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Multi Dataset (#2120)
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* Fix bug with cross platform compatibility of references within vlens.
No testing yet.

* Merge from multi_rd_wd_coll_io to a more recent branch from develop.
Untested, probably does not work yet.

* Committing clang-format changes

* Committing clang-format changes

* Fix many bugs in multi dataset branch.  Mostly works, some issues in
SWMR tests.

* Committing clang-format changes

* Disable test in swmr.c that was failing due to bug in HDF5 unrelated to
multi dataset.

* Committing clang-format changes

* Fixed fortran multi-dataset tests

* Fixed xlf errors

* Added benchmark code for multi-datasets

* loops over datasets

* added missing error arg.

* Added gnuplot formatting

* Jonathan Kim original MD benchmarking code

* updated MD benchmarking code

* code clean-up

* Only make files in feature test mode

* misc clean-up

* removed TEST_MDSET_NO_LAST_DSET_2ND_PROC option

* Committing clang-format changes

* Change multi dataset API to use arrays of individual parameters instead
of the parameter struct.

* Committing clang-format changes

* Update to new multi dataset Fortran API and tests. (#1724)

* Update to new multi dataset Fortran API and tests.
* Sync Fortran with develop.
* skipping h5pget_mpio_actual_io_mode_f for now

* Fixed issue with dxpl_id, changed to variable size dim. (#1770)

* Remove "is_coll_broken" field from H5D_io_info_t struct

* Committing clang-format changes

* Minor cleanup in multi dataset code.

* Committing clang-format changes

* Clean up in multi dataset code.

* Committing clang-format changes

* Committing clang-format changes

* Fix speeling

* Fix bug in parallel compression. Switch base_maddr in io_info to be a
union.

* Committing clang-format changes

* Implement selection I/O support with multi dataset.  Will be broken in
parallel until PR 1803 is merged to develop then the MDS branch.

* Committing clang-format changes

* Spelling

* Fix bug in multi dataset that could cause errors when only some of the
datasets in the multi dataset I/O used type conversion.

* Committing clang-format changes

* Integrate multi dataset APIs with VOL layer.  Add async versions of
multi dataset APIs.

* Committing clang-format changes

* Spelling fixes

* Fix bug in non-parallel HDF5 compilation.

* Committing clang-format changes

* Fix potential memory/free list error. Minor performance fix. Other minor
changes.

* Committing clang-format changes

* Fix memory leak with memory dataspace for I/O.

* Committing clang-format changes

* Fix stack variables too large.  Rename H5D_dset_info_t to
H5D_dset_io_info_t.

* Committing clang-format changes

* Remove mem_space_alloc field from H5D_dset_io_info_t.  Each function is
now responsible for freeing any spaces it adds to dset_info.

* Committing clang-format changes

* fixed _multi Fortran declaration

* Refactor various things in (mostly) the serial I/O code path to make
things more maintainable.

* Committing clang-format changes

* updated to array based, doxygen, and examples

* Reinstate H5D_chunk_map_t, stored (via pointer) inside
H5D_dset_io_info_t.

* Change from calloc to malloc for H5D_dset_io_info_t and H5D_chunk_map_t.
Switch temporary dset_infos to be local stack variables.

* Committing clang-format changes

* format cleanup

* format cleanup

* added coll and ind

* Modify all parallel I/O paths to take dset_info instead of assuming
dset_info[0].

* Committing clang-format changes

* fixed output

* Rework parallel I/O code to work properly with multi dataset in more
cases.  Fix bug in parallel compression.

* Committing clang-format changes

* Prevent H5D__multi_chunk_collective_io() from messing up collective opt
property for other datasets in I/O.  Other minor cleanup.  Add new test
case to t_pmulti_dset.c for H5FD_MPIO_INDIVIDUAL_IO, disabled for now
due to failures apparently unrelated to multi dataset code.

* Fix spelling

* Committing clang-format changes

* Replace N log N algorithm for finding chunk in
H5D__multi_chunk_collective_io() with O(N) algorithm, and remove use of
io_info->sel_pieces in that function.

* Committing clang-format changes

* Replace sel_pieces skiplist in io_info with flat array of pointers, use
qsort in I/O routine only when necessary.

* Committing clang-format changes

* Add new test case to mdset.c

* Committing clang-format changes

* Fix spelling

* Very minor fix in H5VL__native_dataset_read()

* Fix bug that could affect filtered parallel multi-dataset I/O.

* Add RM entries for H5Dread_multi(), H5Dread_multi_async(),
H5Dwrite_multi(), and H5Dwrite_multi_async()

* Unskip test in swmr.c

* Committing clang-format changes

* Eliminate H5D__pre_read and H5D__pre_write

* Remove examples/ph5mdsettest.c. Will fix and re-add as a test.

* Enable hyperslab combinations in mdset test

* Committing clang-format changes

* Clarify H5Dread/write_multi documentation.

* Fix bugs in multi-dataset I/O.  Expand serial multi dataset test.
Update macro in parallel multi dataset test.

* Committing clang-format changes

* Spelling

* Remove obsolete entry in bin/trace

* Rework type conversion buffer allocation. Only one buffer is shared
between datasets in mdset mode, and it is malloced instead of calloced.

* Committing clang-format changes

* Fix bug in error handling in H5D__read/write

* added multi-dataset fortran check with optional dataset creation id (#2150)

* removed dup. dll entry

* Address comments from code review.

* Remove spurious changes in H5Fmpi.c

* Fix issue with reading unallocated datasets in multi-dataset mode.
Address other comments from code review.

* Committing clang-format changes

* Delay chunk index lookup from io_init to mdio_init so it doesn't add
overhead to single dataset I/O.

* Committing clang-format changes

* Fix inappropriate use of piece_count

* updated copyright on new file, removed benchmark from testing dir.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: M. Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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104 changes: 103 additions & 1 deletion fortran/src/H5Dff.F90
Original file line number Diff line number Diff line change
Expand Up @@ -1098,7 +1098,7 @@ END SUBROUTINE H5Dvlen_reclaim_f
!>
!! \ingroup FH5D
!!
!! \brief Writes raw data from a dataset into a buffer.
!! \brief Writes raw data from a buffer to a dataset.
!!
!! \attention \fortran_approved
!!
Expand Down Expand Up @@ -1762,6 +1762,108 @@ SUBROUTINE h5dfill_char(fill_value, space_id, buf, hdferr)
CALL h5dfill_ptr(f_ptr_fill_value, fill_type_id, f_ptr_buf, mem_type_id, space_id, hdferr)

END SUBROUTINE h5dfill_char
!>
!! \ingroup FH5D
!!
!! \brief Reads data from a file to memory buffers for multiple datasets.
!!
!! \param count Number of datasets to write to.
!! \param dset_id Identifier of the dataset to write to.
!! \param mem_type_id Identifier of the memory datatype.
!! \param mem_space_id Identifier of the memory dataspace.
!! \param file_space_id Identifier of the dataset&apos;s dataspace in the file.
!! \param buf Buffer with data to be written to the file.
!! \param hdferr \fortran_error
!! \param xfer_prp Identifier of a transfer property list for this I/O operation.
!!
SUBROUTINE H5Dread_multi_f(count, dset_id, mem_type_id, mem_space_id, file_space_id, buf, hdferr, xfer_prp)
IMPLICIT NONE

INTEGER(SIZE_T), INTENT(IN) :: count
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: dset_id
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_type_id
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_space_id
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: file_space_id
TYPE(C_PTR), DIMENSION(*) :: buf
INTEGER, INTENT(OUT) :: hdferr
INTEGER(HID_T), INTENT(IN), OPTIONAL :: xfer_prp

INTEGER(HID_T) :: xfer_prp_default

INTERFACE
INTEGER FUNCTION H5Dread_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp, buf) &
BIND(C, NAME='H5Dread_multi')
IMPORT :: SIZE_T
IMPORT :: HID_T
IMPORT :: C_PTR
IMPLICIT NONE
INTEGER(SIZE_T), VALUE :: count
INTEGER(HID_T), DIMENSION(*) :: dset_id
INTEGER(HID_T), DIMENSION(*) :: mem_type_id
INTEGER(HID_T), DIMENSION(*) :: mem_space_id
INTEGER(HID_T), DIMENSION(*) :: file_space_id
INTEGER(HID_T), VALUE :: xfer_prp
TYPE(C_PTR), DIMENSION(*) :: buf
END FUNCTION H5Dread_multi
END INTERFACE

xfer_prp_default = H5P_DEFAULT_F
IF (PRESENT(xfer_prp)) xfer_prp_default = xfer_prp

hdferr = H5Dread_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp_default, buf)

END SUBROUTINE H5Dread_multi_f
!>
!! \ingroup FH5D
!!
!! \brief Writes data in memory to a file for multiple datasets.
!!
!! \param count Number of datasets to write to.
!! \param dset_id Identifier of the dataset to write to.
!! \param mem_type_id Identifier of the memory datatype.
!! \param mem_space_id Identifier of the memory dataspace.
!! \param file_space_id Identifier of the dataset&apos;s dataspace in the file.
!! \param buf Buffer with data to be written to the file.
!! \param hdferr \fortran_error
!! \param xfer_prp Identifier of a transfer property list for this I/O operation.
!!
SUBROUTINE H5Dwrite_multi_f(count, dset_id, mem_type_id, mem_space_id, file_space_id, buf, hdferr, xfer_prp)
IMPLICIT NONE

INTEGER(SIZE_T), INTENT(IN) :: count
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: dset_id
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_type_id
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: mem_space_id
INTEGER(HID_T), INTENT(IN), DIMENSION(*) :: file_space_id
TYPE(C_PTR), DIMENSION(*) :: buf
INTEGER, INTENT(OUT) :: hdferr
INTEGER(HID_T), INTENT(IN), OPTIONAL :: xfer_prp

INTEGER(HID_T) :: xfer_prp_default

INTERFACE
INTEGER FUNCTION H5Dwrite_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp, buf) &
BIND(C, NAME='H5Dwrite_multi')
IMPORT :: SIZE_T
IMPORT :: HID_T
IMPORT :: C_PTR
IMPLICIT NONE
INTEGER(SIZE_T), VALUE :: count
INTEGER(HID_T), DIMENSION(*) :: dset_id
INTEGER(HID_T), DIMENSION(*) :: mem_type_id
INTEGER(HID_T), DIMENSION(*) :: mem_space_id
INTEGER(HID_T), DIMENSION(*) :: file_space_id
INTEGER(HID_T), VALUE :: xfer_prp
TYPE(C_PTR), DIMENSION(*) :: buf
END FUNCTION H5Dwrite_multi
END INTERFACE

xfer_prp_default = H5P_DEFAULT_F
IF (PRESENT(xfer_prp)) xfer_prp_default = xfer_prp

hdferr = H5Dwrite_multi(count, dset_id, mem_type_id, mem_space_id, file_space_id, xfer_prp_default, buf)

END SUBROUTINE H5Dwrite_multi_f

#endif

Expand Down
2 changes: 2 additions & 0 deletions fortran/src/hdf5_fortrandll.def.in
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,8 @@ H5D_mp_H5DGET_ACCESS_PLIST_F
H5D_mp_H5DWRITE_PTR
H5D_mp_H5DREAD_PTR
H5D_mp_H5DVLEN_RECLAIM_F
H5D_mp_H5DREAD_MULTI_F
H5D_mp_H5DWRITE_MULTI_F
; H5E
H5E_mp_H5ECLEAR_F
H5E_mp_H5EPRINT_F
Expand Down
4 changes: 4 additions & 0 deletions fortran/test/fortranlib_test_F03.F90
Original file line number Diff line number Diff line change
Expand Up @@ -151,6 +151,10 @@ PROGRAM fortranlibtest_F03
CALL test_h5p_file_image(ret_total_error)
CALL write_test_status(ret_total_error, ' Testing h5pset/get file image', total_error)

ret_total_error = 0
CALL multiple_dset_rw(ret_total_error)
CALL write_test_status(ret_total_error, ' Testing multi-dataset reads and writes', total_error)

! write(*,*)
! write(*,*) '========================================='
! write(*,*) 'Testing OBJECT interface '
Expand Down
254 changes: 254 additions & 0 deletions fortran/test/tH5T_F03.F90
Original file line number Diff line number Diff line change
Expand Up @@ -3407,4 +3407,258 @@ SUBROUTINE t_enum_conv(total_error)

END SUBROUTINE t_enum_conv

! Tests the reading and writing of multiple datasets using H5Dread_multi and
! H5Dwrite_multi

SUBROUTINE multiple_dset_rw(total_error)

!-------------------------------------------------------------------------
! Subroutine: multiple_dset_rw
!
! Purpose: Tests the reading and writing of multiple datasets
! using H5Dread_multi and H5Dwrite_multi
!
! Return: Success: 0
! Failure: number of errors
!
! Programmer: M. Scot Breitenfeld
! April 2, 2014
!
!-------------------------------------------------------------------------
!
USE iso_c_binding
USE hdf5
IMPLICIT NONE

INTEGER, INTENT(INOUT) :: total_error ! number of errors
INTEGER :: error ! HDF hdferror flag

INTEGER(SIZE_T), PARAMETER :: ndset = 5 ! Number of data sets
INTEGER(HID_T), DIMENSION(:), ALLOCATABLE :: dset_id
INTEGER(HID_T), DIMENSION(:), ALLOCATABLE :: mem_type_id
INTEGER(HID_T), DIMENSION(:), ALLOCATABLE :: mem_space_id
INTEGER(HID_T), DIMENSION(:), ALLOCATABLE :: file_space_id

INTEGER, PARAMETER :: idim=10, idim2=5, idim3=3 ! size of integer array
INTEGER, PARAMETER :: rdim=5 ! size of real array
INTEGER, PARAMETER :: cdim=3 ! size of character array
INTEGER, PARAMETER :: sdim=2 ! length of character string
INTEGER, PARAMETER :: ddim=2 ! size of derived type array
INTEGER :: i,j,k

TYPE(C_PTR), ALLOCATABLE, DIMENSION(:) :: buf_md ! array to hold the multi-datasets

INTEGER, DIMENSION(1:idim), TARGET :: wbuf_int ! integer write buffer
INTEGER, DIMENSION(1:idim,idim2,idim3), TARGET :: wbuf_intmd
REAL, DIMENSION(1:rdim), TARGET :: wbuf_real ! real write buffer
CHARACTER(LEN=sdim), DIMENSION(1:cdim), TARGET :: wbuf_chr ! character write buffer
INTEGER, DIMENSION(1:idim), TARGET :: rbuf_int ! integer read buffer
INTEGER, DIMENSION(1:idim,idim2,idim3), TARGET :: rbuf_intmd ! integer read buffer
REAL, DIMENSION(1:rdim), TARGET :: rbuf_real ! real read buffer
CHARACTER(LEN=sdim), DIMENSION(1:cdim), TARGET :: rbuf_chr ! character read buffer

TYPE derived
REAL :: r
INTEGER :: i
CHARACTER(LEN=sdim) :: c
END TYPE derived

TYPE(derived), DIMENSION(1:ddim), TARGET :: wbuf_derived ! derived type write buffer
TYPE(derived), DIMENSION(1:ddim), TARGET :: rbuf_derived ! derived type read buffer
INTEGER(HSIZE_T), DIMENSION(1:1) :: dims ! dimension of the spaces
INTEGER(HSIZE_T), DIMENSION(1:3) :: dimsmd ! dimension of the spaces
INTEGER(HID_T) :: file_id, strtype ! handles
INTEGER(SIZE_T) :: obj_count

ALLOCATE(buf_md(1:ndset),stat=error)
IF (error .NE. 0) THEN
WRITE(*,*) 'allocate error'
total_error = total_error + 1
RETURN
ENDIF
ALLOCATE(dset_id(1:ndset),stat=error)
IF (error .NE. 0) THEN
WRITE(*,*) 'allocate error'
total_error = total_error + 1
RETURN
ENDIF
ALLOCATE(mem_type_id(1:ndset),stat=error)
IF (error .NE. 0) THEN
WRITE(*,*) 'allocate error'
total_error = total_error + 1
RETURN
ENDIF
ALLOCATE(mem_space_id(1:ndset),stat=error)
IF (error .NE. 0) THEN
WRITE(*,*) 'allocate error'
total_error = total_error + 1
RETURN
ENDIF
ALLOCATE(file_space_id(1:ndset),stat=error)
IF (error .NE. 0) THEN
WRITE(*,*) 'allocate error'
total_error = total_error + 1
RETURN
ENDIF

CALL h5fcreate_f("multidset_rw.h5", H5F_ACC_TRUNC_F, file_id, error)
CALL check("h5fcreate_f", error, total_error)
!
! Create real dataset
!
wbuf_real(1:rdim) = (/(i,i=1,rdim)/)
dims(1) = rdim
buf_md(1) = C_LOC(wbuf_real(1))
mem_type_id(1) = H5T_NATIVE_REAL
CALL h5screate_simple_f(1, dims, file_space_id(1), error)
CALL check("h5screate_simple_f", error, total_error)
CALL h5dcreate_f(file_id, "ds real", mem_type_id(1), file_space_id(1), dset_id(1), error)
CALL check("h5dcreate_f", error, total_error)
mem_space_id(1) = file_space_id(1)

! Create integer dataset (1D)
wbuf_int(1:idim) = (/(i,i=1,idim)/)
dims(1) = idim
buf_md(2) = C_LOC(wbuf_int(1))
mem_type_id(2) = H5T_NATIVE_INTEGER
CALL h5screate_simple_f(1, dims, file_space_id(2), error)
CALL check("h5screate_simple_f", error, total_error)
CALL h5dcreate_f(file_id, "ds int", mem_type_id(2), file_space_id(2), dset_id(2), error)
CALL check("h5dcreate_f", error, total_error)
mem_space_id(2) = file_space_id(2)

! Create character dataset
wbuf_chr(1:cdim) = (/'ab','cd','ef'/)
dims(1) = cdim
buf_md(3) = C_LOC(wbuf_chr(1)(1:1))
CALL H5Tcopy_f(H5T_FORTRAN_S1, mem_type_id(3), error)
CALL check("H5Tcopy_f", error, total_error)
CALL H5Tset_size_f(mem_type_id(3), INT(sdim,SIZE_T), error)
CALL check("H5Tset_size_f", error, total_error)
CALL h5screate_simple_f(1, dims, file_space_id(3), error)
CALL check("h5screate_simple_f", error, total_error)
CALL h5dcreate_f(file_id, "ds chr", mem_type_id(3), file_space_id(3), dset_id(3), error)
CALL check("h5dcreate_f", error, total_error)
mem_space_id(3) = file_space_id(3)

! Create derived type dataset
wbuf_derived(1:ddim)%r = (/10.,20./)
wbuf_derived(1:ddim)%i = (/30,40/)
wbuf_derived(1:ddim)%c = (/'wx','yz'/)
buf_md(4) = C_LOC(wbuf_derived(1)%r)
CALL h5tcreate_f(H5T_COMPOUND_F, H5OFFSETOF(C_LOC(wbuf_derived(1)), C_LOC(wbuf_derived(2))), mem_type_id(4), error)
CALL check("h5tcreate_f", error, total_error)
CALL h5tinsert_f(mem_type_id(4), "real", &
H5OFFSETOF(C_LOC(wbuf_derived(1)),C_LOC(wbuf_derived(1)%r)), H5T_NATIVE_REAL, error)
CALL check("h5tinsert_f", error, total_error)
CALL h5tinsert_f(mem_type_id(4), "int", &
H5OFFSETOF(C_LOC(wbuf_derived(1)),C_LOC(wbuf_derived(1)%i)), H5T_NATIVE_INTEGER, error)
CALL check("h5tinsert_f", error, total_error)
CALL h5tcopy_f(H5T_NATIVE_CHARACTER, strtype, error)
CALL check("h5tcopy_f", error, total_error)
CALL h5tset_size_f(strtype, INT(sdim,size_t), error)
CALL check("h5tset_size_f", error, total_error)
CALL h5tinsert_f(mem_type_id(4), "chr", &
H5OFFSETOF(C_LOC(wbuf_derived(1)),C_LOC(wbuf_derived(1)%c(1:1))), strtype, error)
CALL check("h5tinsert_f", error, total_error)

dims(1) = ddim
CALL h5screate_simple_f(1, dims, file_space_id(4), error)
CALL check("h5screate_simple_f", error, total_error)
CALL h5dcreate_f(file_id, "ds derived", mem_type_id(4), file_space_id(4), dset_id(4), error)
CALL check("h5dcreate_f", error, total_error)
mem_space_id(4) = file_space_id(4)


! Create integer dataset (3D)

DO i = 1, idim
DO j = 1, idim2
DO k = 1, idim3
wbuf_intmd(i,j,k) = i*j
ENDDO
ENDDO
ENDDO

dimsmd(1:3) = (/idim,idim2,idim3/)
buf_md(5) = C_LOC(wbuf_intmd(1,1,1))
mem_type_id(5) = H5T_NATIVE_INTEGER
CALL h5screate_simple_f(3, dimsmd, file_space_id(5), error)
CALL check("h5screate_simple_f", error, total_error)
CALL h5dcreate_f(file_id, "ds int 3d", mem_type_id(5), file_space_id(5), dset_id(5), error)
CALL check("h5dcreate_f", error, total_error)
mem_space_id(5) = file_space_id(5)

! write all the datasets
CALL h5dwrite_multi_f(ndset, dset_id, mem_type_id, mem_space_id, file_space_id, buf_md, error)
CALL check("h5dwrite_multi_f", error, total_error)

! point to read buffers

buf_md(1) = C_LOC(rbuf_real(1))
buf_md(2) = C_LOC(rbuf_int(1))
buf_md(3) = C_LOC(rbuf_chr(1)(1:1))
buf_md(4) = C_LOC(rbuf_derived(1)%r)
buf_md(5) = C_LOC(rbuf_intmd(1,1,1))

! read all the datasets
CALL h5dread_multi_f(ndset, dset_id, mem_type_id, mem_space_id, file_space_id, buf_md, error)
CALL check("h5dread_multi_f", error, total_error)

! check the written and read in values
DO i = 1, rdim
IF(rbuf_real(i).NE.wbuf_real(i))THEN
total_error = total_error + 1
END IF
END DO
DO i = 1, idim
IF(rbuf_int(i).NE.wbuf_int(i))THEN
total_error = total_error + 1
END IF
END DO
DO i = 1, cdim
IF(rbuf_chr(i).NE.wbuf_chr(i))THEN
total_error = total_error + 1
END IF
END DO
DO i = 1, ddim
IF(rbuf_derived(i)%r.NE.wbuf_derived(i)%r)THEN
total_error = total_error + 1
END IF
IF(rbuf_derived(i)%i.NE.wbuf_derived(i)%i)THEN
total_error = total_error + 1
END IF
IF(rbuf_derived(i)%c.NE.wbuf_derived(i)%c)THEN
total_error = total_error + 1
END IF
END DO
DO i = 1, idim
DO j = 1, idim2
DO k = 1, idim3
IF(rbuf_intmd(i,j,k).NE.wbuf_intmd(i,j,k))THEN
total_error = total_error + 1
END IF
END DO
ENDDO
ENDDO

DO i = 1, ndset
CALL H5Dclose_f(dset_id(i), error)
CALL check("H5Dclose_f", error, total_error)
CALL H5Sclose_f(file_space_id(i), error)
CALL check("H5Sclose_f", error, total_error)
ENDDO
CALL H5Tclose_f(mem_type_id(4), error)
CALL check("H5Tclose_f", error, total_error)

CALL h5fget_obj_count_f(file_id, H5F_OBJ_ALL_F, obj_count, error)
IF(obj_count.NE.1)THEN
total_error = total_error + 1
END IF

CALL H5Fclose_f(file_id, error)

END SUBROUTINE multiple_dset_rw


END MODULE TH5T_F03
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