Fix bug with chunk data updating

1 files changed, 68 insertions, 67 deletions

diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index 70a859e..39a5e15 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -2661,12 +2661,12 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
     H5D_filtered_collective_io_info_t *local_info_array = NULL;
     H5D_filtered_collective_io_info_t *overlap_info_array = NULL;
     H5S_sel_iter_t                    *mem_iter = NULL;
+    unsigned char                     *mod_data = NULL;
     H5SL_node_t                       *chunk_node;
     MPI_Request                       *send_requests = NULL;
     MPI_Status                        *send_statuses = NULL;
     hbool_t                            no_overlap = FALSE;
     hbool_t                            mem_iter_init = FALSE;
-    uint8_t                           *mod_data = NULL;
     size_t                             num_send_requests;
     size_t                             num_chunks_selected;
     size_t                             overlap_info_array_num_entries;
@@ -2680,6 +2680,8 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
     HDassert(type_info);
     HDassert(fm);
     HDassert(chunk_list);
+    HDassert(num_entries);
+    HDassert(_num_chunks_selected_array);
 
     if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0)
         HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank")
@@ -2723,10 +2725,7 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
         HDfprintf(debug_file, "|  - Chunk Num Elmts Sel.: %zd\n", H5S_GET_SELECT_NPOINTS(local_info_array[j].chunk_info.mspace));
     }
     HDfprintf(debug_file, "------------------------------\n\n");
-#endif
-
 
-#ifdef PARALLEL_COMPRESS_DEBUG
     HDfprintf(debug_file, "Testing mem/file space addresses:\n");
     HDfprintf(debug_file, "-----------------------------------\n");
 
@@ -2805,19 +2804,23 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
                 overlap_info_array[num_chunks_selected++] = chunk_entry;
             } /* end if */
             else {
+                unsigned char *mod_data_p = NULL;
                 hssize_t       iter_nelmts;
-                hssize_t       mod_data_size;
-                uint8_t       *mod_data_p = NULL;
+                size_t         mod_data_size;
 
                 /* XXX: Need some way of checking chunk entry to validate that this process
                  * is actually contributing some data for this chunk update
                  */
 
-                /* Determine size of serialized chunk selection plus the size
+                /* Determine size of serialized chunk memory dataspace plus the size
                  * of the data being written
                  */
-                if ((mod_data_size = H5S_SELECT_SERIAL_SIZE(chunk_entry.chunk_info.mspace)) < 0)
-                    HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to check dataspace selection size")
+                /* XXX: Using the file dataspace seems to work here, presumably because the file
+                 * space reflects how the data is actually stored in the file, not in memory. e.g.
+                 * it reflects the chunking setup
+                 */
+                if (H5S_encode(chunk_entry.chunk_info.fspace, &mod_data, &mod_data_size) < 0)
+                    HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to get encoded dataspace size")
 
                 if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_entry.chunk_info.mspace)) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
@@ -2828,16 +2831,16 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
                 mod_data_size += iter_nelmts * type_info->src_type_size;
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Allocing %zd bytes for mod. data buffer.\n", (size_t) mod_data_size);
+                HDfprintf(debug_file, "| Allocing %zd bytes for mod. data buffer.\n", (size_t) mod_data_size);
 #endif
 
-                if (NULL == (mod_data = (uint8_t *) H5MM_malloc(mod_data_size)))
+                if (NULL == (mod_data = (unsigned char *) H5MM_malloc(mod_data_size)))
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk modification send buffer")
 
-                /* Serialize the current selection into the buffer */
+                /* Serialize the chunk's file dataspace into the buffer */
                 mod_data_p = mod_data;
-                if (H5S_SELECT_SERIALIZE(chunk_entry.chunk_info.mspace, &mod_data_p) < 0)
-                    HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to serialize dataspace selection")
+                if (H5S_encode(chunk_entry.chunk_info.fspace, &mod_data_p, &mod_data_size) < 0)
+                    HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to encode dataspace")
 
                 /* Initialize iterator for memory selection */
                 if (H5S_select_iter_init(mem_iter, chunk_entry.chunk_info.mspace, type_info->src_type_size) < 0)
@@ -2845,7 +2848,7 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
                 mem_iter_init = TRUE;
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Iterating over %lld elements.\n", iter_nelmts);
+                HDfprintf(debug_file, "| Iterating over %lld elements.\n", iter_nelmts);
 #endif
 
                 /* Collect the modification data into the buffer */
@@ -2862,27 +2865,28 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
                 }
                 HDfprintf(debug_file, "]\n|\n");
 
-                HDfprintf(debug_file, "Sending modification data for chunk at address %a to process %d.\n", chunk_entry.old_chunk.offset, new_owner);
+                HDfprintf(debug_file, "| Sending modification data for chunk at address %a to process %d.\n", chunk_entry.old_chunk.offset, new_owner);
 #endif
 
                 /* Send modification data to new owner */
-                H5_CHECK_OVERFLOW(mod_data_size, hssize_t, int)
+                H5_CHECK_OVERFLOW(mod_data_size, size_t, int)
                 if (MPI_SUCCESS != (mpi_code = MPI_Isend(mod_data, (int) mod_data_size, MPI_BYTE, new_owner,
                         chunk_entry.chunk_info.index, io_info->comm, &send_requests[num_send_requests++])))
                     HMPI_GOTO_ERROR(FAIL, "MPI_Isend failed", mpi_code)
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Mod. data sent.\n");
+                HDfprintf(debug_file, "| Mod. data sent.\n|\n");
 #endif
 
                 if (mod_data)
-                    mod_data = (uint8_t *) H5MM_free(mod_data);
+                    mod_data = (unsigned char *) H5MM_free(mod_data);
                 if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
+                mem_iter_init = FALSE;
             } /* end else */
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-            HDfprintf(debug_file, "Chunk at address %a re-assigned to process %d.\n", chunk_addr, new_owner);
+            HDfprintf(debug_file, "| Chunk at address %a re-assigned to process %d.\n|\n", chunk_addr, new_owner);
 #endif
         } /* end for */
 
@@ -2902,9 +2906,9 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
             HDfprintf(debug_file, "| Chunk Entry %zd:\n", j);
             HDfprintf(debug_file, "|  - Chunk Address: %a\n", local_info_array[j].old_chunk.offset);
             HDfprintf(debug_file, "|  - Chunk Length: %zd\n", local_info_array[j].old_chunk.length);
-            HDfprintf(debug_file, "|  - Address of mspace: %x\n", local_info_array[j].chunk_info.mspace);
-            HDfprintf(debug_file, "|  - Chunk Selection Type: %d\n", H5S_GET_SELECT_TYPE(local_info_array[j].chunk_info.mspace));
-            HDfprintf(debug_file, "|  - Chunk Num Elmts Sel.: %zd\n", H5S_GET_SELECT_NPOINTS(local_info_array[j].chunk_info.mspace));
+            HDfprintf(debug_file, "|  - Address of mspace: %x\n", local_info_array[j].chunk_info.fspace);
+            HDfprintf(debug_file, "|  - Chunk Selection Type: %d\n", H5S_GET_SELECT_TYPE(local_info_array[j].chunk_info.fspace));
+            HDfprintf(debug_file, "|  - Chunk Num Elmts Sel.: %zd\n", H5S_GET_SELECT_NPOINTS(local_info_array[j].chunk_info.fspace));
         }
         HDfprintf(debug_file, "------------------------------\n\n");
 #endif
@@ -2947,6 +2951,8 @@ done:
         H5MM_free(send_statuses);
     if (mod_data)
         H5MM_free(mod_data);
+    if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
     if (mem_iter)
         H5MM_free(mem_iter);
 
@@ -3076,11 +3082,13 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
     const H5D_io_info_t *io_info, const H5D_type_info_t *type_info)
 {
     H5S_sel_iter_t *mem_iter = NULL;
+    unsigned char  *mod_data = NULL;
     unsigned        filter_mask = 0;
     hssize_t        iter_nelmts;
     hbool_t         full_overwrite = FALSE;
     hbool_t         mem_iter_init = FALSE;
     size_t          buf_size;
+    H5S_t          *dataspace = NULL;
     herr_t          ret_value = SUCCEED;
     
     FUNC_ENTER_STATIC
@@ -3179,12 +3187,10 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
 
             /* Update the chunk data with any modifications from other processes */
             while (chunk_entry->num_writers > 1) {
-                MPI_Status status;
-                uint8_t   *buf = NULL;
-                uint8_t   *buf_p = NULL;
-                H5S_t     *selection = NULL;
-                int        count;
-                int        mpi_code;
+                unsigned char *mod_data_p = NULL;
+                MPI_Status     status;
+                int            count;
+                int            mpi_code;
 
                 /* XXX: Since the receive tag needs to be an int, it is possible that a chunk's index
                  * may fall outside the range of an int and cause an overflow problem when casting down
@@ -3196,7 +3202,7 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
                     HMPI_GOTO_ERROR(FAIL, "MPI_Probe failed", mpi_code)
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Found message from source %d with tag %d.\n", status.MPI_SOURCE, status.MPI_TAG);
+                HDfprintf(debug_file, "| - Found message from source %d with tag %d.\n", status.MPI_SOURCE, status.MPI_TAG);
 #endif
 
                 /* Retrieve the message size */
@@ -3204,81 +3210,73 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
                     HMPI_GOTO_ERROR(FAIL, "MPI_Get_count failed", mpi_code)
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Message size is %d bytes.\n", count);
+                HDfprintf(debug_file, "| - Message size is %d bytes.\n", count);
 #endif
 
-                if (NULL == (buf = (uint8_t *) H5MM_malloc(count)))
+                if (NULL == (mod_data = (unsigned char *) H5MM_malloc(count)))
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate modification data receive buffer")
-                buf_p = buf;
+                mod_data_p = mod_data;
 
-                if (MPI_SUCCESS != (mpi_code = MPI_Recv(buf, count, MPI_BYTE, MPI_ANY_SOURCE,
+                if (MPI_SUCCESS != (mpi_code = MPI_Recv(mod_data, count, MPI_BYTE, MPI_ANY_SOURCE,
                         chunk_entry->chunk_info.index, io_info->comm, &status)))
                     HMPI_GOTO_ERROR(FAIL, "MPI_Recv failed", mpi_code)
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Received the message.\n");
+                HDfprintf(debug_file, "| - Received the message.\n");
 #endif
 
-                /* Deserialize the selection in the chunk's dataspace */
-                if (H5S_SELECT_DESERIALIZE(&selection, &buf_p) < 0)
-                    HGOTO_ERROR(H5E_DATASET, H5E_CANTDECODE, FAIL, "unable to deserialize dataspace selection")
-
-                /* H5S_extent_copy(selection, chunk_entry->chunk_info.mspace); */
+                /* Decode the chunk's memory dataspace */
+                if (NULL == (dataspace = H5S_decode(&mod_data_p)))
+                    HGOTO_ERROR(H5E_DATASET, H5E_CANTDECODE, FAIL, "unable to decode dataspace")
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Deserialized selection info:\n");
+                HDfprintf(debug_file, "| Deserialized selection info:\n");
                 HDfprintf(debug_file, "| Mem Space:\n");
-                HDfprintf(debug_file, "|  - Extent Num elements: %zd\n", H5S_GET_EXTENT_NPOINTS(selection));
-                HDfprintf(debug_file, "|  - Extent type: %d\n", H5S_GET_EXTENT_TYPE(selection));
-                HDfprintf(debug_file, "|  - Selection Num elements: %zd\n", H5S_GET_SELECT_NPOINTS(selection));
-                HDfprintf(debug_file, "|  - Selection type: %d\n", H5S_GET_SELECT_TYPE(selection));
+                HDfprintf(debug_file, "|  - Extent Num elements: %zd\n", H5S_GET_EXTENT_NPOINTS(dataspace));
+                HDfprintf(debug_file, "|  - Extent type: %d\n", H5S_GET_EXTENT_TYPE(dataspace));
+                HDfprintf(debug_file, "|  - Selection Num elements: %zd\n", H5S_GET_SELECT_NPOINTS(dataspace));
+                HDfprintf(debug_file, "|  - Selection type: %d\n", H5S_GET_SELECT_TYPE(dataspace));
 #endif
 
-                /* XXX: After receiving the selection information, the extent is not
-                 * set/valid. Possibly copy the selection information directly into
-                 * chunk entry mem space, or copy extent into received selection H5S type
-                 */
-
-
-                if (H5S_select_iter_init(mem_iter, selection, type_info->dst_type_size) < 0)
+                if (H5S_select_iter_init(mem_iter, dataspace, type_info->dst_type_size) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
                 mem_iter_init = TRUE;
 
-                if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(selection)) < 0)
+                if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(dataspace)) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Contents of message:\n[");
+                HDfprintf(debug_file, "| Contents of message:\n| [");
                 for (size_t j = 0; j < iter_nelmts; j++) {
                     if (j > 0) HDfprintf(debug_file, ", ");
-                    HDfprintf(debug_file, "%lld", ((long *) buf_p)[j]);
+                    HDfprintf(debug_file, "%lld", ((long *) mod_data_p)[j]);
                 }
                 HDfprintf(debug_file, "]\n");
 #endif
 
 #ifdef PARALLEL_COMPRESS_DEBUG
-                HDfprintf(debug_file, "Iter nelmts=%lld.\n", iter_nelmts);
-                HDfprintf(debug_file, "Mem space selected points: %zd.\n", H5S_GET_SELECT_NPOINTS(selection));
+                HDfprintf(debug_file, "| Iter nelmts=%lld.\n", iter_nelmts);
+                HDfprintf(debug_file, "| Mem space selected points: %zd.\n| \n", H5S_GET_SELECT_NPOINTS(dataspace));
 #endif
 
                 /* Update the chunk data with the received modification data */
-                /* if (!H5D__gather_mem(buf_p, selection, mem_iter, (size_t) iter_nelmts,
-                        io_info->dxpl_cache, chunk_entry->buf))
-                    HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't gather to write buffer") */
-                if (H5D__scatter_mem(buf_p, selection, mem_iter, (size_t) iter_nelmts,
+                if (H5D__scatter_mem(mod_data_p, dataspace, mem_iter, (size_t) iter_nelmts,
                         io_info->dxpl_cache, chunk_entry->buf) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't scatter to write buffer")
 
                 chunk_entry->num_writers--;
 
-                if (buf)
-                    H5MM_free(buf);
-                if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
+                if (mod_data)
+                    H5MM_free(mod_data);
+                if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
-                if (selection)
-                    if (H5S_close(selection) < 0)
+                if (dataspace) {
+                    if (H5S_close(dataspace) < 0)
                         HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace")
-            }
+                    dataspace = NULL;
+                }
+                mem_iter_init = FALSE;
+            } /* end while */
 
 
 #ifdef PARALLEL_COMPRESS_DEBUG
@@ -3314,6 +3312,9 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
 done:
     if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
+    if (dataspace)
+        if (H5S_close(dataspace) < 0)
+            HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace")
     if (mem_iter)
         H5MM_free(mem_iter)