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, 103 insertions, 1 deletions

diff --git a/fortran/src/H5Dff.F90 b/fortran/src/H5Dff.F90
index d15e59e..1e88399 100644
--- a/fortran/src/H5Dff.F90
+++ b/fortran/src/H5Dff.F90
@@ -1098,7 +1098,7 @@ CONTAINS
 !>
 !! \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
 !!
@@ -1762,6 +1762,108 @@ CONTAINS
     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'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'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