Multi Dataset (#2120)

* 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>

1 files changed, 254 insertions, 0 deletions

diff --git a/fortran/test/tH5T_F03.F90 b/fortran/test/tH5T_F03.F90
index 200c674..02e848e 100644
--- a/fortran/test/tH5T_F03.F90
+++ b/fortran/test/tH5T_F03.F90
@@ -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