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authorNeil Fortner <nfortne2@hdfgroup.org>2010-05-25 20:39:52 (GMT)
committerNeil Fortner <nfortne2@hdfgroup.org>2010-05-25 20:39:52 (GMT)
commit3f837fc3236a7f55004778e4f22f6e12f26c0b70 (patch)
tree489b7a248f0dd0b7ae9467a7585fa71365799525
parentef292895e9817f7134da9d4a6c7c0c699e01ae9e (diff)
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[svn-r18894] Purpose: Improve allocation performance of filtered datasets with non-default VL
fill values. Description: Previously, H5D_chunk_allocate would, if a dataset were filtered and had a non-default VL fill value, allocate a new buffer for every chunk. Changed H5D_chunk_allocate to reuse the existing buffer if possible. Also other miscellaneous cleanup. Tested: jam, linew, amani (h5committest)
-rw-r--r--src/H5Dchunk.c117
-rw-r--r--src/H5Dcompact.c2
-rw-r--r--src/H5Dcontig.c2
-rw-r--r--src/H5Dfill.c29
-rw-r--r--src/H5Dint.c8
-rw-r--r--src/H5Dpkg.h2
-rw-r--r--src/H5Pdcpl.c2
-rw-r--r--test/set_extent.c7
8 files changed, 95 insertions, 74 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index b0cb0b1..f932a6c 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -188,6 +188,8 @@ static herr_t H5D_chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims
const hsize_t *curr_dims);
static void *H5D_chunk_alloc(size_t size, const H5O_pline_t *pline);
static void *H5D_chunk_xfree(void *chk, const H5O_pline_t *pline);
+static void *H5D_chunk_realloc(void *chk, size_t size,
+ const H5O_pline_t *pline);
static herr_t H5D_chunk_cinfo_cache_update(H5D_chunk_cached_t *last,
const H5D_chunk_ud_t *udata);
static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata);
@@ -889,6 +891,39 @@ H5D_chunk_xfree(void *chk, const H5O_pline_t *pline)
} /* H5D_chunk_xfree() */
+/*-------------------------------------------------------------------------
+ * Function: H5D_chunk_realloc
+ *
+ * Purpose: Reallocate space for a chunk in memory. This routine allocates
+ * memory space for non-filtered chunks from a block free list
+ * and uses malloc()/free() for filtered chunks.
+ *
+ * Return: Pointer to memory for chunk on success/NULL on failure
+ *
+ * Programmer: Neil Fortner
+ * May 3, 2010
+ *
+ *-------------------------------------------------------------------------
+ */
+static void *
+H5D_chunk_realloc(void *chk, size_t size, const H5O_pline_t *pline)
+{
+ void *ret_value = NULL; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_chunk_realloc)
+
+ HDassert(size);
+ HDassert(pline);
+
+ if(pline->nused > 0)
+ ret_value = H5MM_realloc(chk, size);
+ else
+ ret_value = H5FL_BLK_REALLOC(chunk, chk, size);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D_chunk_realloc() */
+
+
/*--------------------------------------------------------------------------
NAME
H5D_free_chunk_info
@@ -2744,6 +2779,9 @@ H5D_chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
else {
H5D_fill_value_t fill_status;
+ /* Sanity check */
+ HDassert(fill->alloc_time != H5D_ALLOC_TIME_EARLY);
+
/* Chunk size on disk isn't [likely] the same size as the final chunk
* size in memory, so allocate memory big enough. */
if(NULL == (chunk = H5D_chunk_alloc(chunk_size, pline)))
@@ -2761,8 +2799,7 @@ H5D_chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
/* Initialize the fill value buffer */
/* (use the compact dataset storage buffer as the fill value buffer) */
- if(H5D_fill_init(&fb_info, chunk, FALSE,
- NULL, NULL, NULL, NULL,
+ if(H5D_fill_init(&fb_info, chunk, NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, chunk_size, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize fill buffer info")
@@ -3124,6 +3161,9 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple dataspace info")
space_dim[space_ndims] = layout->u.chunk.dim[space_ndims];
+ /* The last dimension in chunk_offset is always 0 */
+ chunk_offset[space_ndims] = (hsize_t)0;
+
/* Check if any space dimensions are 0, if so we do not have to do anything
*/
for(op_dim=0; op_dim<space_ndims; op_dim++)
@@ -3184,30 +3224,29 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
/* Initialize the fill value buffer */
/* (delay allocating fill buffer for VL datatypes until refilling) */
/* (casting away const OK - QAK) */
- if(H5D_fill_init(&fb_info, NULL, (hbool_t)(pline->nused > 0),
- (H5MM_allocate_t)H5D_chunk_alloc, (void *)pline,
- (H5MM_free_t)H5D_chunk_xfree, (void *)pline,
+ if(H5D_fill_init(&fb_info, NULL, (H5MM_allocate_t)H5D_chunk_alloc,
+ (void *)pline, (H5MM_free_t)H5D_chunk_xfree, (void *)pline,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, orig_chunk_size, data_dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
fb_info_init = TRUE;
- /* Check if there are filters which need to be applied to the chunk */
- /* (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(!fb_info.has_vlen_fill_type && pline->nused > 0) {
- size_t buf_size = orig_chunk_size;
+ /* Check if there are filters which need to be applied to the chunk */
+ /* (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(!fb_info.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, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0)
- HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
+ /* Push the chunk through the filters */
+ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &orig_chunk_size, &buf_size, &fb_info.fill_buf) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
/* Check for the chunk expanding too much to encode in a 32-bit value */
if(orig_chunk_size > ((size_t)0xffffffff))
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length")
#endif /* H5_SIZEOF_SIZE_T > 4 */
- } /* end if */
+ } /* end if */
} /* end if */
/* Compose chunked index info struct */
@@ -3217,15 +3256,14 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
idx_info.layout = &dset->shared->layout.u.chunk;
idx_info.storage = &dset->shared->layout.storage.u.chunk;
- /* Calculate the minimum and maximum chunk offsets in each dimension */
+ /* Calculate the minimum and maximum chunk offsets in each dimension. Note
+ * that we assume here that all elements of space_dim are > 0. This is
+ * checked at the top of this function */
for(op_dim=0; op_dim<space_ndims; op_dim++) {
min_unalloc[op_dim] = ((old_dim[op_dim] + chunk_dim[op_dim] - 1)
/ chunk_dim[op_dim]) * chunk_dim[op_dim];
- if(space_dim[op_dim] == 0)
- max_unalloc[op_dim] = 0;
- else
- max_unalloc[op_dim] = ((space_dim[op_dim] - 1) / chunk_dim[op_dim])
- * chunk_dim[op_dim];
+ max_unalloc[op_dim] = ((space_dim[op_dim] - 1) / chunk_dim[op_dim])
+ * chunk_dim[op_dim];
} /* end for */
/* Loop over all chunks */
@@ -3255,14 +3293,15 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
continue;
else {
/* Reset the chunk offset indices */
- HDmemset(chunk_offset, 0, (layout->u.chunk.ndims * sizeof(chunk_offset[0])));
+ HDmemset(chunk_offset, 0, ((unsigned)space_ndims
+ * sizeof(chunk_offset[0])));
chunk_offset[op_dim] = min_unalloc[op_dim];
carry = FALSE;
} /* end if */
while(!carry) {
- size_t chunk_size; /* Size of chunk in bytes, possibly filtered */
+ size_t chunk_size = orig_chunk_size; /* Size of chunk in bytes, possibly filtered */
#ifndef NDEBUG
/* None of the chunks should be allocated */
@@ -3288,17 +3327,26 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
/* Sanity check */
HDassert(should_fill);
+ /* Check to make sure the buffer is large enough. It is
+ * possible (though ill-advised) for the filter to shrink the
+ * buffer. */
+ if(fb_info.fill_buf_size < orig_chunk_size) {
+ if(NULL == (fb_info.fill_buf = H5D_chunk_realloc(
+ fb_info.fill_buf, orig_chunk_size, pline)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory reallocation failed for raw data chunk")
+ fb_info.fill_buf_size = orig_chunk_size;
+ } /* end if */
+
/* Fill the buffer with VL datatype fill values */
if(H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, data_dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer")
/* 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 = fb_info.fill_buf_size;
+ size_t nbytes = 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, &fb_info.fill_buf) < 0)
+ if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &fb_info.fill_buf_size, &fb_info.fill_buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
@@ -3310,11 +3358,7 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
/* Keep the number of bytes the chunk turned in to */
chunk_size = nbytes;
} /* end if */
- else
- H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t);
} /* end if */
- else
- chunk_size = orig_chunk_size;
/* Initialize the chunk information */
udata.common.layout = &layout->u.chunk;
@@ -3356,10 +3400,6 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
#endif /* H5_HAVE_PARALLEL */
} /* end if */
- /* Release the fill buffer if we need to re-allocate it each time */
- if(fb_info_init && fb_info.has_vlen_fill_type && pline->nused > 0)
- H5D_fill_release(&fb_info);
-
/* Increment indices */
carry = TRUE;
for(i = (int)(space_ndims - 1); i >= 0; --i) {
@@ -3377,8 +3417,8 @@ H5D_chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite,
} /* end while(!carry) */
/* Adjust max_unalloc_dim_idx so we don't allocate the same chunk twice.
- * Also check if this dimension started from 0 (and hence allocated all
- * of the chunks. */
+ * Also check if this dimension started from 0 (and hence allocated all
+ * of the chunks. */
if(min_unalloc[op_dim] == 0)
break;
else
@@ -3457,7 +3497,7 @@ H5D_chunk_prune_fill(H5D_chunk_it_ud1_t *udata)
/* Initialize the fill value buffer, if necessary */
if(!udata->fb_info_init) {
H5_CHECK_OVERFLOW(udata->elmts_per_chunk, uint32_t, size_t);
- if(H5D_fill_init(&udata->fb_info, NULL, FALSE, NULL, NULL, NULL, NULL,
+ if(H5D_fill_init(&udata->fb_info, NULL, NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill,
dset->shared->type, dset->shared->type_id, (size_t)udata->elmts_per_chunk,
io_info->dxpl_cache->max_temp_buf, io_info->dxpl_id) < 0)
@@ -4990,8 +5030,7 @@ H5D_nonexistent_readvv(const H5D_io_info_t *io_info,
buf = (unsigned char *)io_info->u.rbuf + mem_offset_arr[u];
/* Initialize the fill value buffer */
- if(H5D_fill_init(&fb_info, buf, FALSE,
- NULL, NULL, NULL, NULL,
+ if(H5D_fill_init(&fb_info, buf, NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, size, io_info->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info")
diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c
index 128b07e..4f56833 100644
--- a/src/H5Dcompact.c
+++ b/src/H5Dcompact.c
@@ -134,7 +134,7 @@ H5D_compact_fill(H5D_t *dset, hid_t dxpl_id)
/* Initialize the fill value buffer */
/* (use the compact dataset storage buffer as the fill value buffer) */
- if(H5D_fill_init(&fb_info, dset->shared->layout.storage.u.compact.buf, FALSE,
+ if(H5D_fill_init(&fb_info, dset->shared->layout.storage.u.compact.buf,
NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill, dset->shared->type,
dset->shared->type_id, (size_t)0, dset->shared->layout.storage.u.compact.size, dxpl_id) < 0)
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c
index 567f4c9..b674f44 100644
--- a/src/H5Dcontig.c
+++ b/src/H5Dcontig.c
@@ -222,7 +222,7 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
H5_ASSIGN_OVERFLOW(npoints, snpoints, hssize_t, size_t);
/* Initialize the fill value buffer */
- if(H5D_fill_init(&fb_info, NULL, FALSE, NULL, NULL, NULL, NULL,
+ if(H5D_fill_init(&fb_info, NULL, NULL, NULL, NULL, NULL,
&dset->shared->dcpl_cache.fill,
dset->shared->type, dset->shared->type_id, npoints,
dxpl_cache->max_temp_buf, my_dxpl_id) < 0)
diff --git a/src/H5Dfill.c b/src/H5Dfill.c
index 1db2976..1929a5a 100644
--- a/src/H5Dfill.c
+++ b/src/H5Dfill.c
@@ -363,7 +363,6 @@ done:
*/
herr_t
H5D_fill_init(H5D_fill_buf_info_t *fb_info, void *caller_fill_buf,
- hbool_t alloc_vl_during_refill,
H5MM_allocate_t alloc_func, void *alloc_info,
H5MM_free_t free_func, void *free_info,
const H5O_fill_t *fill, const H5T_t *dset_type, hid_t dset_type_id,
@@ -386,7 +385,6 @@ H5D_fill_init(H5D_fill_buf_info_t *fb_info, void *caller_fill_buf,
fb_info->fill = fill;
fb_info->file_type = dset_type;
fb_info->file_tid = dset_type_id;
- fb_info->alloc_vl_during_refill = alloc_vl_during_refill;
fb_info->fill_alloc_func = alloc_func;
fb_info->fill_alloc_info = alloc_info;
fb_info->fill_free_func = free_func;
@@ -434,16 +432,12 @@ H5D_fill_init(H5D_fill_buf_info_t *fb_info, void *caller_fill_buf,
fb_info->use_caller_fill_buf = TRUE;
} /* end if */
else {
- if(alloc_vl_during_refill)
- fb_info->fill_buf = NULL;
- else {
- if(alloc_func)
- fb_info->fill_buf = alloc_func(fb_info->fill_buf_size, alloc_info);
- else
- fb_info->fill_buf = H5FL_BLK_MALLOC(non_zero_fill, fb_info->fill_buf_size);
- if(NULL == fb_info->fill_buf)
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
- } /* end else */
+ if(alloc_func)
+ fb_info->fill_buf = alloc_func(fb_info->fill_buf_size, alloc_info);
+ else
+ fb_info->fill_buf = H5FL_BLK_MALLOC(non_zero_fill, fb_info->fill_buf_size);
+ if(NULL == fb_info->fill_buf)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
} /* end else */
/* Get the datatype conversion path for this operation */
@@ -577,16 +571,7 @@ H5D_fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts, hid_t dxpl_id)
/* Check args */
HDassert(fb_info);
HDassert(fb_info->has_vlen_fill_type);
-
- /* Check if we should allocate the fill buffer now */
- if(fb_info->alloc_vl_during_refill) {
- if(fb_info->fill_alloc_func)
- fb_info->fill_buf = fb_info->fill_alloc_func(fb_info->fill_buf_size, fb_info->fill_alloc_info);
- else
- fb_info->fill_buf = H5FL_BLK_MALLOC(non_zero_fill, fb_info->fill_buf_size);
- if(NULL == fb_info->fill_buf)
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
- } /* end if */
+ HDassert(fb_info->fill_buf);
/* Make a copy of the (disk-based) fill value into the buffer */
HDmemcpy(fb_info->fill_buf, fb_info->fill->buf, fb_info->file_elmt_size);
diff --git a/src/H5Dint.c b/src/H5Dint.c
index 6253aa6..538ff80 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -2190,10 +2190,10 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id)
*/
if(shrink && H5D_CHUNKED == dset->shared->layout.type &&
(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) {
- /* Remove excess chunks */
- if(H5D_chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ")
- } /* end if */
+ /* Remove excess chunks */
+ if(H5D_chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks")
+ } /* end if */
/* Mark the dataspace as dirty, for later writing to the file */
dset->shared->space_dirty = TRUE;
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index bb8fd71..0dc9a9f 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -450,7 +450,6 @@ typedef struct {
/* Typedef for filling a buffer with a fill value */
typedef struct H5D_fill_buf_info_t {
- hbool_t alloc_vl_during_refill; /* Whether to allocate VL-datatype fill buffer during refill */
H5MM_allocate_t fill_alloc_func; /* Routine to call for allocating fill buffer */
void *fill_alloc_info; /* Extra info for allocation routine */
H5MM_free_t fill_free_func; /* Routine to call for freeing fill buffer */
@@ -645,7 +644,6 @@ H5_DLL herr_t H5D_efl_bh_info(H5F_t *f, hid_t dxpl_id, H5O_efl_t *efl,
H5_DLL herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf,
const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id);
H5_DLL herr_t H5D_fill_init(H5D_fill_buf_info_t *fb_info, void *caller_fill_buf,
- hbool_t alloc_vl_during_refill,
H5MM_allocate_t alloc_func, void *alloc_info,
H5MM_free_t free_func, void *free_info,
const H5O_fill_t *fill, const H5T_t *dset_type, hid_t dset_type_id,
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index 4b3e0a8..6fe1b39 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -1363,7 +1363,7 @@ H5Pset_scaleoffset(hid_t plist_id, H5Z_SO_scale_type_t scale_type, int scale_fac
HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
if(scale_factor < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "scale factor must be > 0")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "scale factor must be >= 0")
if(scale_type!=H5Z_SO_FLOAT_DSCALE && scale_type!=H5Z_SO_FLOAT_ESCALE && scale_type!=H5Z_SO_INT)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid scale type")
diff --git a/test/set_extent.c b/test/set_extent.c
index 172c0ee..0582c41 100644
--- a/test/set_extent.c
+++ b/test/set_extent.c
@@ -55,11 +55,10 @@ const char *FILENAME[] = {
#define DO_RANKS_PRINT_CONFIG(TEST) { \
printf(" Config:\n"); \
printf(" Test: %s\n", TEST); \
- printf(" Compression: %s\n", (config & CONFIG_COMPRESS ? "yes" \
- : "no")); \
+ printf(" Compression: %s\n", (config & CONFIG_COMPRESS ? "yes" : "no")); \
printf(" Fill value: %s\n", (do_fillvalue ? "yes" : "no")); \
- printf(" Early allocation: %s\n", (config & CONFIG_EARLY_ALLOC \
- ? "yes" : "no")); \
+ printf(" Early allocation: %s\n", (config & CONFIG_EARLY_ALLOC ? "yes" \
+ : "no")); \
} /* end DO_RANKS_PRINT_CONFIG */
#define RANK1 1