Implement selection vector I/O with collective chunk filling (HDFGroup#3826)

* Changes for ECP-344: Implement selection vector I/O with collective chunk filling.
Also fix a bug in H5FD__mpio_write_vector() to account for fixed size optimization
when computing max address.

* Fixes based on PR review comments:
For H5Dchunk.c: fix H5MM_xfree()
For H5FDmpio.c:
1) Revert the fix to H5FD__mpio_write_vector()
2) Apply the patch from Neil on the proper length of s_sizes reported by H5FD__mpio_vector_build_types()

* Put back the logic of dividing up the work among all the mpi ranks similar to the
original H5D__chunk_collective_fill() routine.

* Add a test to verify the fix for the illegal reference problem in H5FD__mpio_write_vector().

Author: vchoi-hdfgroup

src/H5Dchunk.c

@@ -5536,11 +5536,9 @@ H5D__chunk_update_old_edge_chunks(H5D_t *dset, hsize_t old_dim[])
 /*-------------------------------------------------------------------------
  * Function:    H5D__chunk_collective_fill
  *
- * Purpose:     Use MPIO collective write to fill the chunks (if number of
- *              chunks to fill is greater than the number of MPI procs;
- *              otherwise use independent I/O).
+ * Purpose:     Use MPIO selection vector I/O for writing fill chunks
  *
- * Return:    Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
  *-------------------------------------------------------------------------
  */
@@ -5554,19 +5552,24 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_
     int              mpi_code;                 /* MPI return code */
     size_t           num_blocks;               /* Number of blocks between processes. */
     size_t           leftover_blocks;          /* Number of leftover blocks to handle */
-    int              blocks, leftover;         /* converted to int for MPI */
-    MPI_Aint        *chunk_disp_array = NULL;
-    MPI_Aint        *block_disps      = NULL;
-    int             *block_lens       = NULL;
-    MPI_Datatype     mem_type = MPI_BYTE, file_type = MPI_BYTE;
-    H5FD_mpio_xfer_t prev_xfer_mode;         /* Previous data xfer mode */
-    bool             have_xfer_mode = false; /* Whether the previous xffer mode has been retrieved */
-    bool             need_sort      = false;
-    size_t           i;                   /* Local index variable */
+    int              blocks;                   /* converted to int for MPI */
+    int              leftover;                 /* converted to int for MPI */
+    H5FD_mpio_xfer_t prev_xfer_mode;           /* Previous data xfer mode */
+    bool             have_xfer_mode = false;   /* Whether the previous xffer mode has been retrieved */
+    size_t           i;                        /* Local index variable */
+    haddr_t         *io_addrs = NULL;
+    size_t          *io_sizes = NULL;
+    const void     **io_wbufs = NULL;
+    H5FD_mem_t       io_types[2];
+    bool             all_same_block_len = true;
+    bool             need_sort          = false;
+    size_t           io_2sizes[2];
     herr_t           ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_PACKAGE
 
+    assert(chunk_fill_info->num_chunks != 0);
+
     /*
      * If a separate fill buffer is provided for partial chunks, ensure
      * that the "don't filter partial edge chunks" flag is set.
@@ -5589,6 +5592,7 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_
     /* Distribute evenly the number of blocks between processes. */
     if (mpi_size == 0)
         HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "Resulted in division by zero");
+
     num_blocks =
         (size_t)(chunk_fill_info->num_chunks / (size_t)mpi_size); /* value should be the same on all procs */
 
@@ -5602,157 +5606,97 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_
     H5_CHECKED_ASSIGN(leftover, int, leftover_blocks, size_t);
 
     /* Check if we have any chunks to write on this rank */
-    if (num_blocks > 0 || (leftover && leftover > mpi_rank)) {
-        MPI_Aint partial_fill_buf_disp = 0;
-        bool     all_same_block_len    = true;
-
-        /* Allocate buffers */
-        if (NULL == (chunk_disp_array = (MPI_Aint *)H5MM_malloc((size_t)(blocks + 1) * sizeof(MPI_Aint))))
-            HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file displacement buffer");
-
-        if (partial_chunk_fill_buf) {
-            MPI_Aint fill_buf_addr;
-            MPI_Aint partial_fill_buf_addr;
-
-            /* Calculate the displacement between the fill buffer and partial chunk fill buffer */
-            if (MPI_SUCCESS != (mpi_code = MPI_Get_address(fill_buf, &fill_buf_addr)))
-                HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code)
-            if (MPI_SUCCESS != (mpi_code = MPI_Get_address(partial_chunk_fill_buf, &partial_fill_buf_addr)))
-                HMPI_GOTO_ERROR(FAIL, "MPI_Get_address failed", mpi_code)
-
-#if H5_CHECK_MPI_VERSION(3, 1)
-            partial_fill_buf_disp = MPI_Aint_diff(partial_fill_buf_addr, fill_buf_addr);
-#else
-            partial_fill_buf_disp = partial_fill_buf_addr - fill_buf_addr;
-#endif
+    if (num_blocks > 0 || leftover > mpi_rank) {
 
-            /*
-             * Allocate all-zero block displacements array. If a block's displacement
-             * is left as zero, that block will be written to from the regular fill
-             * buffer. If a block represents an unfiltered partial edge chunk, its
-             * displacement will be set so that the block is written to from the
-             * unfiltered fill buffer.
-             */
-            if (NULL == (block_disps = (MPI_Aint *)H5MM_calloc((size_t)(blocks + 1) * sizeof(MPI_Aint))))
-                HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate block displacements buffer");
-        }
+        if (NULL == (io_addrs = H5MM_malloc((size_t)(blocks + 1) * sizeof(*io_addrs))))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
+                        "couldn't allocate space for I/O addresses vector");
 
-        /*
-         * Perform initial scan of chunk info list to:
-         *  - make sure that chunk addresses are monotonically non-decreasing
-         *  - check if all blocks have the same length
-         */
-        for (i = 1; i < chunk_fill_info->num_chunks; i++) {
-            if (chunk_fill_info->chunk_info[i].addr < chunk_fill_info->chunk_info[i - 1].addr)
-                need_sort = true;
-
-            if (chunk_fill_info->chunk_info[i].chunk_size != chunk_fill_info->chunk_info[i - 1].chunk_size)
-                all_same_block_len = false;
-        }
+        if (NULL == (io_wbufs = H5MM_malloc((size_t)(blocks + 1) * sizeof(*io_wbufs))))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate space for I/O buffers vector");
+    }
 
-        if (need_sort)
-            qsort(chunk_fill_info->chunk_info, chunk_fill_info->num_chunks,
-                  sizeof(struct chunk_coll_fill_info), H5D__chunk_cmp_coll_fill_info);
+    /*
+     * Perform initial scan of chunk info list to:
+     *  - make sure that chunk addresses are monotonically non-decreasing
+     *  - check if all blocks have the same length
+     */
+    for (i = 1; i < chunk_fill_info->num_chunks; i++) {
+        if (chunk_fill_info->chunk_info[i].addr < chunk_fill_info->chunk_info[i - 1].addr)
+            need_sort = true;
 
-        /* Allocate buffer for block lengths if necessary */
-        if (!all_same_block_len)
-            if (NULL == (block_lens = (int *)H5MM_malloc((size_t)(blocks + 1) * sizeof(int))))
-                HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk lengths buffer");
+        if (chunk_fill_info->chunk_info[i].chunk_size != chunk_fill_info->chunk_info[i - 1].chunk_size)
+            all_same_block_len = false;
+    }
 
-        for (i = 0; i < (size_t)blocks; i++) {
-            size_t idx = i + (size_t)(mpi_rank * blocks);
+    /*
+     * Note that we sort all of the chunks here, and not just a subset
+     * corresponding to this rank. We do this since we have found MPI I/O to work
+     * better when each rank writes blocks that are contiguous in the file,
+     * and by sorting the full list we maximize the chance of that happening.
+     */
+    if (need_sort)
+        qsort(chunk_fill_info->chunk_info, chunk_fill_info->num_chunks, sizeof(struct chunk_coll_fill_info),
+              H5D__chunk_cmp_coll_fill_info);
 
-            /* store the chunk address as an MPI_Aint */
-            chunk_disp_array[i] = (MPI_Aint)(chunk_fill_info->chunk_info[idx].addr);
+    /*
+     * If all the chunks have the same length, use the compressed feature
+     * to store the size.
+     * Otherwise, allocate the array of sizes for storing chunk sizes.
+     */
+    if (all_same_block_len) {
+        io_2sizes[0] = chunk_fill_info->chunk_info[0].chunk_size;
+        io_2sizes[1] = 0;
+    }
+    else {
+        if (NULL == (io_sizes = H5MM_malloc((size_t)(blocks + 1) * sizeof(*io_sizes))))
+            HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate space for I/O sizes vector");
+    }
 
-            if (!all_same_block_len)
-                H5_CHECKED_ASSIGN(block_lens[i], int, chunk_fill_info->chunk_info[idx].chunk_size, size_t);
+    /*
+     * Since the type of all chunks is raw data, use the compressed feature
+     * to store the chunk type.
+     */
+    io_types[0] = H5FD_MEM_DRAW;
+    io_types[1] = H5FD_MEM_NOLIST;
 
-            if (chunk_fill_info->chunk_info[idx].unfiltered_partial_chunk) {
-                assert(partial_chunk_fill_buf);
-                block_disps[i] = partial_fill_buf_disp;
-            }
-        } /* end for */
+    /*
+     * For the chunks corresponding to this rank, fill in the
+     * address, size and buf pointer for each chunk.
+     */
+    for (i = 0; i < (size_t)blocks; i++) {
+        size_t idx = i + (size_t)(mpi_rank * blocks);
 
-        /* Calculate if there are any leftover blocks after evenly
-         * distributing. If there are, then round-robin the distribution
-         * to processes 0 -> leftover.
-         */
-        if (leftover && leftover > mpi_rank) {
-            chunk_disp_array[blocks] =
-                (MPI_Aint)chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].addr;
-
-            if (!all_same_block_len)
-                H5_CHECKED_ASSIGN(block_lens[blocks], int,
-                                  chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].chunk_size,
-                                  size_t);
-
-            if (chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].unfiltered_partial_chunk) {
-                assert(partial_chunk_fill_buf);
-                block_disps[blocks] = partial_fill_buf_disp;
-            }
+        io_addrs[i] = chunk_fill_info->chunk_info[idx].addr;
 
-            blocks++;
-        }
+        if (!all_same_block_len)
+            io_sizes[i] = chunk_fill_info->chunk_info[idx].chunk_size;
 
-        /* Create file and memory types for the write operation */
-        if (all_same_block_len) {
-            int block_len;
+        if (chunk_fill_info->chunk_info[idx].unfiltered_partial_chunk)
+            io_wbufs[i] = partial_chunk_fill_buf;
+        else
+            io_wbufs[i] = fill_buf;
+    }
 
-            H5_CHECKED_ASSIGN(block_len, int, chunk_fill_info->chunk_info[0].chunk_size, size_t);
+    /*
+     * For the leftover chunk corresponding to this rank, fill in the
+     * address, size and buf pointer for the chunk.
+     */
+    if (leftover > mpi_rank) {
+        io_addrs[blocks] = chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].addr;
 
-            mpi_code =
-                MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, &file_type);
-            if (mpi_code != MPI_SUCCESS)
-                HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code)
+        if (!all_same_block_len)
+            io_sizes[blocks] = chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].chunk_size;
 
-            if (partial_chunk_fill_buf) {
-                /*
-                 * If filters are disabled for partial edge chunks, those chunks could
-                 * potentially have the same block length as the other chunks, but still
-                 * need to be written to using the unfiltered fill buffer. Use an hindexed
-                 * block type rather than an hvector.
-                 */
-                mpi_code =
-                    MPI_Type_create_hindexed_block(blocks, block_len, block_disps, MPI_BYTE, &mem_type);
-                if (mpi_code != MPI_SUCCESS)
-                    HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code)
-            }
-            else {
-                mpi_code = MPI_Type_create_hvector(blocks, block_len, 0, MPI_BYTE, &mem_type);
-                if (mpi_code != MPI_SUCCESS)
-                    HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code)
-            }
-        }
-        else {
-            /*
-             * Currently, different block lengths implies that there are partial
-             * edge chunks and the "don't filter partial edge chunks" flag is set.
-             */
+        if (chunk_fill_info->chunk_info[(blocks * mpi_size) + mpi_rank].unfiltered_partial_chunk) {
             assert(partial_chunk_fill_buf);
-            assert(block_lens);
-            assert(block_disps);
-
-            mpi_code = MPI_Type_create_hindexed(blocks, block_lens, chunk_disp_array, MPI_BYTE, &file_type);
-            if (mpi_code != MPI_SUCCESS)
-                HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
-
-            mpi_code = MPI_Type_create_hindexed(blocks, block_lens, block_disps, MPI_BYTE, &mem_type);
-            if (mpi_code != MPI_SUCCESS)
-                HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
+            io_wbufs[blocks] = partial_chunk_fill_buf;
         }
+        else
+            io_wbufs[blocks] = fill_buf;
 
-        if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&file_type)))
-            HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
-        if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&mem_type)))
-            HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
-    } /* end if */
-
-    /* Set MPI-IO VFD properties */
-
-    /* Set MPI datatypes for operation */
-    if (H5CX_set_mpi_coll_datatypes(mem_type, file_type) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O properties");
+        blocks++;
+    }
 
     /* Get current transfer mode */
     if (H5CX_get_io_xfer_mode(&prev_xfer_mode) < 0)
@@ -5763,31 +5707,24 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_
     if (H5CX_set_io_xfer_mode(H5FD_MPIO_COLLECTIVE) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set transfer mode");
 
-    /* Low-level write (collective) */
-    if (H5F_shared_block_write(H5F_SHARED(dset->oloc.file), H5FD_MEM_DRAW, (haddr_t)0,
-                               (blocks) ? (size_t)1 : (size_t)0, fill_buf) < 0)
-        HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file");
-
     /* Barrier so processes don't race ahead */
     if (MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm)))
         HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
 
+    /* Perform the selection vector I/O for the chunks */
+    if (H5F_shared_vector_write(H5F_SHARED(dset->oloc.file), (uint32_t)blocks, io_types, io_addrs,
+                                all_same_block_len ? io_2sizes : io_sizes, io_wbufs) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "vector write call failed");
+
 done:
     if (have_xfer_mode)
-        /* Set transfer mode */
+        /* Restore transfer mode */
         if (H5CX_set_io_xfer_mode(prev_xfer_mode) < 0)
             HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set transfer mode");
 
-    /* free things */
-    if (MPI_BYTE != file_type)
-        if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&file_type)))
-            HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
-    if (MPI_BYTE != mem_type)
-        if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type)))
-            HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
-    H5MM_xfree(chunk_disp_array);
-    H5MM_xfree(block_disps);
-    H5MM_xfree(block_lens);
+    H5MM_xfree(io_addrs);
+    H5MM_xfree(io_wbufs);
+    H5MM_xfree(io_sizes);
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5D__chunk_collective_fill() */
@@ -5805,6 +5742,7 @@ H5D__chunk_cmp_coll_fill_info(const void *_entry1, const void *_entry2)
 
     FUNC_LEAVE_NOAPI(H5_addr_cmp(entry1->addr, entry2->addr))
 } /* end H5D__chunk_cmp_coll_fill_info() */
+
 #endif /* H5_HAVE_PARALLEL */
 
 /*-------------------------------------------------------------------------