,1)))
#ifdef PETSC
if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) error stop 'MPI error'
endif
#endif
myStart = int(0,HSIZE_T)
myStart(ubound(myStart)) = int(sum(readSize(1:worldrank)),HSIZE_T)
globalShape = [localShape(1:ubound(localShape,1)-1),int(sum(readSize),HSIZE_T)]
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
! creating a property list for IO and set it to collective
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSC
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
#endif
!--------------------------------------------------------------------------------------------------
! open the dataset in the file and get the space ID
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if(hdferr < 0) error stop 'HDF5 error'
call h5dget_space_f(dset_id, filespace_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine initialize_read
!--------------------------------------------------------------------------------------------------
!> @brief closes HDF5 handles
!--------------------------------------------------------------------------------------------------
subroutine finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer :: hdferr
call h5pclose_f(plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5pclose_f(aplist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5dclose_f(dset_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(filespace_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(memspace_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine finalize_read
!--------------------------------------------------------------------------------------------------
!> @brief initialize HDF5 handles, determines global shape and start for parallel write
!--------------------------------------------------------------------------------------------------
subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, &
loc_id,myShape,datasetName,datatype,parallel)
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in) :: parallel
integer(HID_T), intent(in) :: datatype
integer(HSIZE_T), intent(in), dimension(:) :: &
myShape
integer(HSIZE_T), intent(out), dimension(size(myShape,1)):: &
myStart, &
totalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id
integer, dimension(worldsize) :: writeSize !< contribution of all processes
integer(HID_T) :: dcpl
integer :: ierr, hdferr, HDF5_major, HDF5_minor, HDF5_release
integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective when reading in parallel)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSC
if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif
#endif
!--------------------------------------------------------------------------------------------------
! determine the global data layout among all processes
writeSize = 0
writeSize(worldrank+1) = int(myShape(ubound(myShape,1)))
#ifdef PETSC
if (parallel) then
call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) error stop 'MPI error'
endif
#endif
myStart = int(0,HSIZE_T)
myStart(ubound(myStart)) = int(sum(writeSize(1:worldrank)),HSIZE_T)
totalShape = [myShape(1:ubound(myShape,1)-1),int(sum(writeSize),HSIZE_T)]
!--------------------------------------------------------------------------------------------------
! compress (and chunk) larger datasets
call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
if(product(totalShape) >= chunkSize*2_HSIZE_T) then
call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr)
if (hdferr < 0) error stop 'HDF5 error'
if (HDF5_major == 1 .and. HDF5_minor >= 12) then ! https://forum.hdfgroup.org/t/6186
call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_shuffle_f(dcpl, hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_deflate_f(dcpl, 6, hdferr)
if (hdferr < 0) error stop 'HDF5 error'
call h5pset_Fletcher32_f(dcpl,hdferr)
if (hdferr < 0) error stop 'HDF5 error'
endif
endif
!--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) and in file (global shape)
call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape)
if(hdferr < 0) error stop 'HDF5 error'
call h5screate_simple_f(size(totalShape), totalShape, filespace_id, hdferr, totalShape)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
! create dataset in the file and select a hyperslab from it (the portion of the current process)
call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr, dcpl)
if(hdferr < 0) error stop 'HDF5 error'
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, myShape, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5pclose_f(dcpl , hdferr)
if(hdferr < 0) error stop 'HDF5 error'
contains
!------------------------------------------------------------------------------------------------
!> @brief determine chunk layout
!------------------------------------------------------------------------------------------------
pure function getChunks(totalShape,chunkSize)
integer(HSIZE_T), dimension(:), intent(in) :: totalShape
integer(HSIZE_T), intent(in) :: chunkSize
integer(HSIZE_T), dimension(size(totalShape)) :: getChunks
getChunks = [totalShape(1:size(totalShape)-1),&
chunkSize/product(totalShape(1:size(totalShape)-1))]
end function getChunks
end subroutine initialize_write
!--------------------------------------------------------------------------------------------------
!> @brief closes HDF5 handles
!--------------------------------------------------------------------------------------------------
subroutine finalize_write(plist_id, dset_id, filespace_id, memspace_id)
integer(HID_T), intent(in) :: dset_id, filespace_id, memspace_id, plist_id
integer :: hdferr
call h5pclose_f(plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5dclose_f(dset_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(filespace_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(memspace_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
end subroutine finalize_write
end module HDF5_Utilities
Reference in New Issue View Git Blame Copy Permalink