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authorQuincey Koziol <koziol@hdfgroup.org>2007-06-19 17:35:24 (GMT)
committerQuincey Koziol <koziol@hdfgroup.org>2007-06-19 17:35:24 (GMT)
commit32d09759bdf082d1a5d87903a58b0ed6c03dbe8c (patch)
tree6e6d049a968fe96c516c81638b99eb4f0828c477 /src
parentb2318f778aaa3aa2706b4e5b41b25a791bc9e0a7 (diff)
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[svn-r13883] Description:
Fixed bugs w/VL-datatype fill values for chunked dataset storage. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
Diffstat (limited to 'src')
-rw-r--r--src/H5Distore.c398
1 files changed, 309 insertions, 89 deletions
diff --git a/src/H5Distore.c b/src/H5Distore.c
index 0807a76..3246467 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -1843,13 +1843,101 @@ H5D_istore_lock(const H5D_io_info_t *io_info, H5D_istore_ud1_t *udata,
if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
+ /*
+ * The chunk doesn't exist in the file. Replicate the fill
+ * value throughout the chunk, if the fill value is defined.
+ */
if(fill->buf) {
- /*
- * The chunk doesn't exist in the file. Replicate the fill
- * value throughout the chunk.
- */
- HDassert(0 == (chunk_size % (size_t)fill->size));
- H5V_array_fill(chunk, fill->buf, (size_t)fill->size, chunk_size / fill->size);
+ size_t elmts_per_chunk; /* # of elements per chunk */
+
+ /* Sanity check */
+ HDassert(0 == (chunk_size % fill->size));
+ elmts_per_chunk = chunk_size / fill->size;
+
+ /* If necessary, convert fill value datatypes (which copies VL components, etc.) */
+ if(H5T_detect_class(dset->shared->type, H5T_VLEN) > 0) {
+ H5T_path_t *tpath; /* Datatype conversion path */
+ uint8_t *bkg_buf = NULL; /* Background conversion buffer */
+ H5T_t *mem_type; /* Pointer to memory datatype */
+ size_t mem_type_size, file_type_size; /* Size of datatype in memory and on disk */
+ hid_t mem_tid; /* Memory version of disk datatype */
+
+ /* Create temporary datatype for conversion operation */
+ if(NULL == (mem_type = H5T_copy(dset->shared->type, H5T_COPY_REOPEN)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, NULL, "unable to copy file datatype")
+ if((mem_tid = H5I_register(H5I_DATATYPE, mem_type)) < 0) {
+ H5T_close(mem_type);
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL, "unable to register memory datatype")
+ } /* end if */
+
+ /* Retrieve sizes of memory & file datatypes */
+ mem_type_size = H5T_get_size(mem_type);
+ HDassert(mem_type_size > 0);
+ file_type_size = H5T_get_size(dset->shared->type);
+ HDassert(file_type_size == (size_t)fill->size);
+
+ /* Get the datatype conversion path for this operation */
+ if(NULL == (tpath = H5T_path_find(dset->shared->type, mem_type, NULL, NULL, io_info->dxpl_id, FALSE))) {
+ H5I_dec_ref(mem_tid);
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to convert between src and dst datatypes")
+ } /* end if */
+
+ /* Allocate a background buffer, if necessary */
+ if(H5T_path_bkg(tpath) && NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, (elmts_per_chunk * MAX(mem_type_size, file_type_size))))) {
+ H5I_dec_ref(mem_tid);
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
+ } /* end if */
+
+ /* Make a copy of the (disk-based) fill value into the chunk buffer */
+ HDmemcpy(chunk, fill->buf, file_type_size);
+
+ /* Type convert the chunk buffer, to copy any VL components */
+ if(H5T_convert(tpath, dset->shared->type_id, mem_tid, (size_t)1, (size_t)0, (size_t)0, chunk, bkg_buf, io_info->dxpl_id) < 0) {
+ if(bkg_buf)
+ H5FL_BLK_FREE(type_conv, bkg_buf);
+ H5I_dec_ref(mem_tid);
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, NULL, "data type conversion failed")
+ } /* end if */
+
+ /* Replicate the fill value into the cached buffer */
+ H5V_array_fill(chunk, chunk, mem_type_size, elmts_per_chunk);
+
+ /* Get the inverse datatype conversion path for this operation */
+ if(NULL == (tpath = H5T_path_find(mem_type, dset->shared->type, NULL, NULL, io_info->dxpl_id, FALSE))) {
+ if(bkg_buf)
+ H5FL_BLK_FREE(type_conv, bkg_buf);
+ H5I_dec_ref(mem_tid);
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to convert between src and dst datatypes")
+ } /* end if */
+
+ /* Allocate or reset the background buffer, if necessary */
+ if(H5T_path_bkg(tpath)) {
+ if(bkg_buf)
+ HDmemset(bkg_buf, 0, MAX(mem_type_size, file_type_size));
+ else {
+ if(NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, (elmts_per_chunk * MAX(mem_type_size, file_type_size))))) {
+ H5I_dec_ref(mem_tid);
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
+ } /* end if */
+ } /* end else */
+ } /* end if */
+
+ /* Type convert the chunk buffer, to copy any VL components */
+ if(H5T_convert(tpath, mem_tid, dset->shared->type_id, elmts_per_chunk, (size_t)0, (size_t)0, chunk, bkg_buf, io_info->dxpl_id) < 0) {
+ if(bkg_buf)
+ H5FL_BLK_FREE(type_conv, bkg_buf);
+ H5I_dec_ref(mem_tid);
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, NULL, "data type conversion failed")
+ } /* end if */
+
+ /* Release resources used */
+ if(bkg_buf)
+ H5FL_BLK_FREE(type_conv, bkg_buf);
+ H5I_dec_ref(mem_tid);
+ } /* end if */
+ else
+ /* Replicate the [non-VL] fill value into chunk */
+ H5V_array_fill(chunk, fill->buf, (size_t)fill->size, elmts_per_chunk);
} /* end if */
else {
/*
@@ -2715,13 +2803,14 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
H5D_io_info_t io_info; /* Dataset I/O info */
H5D_storage_t store; /* Dataset storage information */
hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
- hsize_t chunk_size; /* Size of chunk in bytes */
- unsigned filter_mask = 0; /* Filter mask for chunks that have them */
+ size_t elmts_per_chunk; /* # of elements which fit in a chunk */
+ size_t orig_chunk_size; /* Original size of chunk in bytes */
+ unsigned filter_mask = 0; /* Filter mask for chunks that have them */
const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status; /* The fill value status */
- hbool_t should_fill = FALSE; /* Whether fill values should be written */
- void *chunk = NULL; /* Chunk buffer for writing fill values */
+ hbool_t should_fill = FALSE; /* Whether fill values should be written */
+ void *chunk = NULL; /* Chunk buffer for writing fill values */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
#ifdef H5_HAVE_PARALLEL
@@ -2734,8 +2823,15 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
int space_ndims; /* Dataset's space rank */
hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
- int i; /* Local index variable */
- unsigned u; /* Local index variable */
+ H5T_path_t *fill_to_mem_tpath; /* Datatype conversion path for converting the fill value to the memory buffer */
+ H5T_path_t *mem_to_dset_tpath; /* Datatype conversion path for converting the memory buffer to the dataset elements */
+ uint8_t *bkg_buf = NULL; /* Background conversion buffer */
+ H5T_t *mem_type = NULL; /* Pointer to memory datatype */
+ size_t mem_type_size, file_type_size; /* Size of datatype in memory and on disk */
+ size_t elmt_size; /* Size of each element */
+ hid_t mem_tid = (-1); /* Memory version of disk datatype */
+ size_t bkg_buf_size; /* Size of background buffer */
+ hbool_t has_vlen_fill_type = FALSE; /* Whether the datatype for the fill value has a variable-length component */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_allocate, FAIL)
@@ -2746,9 +2842,9 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
HDassert(H5F_addr_defined(dset->shared->layout.u.chunk.addr));
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
- /* We only handle simple data spaces so far */
+ /* Retrieve the dataset dimensions */
if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info")
space_dim[space_ndims] = dset->shared->layout.u.chunk.dim[space_ndims];
/* Fill the DXPL cache values for later use */
@@ -2771,13 +2867,9 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
} /* end if */
#endif /* H5_HAVE_PARALLEL */
- /*
- * Setup indice to go through all chunks. (Future improvement:
- * should allocate only chunks that have no file space assigned yet).
- */
- for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
- chunk_offset[u] = 0;
- chunk_size = dset->shared->layout.u.chunk.size;
+ /* Get original chunk size */
+ H5_CHECK_OVERFLOW(dset->shared->layout.u.chunk.size, hsize_t, size_t);
+ orig_chunk_size = (size_t)dset->shared->layout.u.chunk.size;
/* Check the dataset's fill-value status */
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
@@ -2793,34 +2885,92 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
|| pline->nused > 0)
should_fill = TRUE;
- /* Check if fill values should be written to blocks */
+ /* Check if fill values should be written to chunks */
if(should_fill) {
- /* Allocate chunk buffer for processes to use when writing fill values */
- H5_CHECK_OVERFLOW(chunk_size, hsize_t, size_t);
- if(NULL == (chunk = H5D_istore_chunk_alloc((size_t)chunk_size, pline)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk")
-
/* Fill the chunk with the proper values */
if(fill->buf) {
- /* Replicate the fill value throughout the chunk */
- HDassert(0 == (chunk_size % (size_t)fill->size));
- H5V_array_fill(chunk, fill->buf, (size_t)fill->size, (size_t)(chunk_size / fill->size));
+ /* Detect whether the datatype has a VL component */
+ has_vlen_fill_type = H5T_detect_class(dset->shared->type, H5T_VLEN);
+
+ /* If necessary, convert fill value datatypes (which copies VL components, etc.) */
+ if(has_vlen_fill_type) {
+ /* Create temporary datatype for conversion operation */
+ if(NULL == (mem_type = H5T_copy(dset->shared->type, H5T_COPY_REOPEN)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype")
+ if((mem_tid = H5I_register(H5I_DATATYPE, mem_type)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
+
+ /* Retrieve sizes of memory & file datatypes */
+ mem_type_size = H5T_get_size(mem_type);
+ HDassert(mem_type_size > 0);
+ file_type_size = H5T_get_size(dset->shared->type);
+ HDassert(file_type_size == (size_t)fill->size);
+
+ /* Compute the base size for a chunk to operate on */
+ elmt_size = MAX(mem_type_size, file_type_size);
+ elmts_per_chunk = dset->shared->layout.u.chunk.size / file_type_size;
+ orig_chunk_size = elmts_per_chunk * elmt_size;
+
+ /* Allocate a chunk buffer now, if _no_ filters are used */
+ if(pline->nused == 0)
+ if(NULL == (chunk = H5D_istore_chunk_alloc(orig_chunk_size, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk")
+
+ /* Get the datatype conversion path for this operation */
+ if(NULL == (fill_to_mem_tpath = H5T_path_find(dset->shared->type, mem_type, NULL, NULL, dxpl_id, FALSE)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and dst datatypes")
+
+ /* Get the inverse datatype conversion path for this operation */
+ if(NULL == (mem_to_dset_tpath = H5T_path_find(mem_type, dset->shared->type, NULL, NULL, dxpl_id, FALSE)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and dst datatypes")
+
+ /* Check if we need to allocate a background buffer */
+ if(H5T_path_bkg(fill_to_mem_tpath) || H5T_path_bkg(mem_to_dset_tpath)) {
+ /* Check for inverse datatype conversion needing a background buffer */
+ /* (do this first, since it needs a larger buffer) */
+ if(H5T_path_bkg(mem_to_dset_tpath))
+ bkg_buf_size = elmts_per_chunk * elmt_size;
+ else
+ bkg_buf_size = elmt_size;
+
+ /* Allocate the background buffer */
+ if(NULL == (bkg_buf = H5FL_BLK_MALLOC(type_conv, bkg_buf_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+ } /* end if */
+ } /* end if */
+ else {
+ /* Allocate chunk buffer for processes to use when writing fill values */
+ if(NULL == (chunk = H5D_istore_chunk_alloc(orig_chunk_size, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk")
+
+ /*
+ * Replicate the fill value throughout the chunk.
+ */
+ HDassert(0 == (orig_chunk_size % fill->size));
+ H5V_array_fill(chunk, fill->buf, (size_t)fill->size, (size_t)(orig_chunk_size / fill->size));
+ } /* end else */
} /* end if */
- else
- /* No fill value was specified, assume all zeros. */
- HDmemset(chunk, 0, (size_t)chunk_size);
+ else {
+ /* Allocate chunk buffer for processes to use when writing fill values */
+ if(NULL == (chunk = H5D_istore_chunk_alloc(orig_chunk_size, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk")
+
+ /*
+ * No fill value was specified, assume all zeros.
+ */
+ HDmemset(chunk, 0, orig_chunk_size);
+ } /* end else */
/* Check if there are filters which need to be applied to the chunk */
- if(pline->nused > 0) {
- size_t buf_size = (size_t)chunk_size;
- size_t nbytes = (size_t)chunk_size;
+ /* (only do this in advance when the chunk info can be re-used (i.e.
+ * it doesn't contain any non-default VL datatype fill values)
+ */
+ if(!has_vlen_fill_type && pline->nused > 0) {
+ size_t buf_size = orig_chunk_size;
/* Push the chunk through the filters */
- if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &chunk) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed")
-
- /* Keep the number of bytes the chunk turned in to */
- chunk_size = nbytes;
+ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &orig_chunk_size, &buf_size, &chunk) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
} /* end if */
} /* end if */
@@ -2828,16 +2978,20 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
store.chunk.offset = chunk_offset;
H5D_BUILD_IO_INFO(&io_info, dset, dxpl_cache, dxpl_id, &store);
+ /* Reset the chunk offset indices */
+ HDmemset(chunk_offset, 0, (dset->shared->layout.u.chunk.ndims * sizeof(chunk_offset[0])));
+
/* Loop over all chunks */
carry = FALSE;
while(!carry) {
- hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */
+ int i; /* Local index variable */
/* Check if the chunk exists yet on disk */
- chunk_exists = TRUE;
- if(H5D_istore_get_addr(&io_info, NULL) == HADDR_UNDEF) {
- const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
- H5D_rdcc_ent_t *ent; /*cache entry */
+ if(!H5F_addr_defined(H5D_istore_get_addr(&io_info, NULL))) {
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* Raw data chunk cache */
+ H5D_rdcc_ent_t *ent; /* Cache entry */
+ hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */
+ unsigned u; /* Local index variable */
/* Didn't find the chunk on disk */
chunk_exists = FALSE;
@@ -2846,72 +3000,128 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
/* Assume a match */
chunk_exists = TRUE;
- for(u = 0; u < dset->shared->layout.u.chunk.ndims && chunk_exists; u++) {
- if(ent->offset[u] != chunk_offset[u])
+ for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
+ if(ent->offset[u] != chunk_offset[u]) {
chunk_exists = FALSE; /* Reset if no match */
- } /* end for */
+ break;
+ } /* end if */
} /* end for */
- } /* end if */
-
- if(!chunk_exists) {
- H5D_istore_ud1_t udata; /* B-tree pass-through for creating chunk */
-
- /* Initialize the chunk information */
- udata.common.mesg = &dset->shared->layout;
- udata.common.key.filter_mask = filter_mask;
- udata.addr = HADDR_UNDEF;
- H5_CHECK_OVERFLOW(chunk_size,hsize_t,size_t);
- udata.common.key.nbytes = (size_t)chunk_size;
- for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
- udata.common.key.offset[u] = chunk_offset[u];
- /* Allocate the chunk with all processes */
- if(H5B_insert(dset->oloc.file, dxpl_id, H5B_ISTORE, dset->shared->layout.u.chunk.addr, &udata)<0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk")
-
- /* Check if fill values should be written to blocks */
- if(should_fill) {
-#ifdef H5_HAVE_PARALLEL
- /* Check if this file is accessed with an MPI-capable file driver */
- if(using_mpi) {
- /* Write the chunks out from only one process */
- /* !! Use the internal "independent" DXPL!! -QAK */
- if(H5_PAR_META_WRITE == mpi_rank)
- if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, H5AC_ind_dxpl_id, chunk) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
-
- /* Indicate that blocks are being written */
- blocks_written = TRUE;
+ /* Chunk wasn't in cache either, create it now */
+ if(!chunk_exists) {
+ H5D_istore_ud1_t udata; /* B-tree pass-through for creating chunk */
+ size_t chunk_size; /* Size of chunk in bytes, possibly filtered */
+
+ /* Check for VL datatype & non-default fill value */
+ if(has_vlen_fill_type) {
+ /* Allocate a new chunk buffer each time, if filters are used */
+ if(pline->nused > 0)
+ if(NULL == (chunk = H5D_istore_chunk_alloc(orig_chunk_size, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk")
+
+ /* Make a copy of the (disk-based) fill value into the buffer */
+ HDmemcpy(chunk, fill->buf, file_type_size);
+
+ /* Reset first element of background buffer, if necessary */
+ if(H5T_path_bkg(fill_to_mem_tpath))
+ HDmemset(bkg_buf, 0, elmt_size);
+
+ /* Type convert the dataset buffer, to copy any VL components */
+ if(H5T_convert(fill_to_mem_tpath, dset->shared->type_id, mem_tid, (size_t)1, (size_t)0, (size_t)0, chunk, bkg_buf, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
+
+ /* Replicate the fill value into the cached buffer */
+ H5V_array_fill(chunk, chunk, mem_type_size, elmts_per_chunk);
+
+ /* Reset the entire background buffer, if necessary */
+ if(H5T_path_bkg(mem_to_dset_tpath))
+ HDmemset(bkg_buf, 0, bkg_buf_size);
+
+ /* Type convert the dataset buffer, to copy any VL components */
+ if(H5T_convert(mem_to_dset_tpath, mem_tid, dset->shared->type_id, elmts_per_chunk, (size_t)0, (size_t)0, chunk, bkg_buf, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
+
+ /* Check if there are filters which need to be applied to the chunk */
+ if(pline->nused > 0) {
+ size_t buf_size = orig_chunk_size;
+ size_t nbytes = (size_t)dset->shared->layout.u.chunk.size;
+
+ /* Push the chunk through the filters */
+ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &chunk) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
+
+ /* Keep the number of bytes the chunk turned in to */
+ chunk_size = nbytes;
+ } /* end if */
+ else
+ chunk_size = (size_t)dset->shared->layout.u.chunk.size;
} /* end if */
- else {
+ else
+ chunk_size = orig_chunk_size;
+
+ /* Initialize the chunk information */
+ udata.common.mesg = &dset->shared->layout;
+ udata.common.key.filter_mask = filter_mask;
+ udata.addr = HADDR_UNDEF;
+ udata.common.key.nbytes = chunk_size;
+ for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
+ udata.common.key.offset[u] = chunk_offset[u];
+
+ /* Allocate the chunk with all processes */
+ if(H5B_insert(dset->oloc.file, dxpl_id, H5B_ISTORE, dset->shared->layout.u.chunk.addr, &udata) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to allocate chunk")
+
+ /* Check if fill values should be written to chunks */
+ if(should_fill) {
+#ifdef H5_HAVE_PARALLEL
+ /* Check if this file is accessed with an MPI-capable file driver */
+ if(using_mpi) {
+ /* Write the chunks out from only one process */
+ /* !! Use the internal "independent" DXPL!! -QAK */
+ if(H5_PAR_META_WRITE == mpi_rank)
+ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, H5AC_ind_dxpl_id, chunk) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
+
+ /* Indicate that blocks are being written */
+ blocks_written = TRUE;
+ } /* end if */
+ else {
#endif /* H5_HAVE_PARALLEL */
- if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, dxpl_id, chunk) < 0)
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
+ if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, dxpl_id, chunk) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
#ifdef H5_HAVE_PARALLEL
- } /* end else */
+ } /* end else */
#endif /* H5_HAVE_PARALLEL */
+ } /* end if */
+
+ /* Release the chunk if we need to re-allocate it each time */
+ if(has_vlen_fill_type && pline->nused > 0)
+ chunk = H5D_istore_chunk_xfree(chunk, pline);
} /* end if */
} /* end if */
/* Increment indices */
- for(i = (int)dset->shared->layout.u.chunk.ndims - 1, carry = TRUE; i >= 0 && carry; --i) {
+ carry = TRUE;
+ for(i = (int)dset->shared->layout.u.chunk.ndims - 1; i >= 0; --i) {
chunk_offset[i] += dset->shared->layout.u.chunk.dim[i];
- if (chunk_offset[i] >= space_dim[i])
+ if(chunk_offset[i] >= space_dim[i])
chunk_offset[i] = 0;
- else
+ else {
carry = FALSE;
+ break;
+ } /* end else */
} /* end for */
} /* end while */
#ifdef H5_HAVE_PARALLEL
- /* Only need to block at the barrier if we actually allocated a chunk */
- /* And if we are using an MPI-capable file driver */
+ /* Only need to block at the barrier if we actually initialized a chunk */
+ /* using an MPI-capable file driver */
if(using_mpi && blocks_written) {
/* Wait at barrier to avoid race conditions where some processes are
* still writing out chunks and other processes race ahead to read
* them in, getting bogus data.
*/
- if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
+ if(MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
} /* end if */
#endif /* H5_HAVE_PARALLEL */
@@ -2921,6 +3131,16 @@ done:
if(chunk)
chunk = H5D_istore_chunk_xfree(chunk, pline);
+ /* Free other resources for vlen fill values */
+ if(has_vlen_fill_type) {
+ if(mem_tid > 0)
+ H5I_dec_ref(mem_tid);
+ else if(mem_type)
+ H5T_close(mem_type);
+ if(bkg_buf)
+ H5FL_BLK_FREE(type_conv, bkg_buf);
+ } /* end if */
+
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_istore_allocate() */