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, 235 insertions, 0 deletions

diff --git a/fortran/testpar/multidsetrw.F90 b/fortran/testpar/multidsetrw.F90
new file mode 100644
index 0000000..5d41e4c
--- /dev/null
+++ b/fortran/testpar/multidsetrw.F90
@@ -0,0 +1,235 @@
+! * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+!   Copyright by The HDF Group.                                               *
+!   All rights reserved.                                                      *
+!                                                                             *
+!   This file is part of HDF5.  The full HDF5 copyright notice, including     *
+!   terms governing use, modification, and redistribution, is contained in    *
+!   the files COPYING and Copyright.html.  COPYING can be found at the root   *
+!   of the source code distribution tree; Copyright.html can be found at the  *
+!   root level of an installed copy of the electronic HDF5 document set and   *
+!   is linked from the top-level documents page.  It can also be found at     *
+!   http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+!   access to either file, you may request a copy from help@hdfgroup.org.     *
+! * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+
+!
+! writes/reads dataset by hyperslabs using multi-dataset routines, h5dread_multi and
+! h5dwrite_multi
+!
+
+SUBROUTINE pmultiple_dset_hyper_rw(do_collective, do_chunk, mpi_size, mpi_rank, nerrors)
+
+  USE iso_c_binding
+  USE TH5_MISC
+  USE hdf5
+  USE mpi
+  IMPLICIT NONE
+
+  LOGICAL, INTENT(in) :: do_collective              ! use collective IO
+  LOGICAL, INTENT(in) :: do_chunk                   ! use chunking
+  INTEGER, INTENT(in) :: mpi_size                   ! number of processes in the group of communicator
+  INTEGER, INTENT(in) :: mpi_rank                   ! rank of the calling process in the communicator
+  INTEGER, INTENT(inout) :: nerrors                 ! number of errors
+  CHARACTER(LEN=80):: dsetname ! Dataset name
+  INTEGER(hsize_t), DIMENSION(1:2) :: cdims           ! chunk dimensions
+
+  INTEGER(HID_T) :: file_id       ! File identifier
+  INTEGER(HID_T) :: filespace     ! Dataspace identifier in file 
+  INTEGER(HID_T) :: memspace      ! Dataspace identifier in memory
+  INTEGER(HID_T) :: plist_id      ! Property list identifier 
+  INTEGER(HID_T) :: dcpl_id       ! Dataset creation property list
+  INTEGER(HSIZE_T), DIMENSION(1:2) :: dimsf  ! Dataset dimensions.
+
+  INTEGER(HSIZE_T), DIMENSION(1:2) :: count  
+  INTEGER(HSSIZE_T), DIMENSION(1:2) :: offset 
+  INTEGER, ALLOCATABLE, DIMENSION(:,:,:), TARGET :: DATA  ! Data to write
+  INTEGER, ALLOCATABLE, DIMENSION(:,:,:), TARGET :: rDATA  ! Data to write
+  INTEGER, PARAMETER :: rank = 2 ! Dataset rank 
+  INTEGER :: i
+  INTEGER(HSIZE_T) :: ii, jj, kk, istart
+  INTEGER :: error          ! Error flags
+
+  INTEGER(SIZE_T), PARAMETER :: ndsets = 5
+  INTEGER(HID_T), DIMENSION(1:ndsets) :: dset_id
+  INTEGER(HID_T), DIMENSION(1:ndsets) :: mem_type_id
+  INTEGER(HID_T), DIMENSION(1:ndsets) :: mem_space_id
+  INTEGER(HID_T), DIMENSION(1:ndsets) :: file_space_id
+  TYPE(C_PTR), DIMENSION(1:ndsets) :: buf_md
+  INTEGER(SIZE_T) :: obj_count
+  INTEGER :: data_xfer_mode
+
+  dimsf(1) = 5_hsize_t
+  dimsf(2) = INT(mpi_size, hsize_t)*8_hsize_t
+
+  ! 
+  ! Setup file access property list with parallel I/O access.
+  !
+  CALL h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, error)
+  CALL check("h5pcreate_f", error, nerrors)
+  CALL h5pset_fapl_mpio_f(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL, error)
+  CALL check("h5pset_fapl_mpio_f", error, nerrors)
+  !
+  ! Create the file collectively.
+  ! 
+  CALL h5fcreate_f("parf2.h5", H5F_ACC_TRUNC_F, file_id, error, access_prp = plist_id)
+  CALL check("h5fcreate_f", error, nerrors)
+  CALL h5pclose_f(plist_id, error)
+  CALL check("h5pclose_f", error, nerrors)
+  !
+  ! Create the data space for the  dataset. 
+  !
+  CALL h5screate_simple_f(rank, dimsf, filespace, error)
+  CALL check("h5screate_simple_f", error, nerrors)
+  !
+  ! Each process defines dataset in memory and writes it to the hyperslab
+  ! in the file. 
+  !
+  count(1) = dimsf(1)
+  count(2) = dimsf(2)/mpi_size 
+  offset(1) = 0
+  offset(2) = mpi_rank * count(2) 
+  CALL h5screate_simple_f(rank, count, memspace, error) 
+  CALL check("h5screate_simple_f", error, nerrors)
+
+  !
+  ! Modify dataset creation properties to enable chunking
+  !
+
+  CALL h5pcreate_f(H5P_DATASET_CREATE_F, dcpl_id, error)
+  CALL check("h5pcreate_f", error, nerrors)
+
+  IF (do_chunk) THEN
+     cdims(1) = dimsf(1)
+     cdims(2) = dimsf(2)/mpi_size/2
+     CALL h5pset_chunk_f(dcpl_id, 2, cdims, error)
+     CALL check("h5pset_chunk_f", error, nerrors)
+  ENDIF
+  ! 
+  ! Select hyperslab in the file.
+  !
+  CALL h5sselect_hyperslab_f(filespace, H5S_SELECT_SET_F, offset, count, error)
+  CALL check("h5sselect_hyperslab_f", error, nerrors)
+  !
+  ! Initialize data buffer
+  !
+  ALLOCATE ( DATA(COUNT(1),COUNT(2), ndsets))
+  ALLOCATE ( rdata(COUNT(1),COUNT(2), ndsets))
+
+  ! Create property list for collective dataset write
+  !
+  CALL h5pcreate_f(H5P_DATASET_XFER_F, plist_id, error)
+  CALL check("h5pcreate_f", error, nerrors)
+  IF(do_collective)THEN
+     CALL h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, error)
+     CALL check("h5pset_dxpl_mpio_f", error, nerrors)
+  ELSE
+     CALL h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_INDEPENDENT_F, error)
+     CALL check("h5pset_dxpl_mpio_f", error, nerrors)
+  ENDIF
+     
+  !
+  ! Create the dataset with default properties.
+  !
+  mem_type_id(1:ndsets) = H5T_NATIVE_INTEGER
+  mem_space_id(1:ndsets) = memspace
+  file_space_id(1:ndsets)= filespace
+
+  DO ii = 1, ndsets
+     ! Create the data
+     DO kk = 1, COUNT(1)
+        DO jj = 1, COUNT(2)
+           istart = (kk-1)*dimsf(2) + mpi_rank*COUNT(2)
+           DATA(kk,jj,ii) = INT((istart + jj)*10**(ii-1))
+        ENDDO
+     ENDDO
+     ! Point to te data
+     buf_md(ii) = C_LOC(DATA(1,1,ii))
+
+     ! direct the output of the write statement to unit "dsetname"
+     WRITE(dsetname,'("dataset ",I0)') ii
+     ! create the dataset
+     CALL h5dcreate_f(file_id, dsetname, H5T_NATIVE_INTEGER, filespace, dset_id(ii), error, dcpl_id)
+     CALL check("h5dcreate_f", error, nerrors)
+  ENDDO
+
+  !
+  ! Write the dataset collectively. 
+  !  
+  CALL h5dwrite_multi_f(ndsets, dset_id, mem_type_id, mem_space_id, file_space_id, buf_md, error, plist_id)
+  CALL check("h5dwrite_multi_f", error, nerrors)
+
+  CALL h5pget_dxpl_mpio_f(plist_id, data_xfer_mode, error)
+  CALL check("h5pget_dxpl_mpio_f", error, nerrors)
+
+  IF(do_collective)THEN
+     IF(data_xfer_mode.NE.H5FD_MPIO_COLLECTIVE_F)THEN
+        nerrors = nerrors + 1
+     ENDIF
+  ENDIF
+
+  DO i = 1, ndsets
+     ! Point to the read buffer
+     buf_md(i) = C_LOC(rdata(1,1,i))
+  ENDDO
+
+  CALL H5Dread_multi_f(ndsets, dset_id, mem_type_id, mem_space_id, file_space_id, buf_md, error, plist_id)
+  CALL check("h5dread_multi_f", error, nerrors)
+
+  CALL h5pget_dxpl_mpio_f(plist_id, data_xfer_mode, error)
+  CALL check("h5pget_dxpl_mpio_f", error, nerrors)
+
+  IF(do_collective)THEN
+     IF(data_xfer_mode.NE.H5FD_MPIO_COLLECTIVE_F)THEN
+        nerrors = nerrors + 1
+     ENDIF
+  ENDIF
+
+  DO i = 1, ndsets
+     ! Close all the datasets
+     CALL h5dclose_f(dset_id(i), error)
+     CALL check("h5dclose_f", error, nerrors)
+  ENDDO
+
+  ! check the data read and write buffers
+  DO ii = 1, ndsets
+     ! Create the data
+     DO kk = 1, COUNT(1)
+        DO jj = 1, COUNT(2)
+           IF(rDATA(kk,jj,ii).NE.DATA(kk,jj,ii))THEN
+              nerrors = nerrors + 1
+           ENDIF
+        ENDDO
+     ENDDO
+  ENDDO
+  !
+  ! Deallocate data buffer.
+  !
+  DEALLOCATE(data, rdata)
+
+  !
+  ! Close dataspaces.
+  !
+  CALL h5sclose_f(filespace, error)
+  CALL check("h5sclose_f", error, nerrors)
+  CALL h5sclose_f(memspace, error)
+  CALL check("h5sclose_f", error, nerrors)
+  !
+  ! Close the dataset and property list.
+  !
+  CALL h5pclose_f(dcpl_id, error)
+  CALL check("h5pclose_f", error, nerrors)
+  CALL h5pclose_f(plist_id, error)
+  CALL check("h5pclose_f", error, nerrors)
+
+  CALL h5fget_obj_count_f(file_id, H5F_OBJ_ALL_F, obj_count, error)
+  IF(obj_count.NE.1)THEN
+     nerrors = nerrors + 1
+  END IF
+
+  !
+  ! Close the file.
+  !
+  CALL h5fclose_f(file_id, error)
+  CALL check("h5fclose_f", error, nerrors)
+
+END SUBROUTINE pmultiple_dset_hyper_rw