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, 40 insertions, 37 deletions

diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c
index 8ac1f0a..a9e937f 100644
--- a/src/H5Dcompact.c
+++ b/src/H5Dcompact.c
@@ -63,15 +63,16 @@ typedef struct H5D_compact_iovv_memmanage_ud_t {
 /* Layout operation callbacks */
 static herr_t  H5D__compact_construct(H5F_t *f, H5D_t *dset);
 static hbool_t H5D__compact_is_space_alloc(const H5O_storage_t *storage);
-static herr_t  H5D__compact_io_init(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts,
-                                    H5S_t *file_space, H5S_t *mem_space, H5D_chunk_map_t *cm);
+static herr_t  H5D__compact_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo);
 static herr_t  H5D__compact_iovv_memmanage_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata);
-static ssize_t H5D__compact_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq,
-                                   size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq,
-                                   size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[]);
-static ssize_t H5D__compact_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq,
-                                    size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq,
-                                    size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[]);
+static ssize_t H5D__compact_readvv(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info,
+                                   size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[],
+                                   hsize_t dset_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq,
+                                   size_t mem_size_arr[], hsize_t mem_offset_arr[]);
+static ssize_t H5D__compact_writevv(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info,
+                                    size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[],
+                                    hsize_t dset_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq,
+                                    size_t mem_size_arr[], hsize_t mem_offset_arr[]);
 static herr_t  H5D__compact_flush(H5D_t *dset);
 static herr_t  H5D__compact_dest(H5D_t *dset);
 
@@ -86,17 +87,14 @@ const H5D_layout_ops_t H5D_LOPS_COMPACT[1] = {{
     H5D__compact_is_space_alloc, /* is_space_alloc */
     NULL,                        /* is_data_cached */
     H5D__compact_io_init,        /* io_init */
+    NULL,                        /* mdio_init */
     H5D__contig_read,            /* ser_read */
     H5D__contig_write,           /* ser_write */
-#ifdef H5_HAVE_PARALLEL
-    NULL, /* par_read */
-    NULL, /* par_write */
-#endif
-    H5D__compact_readvv,  /* readvv */
-    H5D__compact_writevv, /* writevv */
-    H5D__compact_flush,   /* flush */
-    NULL,                 /* io_term */
-    H5D__compact_dest     /* dest */
+    H5D__compact_readvv,         /* readvv */
+    H5D__compact_writevv,        /* writevv */
+    H5D__compact_flush,          /* flush */
+    NULL,                        /* io_term */
+    H5D__compact_dest            /* dest */
 }};
 
 /*******************/
@@ -247,14 +245,15 @@ H5D__compact_is_space_alloc(const H5O_storage_t H5_ATTR_UNUSED *storage)
  *-------------------------------------------------------------------------
  */
 static herr_t
-H5D__compact_io_init(H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR_UNUSED *type_info,
-                     hsize_t H5_ATTR_UNUSED nelmts, H5S_t H5_ATTR_UNUSED *file_space,
-                     H5S_t H5_ATTR_UNUSED *mem_space, H5D_chunk_map_t H5_ATTR_UNUSED *cm)
+H5D__compact_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo)
 {
     FUNC_ENTER_PACKAGE_NOERR
 
-    io_info->store->compact.buf   = io_info->dset->shared->layout.storage.u.compact.buf;
-    io_info->store->compact.dirty = &io_info->dset->shared->layout.storage.u.compact.dirty;
+    dinfo->store->compact.buf   = dinfo->dset->shared->layout.storage.u.compact.buf;
+    dinfo->store->compact.dirty = &dinfo->dset->shared->layout.storage.u.compact.dirty;
+
+    /* Disable selection I/O */
+    io_info->use_select_io = FALSE;
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 } /* end H5D__compact_io_init() */
@@ -320,15 +319,17 @@ done:
  *-------------------------------------------------------------------------
  */
 static ssize_t
-H5D__compact_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq,
-                    size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq,
-                    size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[])
+H5D__compact_readvv(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, size_t dset_max_nseq,
+                    size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
+                    size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[],
+                    hsize_t mem_offset_arr[])
 {
     ssize_t ret_value = -1; /* Return value */
 
     FUNC_ENTER_PACKAGE
 
     HDassert(io_info);
+    HDassert(dset_info);
 
     /* Check if file driver wishes to do its own memory management */
     if (H5F_SHARED_HAS_FEATURE(io_info->f_sh, H5FD_FEAT_MEMMANAGE)) {
@@ -336,8 +337,8 @@ H5D__compact_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *
 
         /* Set up udata for memory copy operation */
         udata.f_sh   = io_info->f_sh;
-        udata.dstbuf = io_info->u.rbuf;
-        udata.srcbuf = io_info->store->compact.buf;
+        udata.dstbuf = dset_info->buf.vp;
+        udata.srcbuf = dset_info->store->compact.buf;
 
         /* Request that file driver does the memory copy */
         if ((ret_value = H5VM_opvv(mem_max_nseq, mem_curr_seq, mem_size_arr, mem_offset_arr, dset_max_nseq,
@@ -347,8 +348,8 @@ H5D__compact_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *
     }
     else {
         /* Use the vectorized memory copy routine to do actual work */
-        if ((ret_value = H5VM_memcpyvv(io_info->u.rbuf, mem_max_nseq, mem_curr_seq, mem_size_arr,
-                                       mem_offset_arr, io_info->store->compact.buf, dset_max_nseq,
+        if ((ret_value = H5VM_memcpyvv(dset_info->buf.vp, mem_max_nseq, mem_curr_seq, mem_size_arr,
+                                       mem_offset_arr, dset_info->store->compact.buf, dset_max_nseq,
                                        dset_curr_seq, dset_size_arr, dset_offset_arr)) < 0)
             HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
     }
@@ -379,15 +380,17 @@ done:
  *-------------------------------------------------------------------------
  */
 static ssize_t
-H5D__compact_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq,
-                     size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq,
-                     size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[])
+H5D__compact_writevv(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, size_t dset_max_nseq,
+                     size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[],
+                     size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[],
+                     hsize_t mem_offset_arr[])
 {
     ssize_t ret_value = -1; /* Return value */
 
     FUNC_ENTER_PACKAGE
 
     HDassert(io_info);
+    HDassert(dset_info);
 
     /* Check if file driver wishes to do its own memory management */
     if (H5F_SHARED_HAS_FEATURE(io_info->f_sh, H5FD_FEAT_MEMMANAGE)) {
@@ -395,8 +398,8 @@ H5D__compact_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t
 
         /* Set up udata for memory copy operation */
         udata.f_sh   = io_info->f_sh;
-        udata.dstbuf = io_info->store->compact.buf;
-        udata.srcbuf = io_info->u.wbuf;
+        udata.dstbuf = dset_info->store->compact.buf;
+        udata.srcbuf = dset_info->buf.cvp;
 
         /* Request that file driver does the memory copy */
         if ((ret_value = H5VM_opvv(dset_max_nseq, dset_curr_seq, dset_size_arr, dset_offset_arr, mem_max_nseq,
@@ -406,14 +409,14 @@ H5D__compact_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t
     }
     else {
         /* Use the vectorized memory copy routine to do actual work */
-        if ((ret_value = H5VM_memcpyvv(io_info->store->compact.buf, dset_max_nseq, dset_curr_seq,
-                                       dset_size_arr, dset_offset_arr, io_info->u.wbuf, mem_max_nseq,
+        if ((ret_value = H5VM_memcpyvv(dset_info->store->compact.buf, dset_max_nseq, dset_curr_seq,
+                                       dset_size_arr, dset_offset_arr, dset_info->buf.cvp, mem_max_nseq,
                                        mem_curr_seq, mem_size_arr, mem_offset_arr)) < 0)
             HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed")
     }
 
     /* Mark the compact dataset's buffer as dirty */
-    *io_info->store->compact.dirty = TRUE;
+    *dset_info->store->compact.dirty = TRUE;
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)