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, 111 insertions, 0 deletions

diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 6fad138..8040272 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -852,6 +852,52 @@ H5_DLL herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_
 
 /**
  * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Reads raw data from a set of datasets into the provided buffers
+ *
+ * \param[in] count         Number of datasets to read from
+ * \param[in] dset_id       Identifiers of the datasets to read from
+ * \param[in] mem_type_id   Identifiers of the memory datatypes
+ * \param[in] mem_space_id  Identifiers of the memory dataspaces
+ * \param[in] file_space_id Identifiers of the datasets' dataspaces in the file
+ * \param[in] dxpl_id       Identifier of a transfer property list
+ * \param[out] buf          Buffers to receive data read from file
+ *
+ * \return \herr_t
+ *
+ * \details H5Dread_multi() reads data from \p count datasets, whose identifiers
+ *          are listed in the \p dset_id array, from the file into multiple
+ *          application memory buffers listed in the \p buf array. Data transfer
+ *          properties are defined by the argument \p dxpl_id. The memory
+ *          datatypes of each dataset are listed by identifier in the \p
+ *          mem_type_id array. The parts of each dataset to read are listed by
+ *          identifier in the \p file_space_id array, and the parts of each
+ *          application memory buffer to read to are listed by identifier in the
+ *          \p mem_space_id array. All array parameters have length \p count.
+ *
+ *          This function will produce the same results as \p count calls to
+ *          H5Dread(). Information listed in that function about the specifics
+ *          of its behaviour also apply to H5Dread_multi(). By calling
+ *          H5Dread_multi() instead of multiple calls to H5Dread(), however, the
+ *          library can in some cases pass information about the entire I/O
+ *          operation to the file driver, which can improve performance.
+ *
+ *          All datasets must be in the same HDF5 file, and each unique dataset
+ *          may only be listed once. If this function is called collectively in
+ *          parallel, each rank must pass exactly the same list of datasets in
+ *          \p dset_id , though the other parameters may differ.
+ *
+ * \since 1.13.3
+ *
+ * \see H5Dread()
+ *
+ */
+H5_DLL herr_t H5Dread_multi(size_t count, hid_t dset_id[], hid_t mem_type_id[], hid_t mem_space_id[],
+                            hid_t file_space_id[], hid_t dxpl_id, void *buf[] /*out*/);
+
+/**
+ * --------------------------------------------------------------------------
  * \ingroup ASYNC
  * \async_variant_of{H5Dread}
  */
@@ -861,6 +907,15 @@ H5_DLL herr_t H5Dread_async(const char *app_file, const char *app_func, unsigned
 
 /**
  * --------------------------------------------------------------------------
+ * \ingroup ASYNC
+ * \async_variant_of{H5Dread_multi}
+ */
+H5_DLL herr_t H5Dread_multi_async(const char *app_file, const char *app_func, unsigned app_line, size_t count,
+                                  hid_t dset_id[], hid_t mem_type_id[], hid_t mem_space_id[],
+                                  hid_t file_space_id[], hid_t dxpl_id, void *buf[] /*out*/, hid_t es_id);
+
+/**
+ * --------------------------------------------------------------------------
  * \ingroup H5D
  *
  * \brief Writes raw data from a buffer to a dataset
@@ -977,6 +1032,53 @@ H5_DLL herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid
 
 /**
  * --------------------------------------------------------------------------
+ * \ingroup H5D
+ *
+ * \brief Writes raw data from a set buffers to a set of datasets
+ *
+ * \param[in] count         Number of datasets to write to
+ * \param[in] dset_id       Identifiers of the datasets to write to
+ * \param[in] mem_type_id   Identifiers of the memory datatypes
+ * \param[in] mem_space_id  Identifiers of the memory dataspaces
+ * \param[in] file_space_id Identifiers of the datasets' dataspaces in the file
+ * \param[in] dxpl_id       Identifier of a transfer property list
+ * \param[in] buf           Buffers with data to be written to the file
+ *
+ * \return \herr_t
+ *
+ * \details H5Dwrite_multi() writes data to \p count datasets, whose identifiers
+ *          are listed in the \p dset_id array, from multiple application memory
+ *          buffers listed in the \p buf array. Data transfer properties are
+ *          defined by the argument \p dxpl_id. The memory datatypes of each
+ *          dataset are listed by identifier in the \p mem_type_id array. The
+ *          parts of each dataset to write are listed by identifier in the \p
+ *          file_space_id array, and the parts of each application memory buffer
+ *          to write from are listed by identifier in the \p mem_space_id array.
+ *          All array parameters have length \p count.
+ *
+ *          This function will produce the same results as \p count calls to
+ *          H5Dwrite(). Information listed in that function's documentation
+ *          about the specifics of its behaviour also apply to H5Dwrite_multi().
+ *          By calling H5Dwrite_multi() instead of multiple calls to H5Dwrite(),
+ *          however, the library can in some cases pass information about the
+ *          entire I/O operation to the file driver, which can improve
+ *          performance.
+ *
+ *          All datasets must be in the same HDF5 file, and each unique dataset
+ *          may only be listed once. If this function is called collectively in
+ *          parallel, each rank must pass exactly the same list of datasets in
+ *          \p dset_id , though the other parameters may differ.
+ *
+ * \since 1.13.3
+ *
+ * \see H5Dwrite()
+ *
+ */
+H5_DLL herr_t H5Dwrite_multi(size_t count, hid_t dset_id[], hid_t mem_type_id[], hid_t mem_space_id[],
+                             hid_t file_space_id[], hid_t dxpl_id, const void *buf[]);
+
+/**
+ * --------------------------------------------------------------------------
  * \ingroup ASYNC
  * \async_variant_of{H5Dwrite}
  */
@@ -986,6 +1088,15 @@ H5_DLL herr_t H5Dwrite_async(const char *app_file, const char *app_func, unsigne
 
 /**
  * --------------------------------------------------------------------------
+ * \ingroup ASYNC
+ * \async_variant_of{H5Dwrite_multi}
+ */
+H5_DLL herr_t H5Dwrite_multi_async(const char *app_file, const char *app_func, unsigned app_line,
+                                   size_t count, hid_t dset_id[], hid_t mem_type_id[], hid_t mem_space_id[],
+                                   hid_t file_space_id[], hid_t dxpl_id, const void *buf[], hid_t es_id);
+
+/**
+ * --------------------------------------------------------------------------
  * \ingroup H5D
  *
  * \brief Writes a raw data chunk from a buffer directly to a dataset in a file