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-rw-r--r--src/H5Dchunk.c147
1 files changed, 107 insertions, 40 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 33fc036..d693466 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -188,6 +188,10 @@ typedef struct H5D_chunk_it_ud3_t {
/* needed for copy object pointed by refs */
H5O_copy_t *cpy_info; /* Copy options */
+
+ /* needed for getting raw data from chunk cache */
+ hbool_t chunk_in_cache;
+ uint8_t *chunk; /* the unfiltered chunk data */
} H5D_chunk_it_ud3_t;
/* Callback info for iteration to dump index */
@@ -2280,8 +2284,8 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
void *chunk = NULL; /* Pointer to locked chunk buffer */
htri_t cacheable; /* Whether the chunk is cacheable */
- /* Set chunk's [scaled] coordinates */
- io_info->store->chunk.scaled = chunk_info->scaled;
+ /* Set chunk's [scaled] coordinates */
+ io_info->store->chunk.scaled = chunk_info->scaled;
/* Determine if we should use the chunk cache */
if((cacheable = H5D__chunk_cacheable(io_info, udata.chunk_block.offset, FALSE)) < 0)
@@ -2796,7 +2800,7 @@ H5D__chunk_cinfo_cache_found(const H5D_chunk_cached_t *last, H5D_chunk_ud_t *uda
/* Retrieve the information from the cache */
udata->chunk_block.offset = last->addr;
udata->chunk_block.length = last->nbytes;
- udata->chunk_idx = last->chunk_idx;
+ udata->chunk_idx = last->chunk_idx;
udata->filter_mask = last->filter_mask;
/* Indicate that the data was found */
@@ -3065,19 +3069,19 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t
buf = ent->chunk;
if(ent->dirty) {
- H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
H5D_chunk_ud_t udata; /* pass through B-tree */
hbool_t must_alloc = FALSE; /* Whether the chunk must be allocated */
- hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */
+ hbool_t need_insert = FALSE; /* Whether the chunk needs to be inserted into the index */
/* Set up user data for index callbacks */
udata.common.layout = &dset->shared->layout.u.chunk;
udata.common.storage = &dset->shared->layout.storage.u.chunk;
- udata.common.scaled = ent->scaled;
+ udata.common.scaled = ent->scaled;
udata.chunk_block.offset = ent->chunk_block.offset;
udata.chunk_block.length = dset->shared->layout.u.chunk.size;
udata.filter_mask = 0;
- udata.chunk_idx = ent->chunk_idx;
+ udata.chunk_idx = ent->chunk_idx;
/* Should the chunk be filtered before writing it to disk? */
if(dset->shared->dcpl_cache.pline.nused
@@ -3155,8 +3159,8 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t
/* Create the chunk it if it doesn't exist, or reallocate the chunk
* if its size changed.
*/
- if(H5D__chunk_file_alloc(&idx_info, &(ent->chunk_block), &udata.chunk_block, &need_insert, ent->scaled) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level")
+ if(H5D__chunk_file_alloc(&idx_info, &(ent->chunk_block), &udata.chunk_block, &need_insert, ent->scaled) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk on chunk level")
/* Update the chunk entry's info, in case it was allocated or relocated */
ent->chunk_block.offset = udata.chunk_block.offset;
@@ -3170,7 +3174,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
/* Insert the chunk record into the index */
- if(need_insert && dset->shared->layout.storage.u.chunk.ops->insert)
+ if(need_insert && dset->shared->layout.storage.u.chunk.ops->insert)
if((dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata, dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index")
@@ -3644,7 +3648,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, chunk_addr, my_chunk_alloc, io_info->raw_dxpl_id, chunk) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk")
- if(old_pline && old_pline->nused) {
+ if(old_pline && old_pline->nused) {
if(H5Z_pipeline(old_pline, H5Z_FLAG_REVERSE,
&(udata->filter_mask),
io_info->dxpl_cache->err_detect,
@@ -3733,14 +3737,14 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
if(NULL == (ent = H5FL_CALLOC(H5D_rdcc_ent_t)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't allocate raw data chunk entry")
- ent->edge_chunk_state = disable_filters ? H5D_RDCC_DISABLE_FILTERS : 0;
- if(udata->new_unfilt_chunk)
- ent->edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS;
+ ent->edge_chunk_state = disable_filters ? H5D_RDCC_DISABLE_FILTERS : 0;
+ if(udata->new_unfilt_chunk)
+ ent->edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS;
/* Initialize the new entry */
ent->chunk_block.offset = chunk_addr;
ent->chunk_block.length = chunk_alloc;
- ent->chunk_idx = udata->chunk_idx;
+ ent->chunk_idx = udata->chunk_idx;
HDmemcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims);
H5_CHECKED_ASSIGN(ent->rd_count, uint32_t, chunk_size, size_t);
H5_CHECKED_ASSIGN(ent->wr_count, uint32_t, chunk_size, size_t);
@@ -3761,8 +3765,8 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata,
} /* end if */
else
rdcc->head = rdcc->tail = ent;
- ent->tmp_next = NULL;
- ent->tmp_prev = NULL;
+ ent->tmp_next = NULL;
+ ent->tmp_prev = NULL;
} /* end if */
else
@@ -5658,11 +5662,22 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
H5Z_cb_t cb_struct; /* Filter failure callback struct */
int ret_value = H5_ITER_CONT; /* Return value */
+
FUNC_ENTER_STATIC
/* Get 'size_t' local value for number of bytes in chunk */
H5_CHECKED_ASSIGN(nbytes, size_t, chunk_rec->nbytes, uint32_t);
+ /* Check for filtered chunks */
+ /* Check for an edge chunk that is not filtered */
+ if(pline && pline->nused) {
+ must_filter = TRUE;
+ if( (udata->common.layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) &&
+ (H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, udata->common.layout->dim,
+ chunk_rec->scaled, udata->dset_dims)) )
+ must_filter = FALSE;
+ }
+
/* Check parameter for type conversion */
if(udata->do_convert) {
if(H5T_detect_class(udata->dt_src, H5T_VLEN, FALSE) > 0)
@@ -5673,19 +5688,6 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, H5_ITER_ERROR, "unable to copy dataset elements")
} /* end if */
- /* Check for filtered chunks */
- if((is_vlen || fix_ref) && pline && pline->nused) {
- /* Check if we should disable filters on this chunk */
- if(udata->common.layout->flags
- & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) {
- /* Check if the chunk is an edge chunk, and disable filters if so */
- if(!H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, udata->common.layout->dim, chunk_rec->scaled, udata->dset_dims))
- must_filter = TRUE;
- } /* end if */
- else
- must_filter = TRUE;
- } /* end if */
-
/* Resize the buf if it is too small to hold the data */
if(nbytes > buf_size) {
void *new_buf; /* New buffer for data */
@@ -5708,12 +5710,51 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
udata->buf_size = buf_size = nbytes;
} /* end if */
- /* read chunk data from the source file */
- if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, H5AC_rawdata_dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
+ if(udata->chunk_in_cache && udata->chunk) {
+ HDassert(!H5F_addr_defined(chunk_rec->chunk_addr));
+ HDmemcpy(buf, udata->chunk, nbytes);
+ udata->chunk = NULL;
+ } else {
+ H5D_rdcc_ent_t *ent = NULL; /* Cache entry */
+ unsigned idx; /* Index of chunk in cache, if present */
+ unsigned u; /* Counter */
+ H5D_shared_t *shared_fo = udata->cpy_info->shared_fo;
+
+ /* See if the written chunk is in the chunk cache */
+ if(shared_fo && shared_fo->cache.chunk.nslots > 0) {
+ /* Determine the chunk's location in the hash table */
+ idx = H5D__chunk_hash_val(shared_fo, chunk_rec->scaled);
+
+ /* Get the chunk cache entry for that location */
+ ent = shared_fo->cache.chunk.slot[idx];
+ if(ent) {
+ /* Speculatively set the 'found' flag */
+ udata->chunk_in_cache = TRUE;
+
+ /* Verify that the cache entry is the correct chunk */
+ for(u = 0; u < shared_fo->ndims; u++)
+ if(chunk_rec->scaled[u] != ent->scaled[u]) {
+ udata->chunk_in_cache = FALSE;
+ break;
+ } /* end if */
+ } /* end if */
+ } /* end if */
+
+ if(udata->chunk_in_cache) {
+ HDassert(H5F_addr_defined(chunk_rec->chunk_addr));
+ HDassert(H5F_addr_defined(ent->chunk_block.offset));
+
+ H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t);
+ HDmemcpy(buf, ent->chunk, nbytes);
+ } else {
+ /* read chunk data from the source file */
+ if(H5F_block_read(udata->file_src, H5FD_MEM_DRAW, chunk_rec->chunk_addr, nbytes, H5AC_rawdata_dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk")
+ }
+ }
- /* Need to uncompress variable-length & reference data elements */
- if(must_filter) {
+ /* Need to uncompress filtered variable-length & reference data elements that are not found in chunk cache */
+ if(must_filter && (is_vlen || fix_ref) && !udata->chunk_in_cache) {
unsigned filter_mask = chunk_rec->filter_mask;
cb_struct.func = NULL; /* no callback function when failed */
@@ -5777,8 +5818,8 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
udata_dst.chunk_block.length = chunk_rec->nbytes;
udata_dst.filter_mask = chunk_rec->filter_mask;
- /* Need to compress variable-length & reference data elements before writing to file */
- if(must_filter) {
+ /* Need to compress variable-length or reference data elements or a chunk found in cache before writing to file */
+ if(must_filter && (is_vlen || fix_ref || udata->chunk_in_cache) ) {
if(H5Z_pipeline(pline, 0, &(udata_dst.filter_mask), H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, H5_ITER_ERROR, "output pipeline failed")
#if H5_SIZEOF_SIZE_T > 4
@@ -5787,12 +5828,14 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, H5_ITER_ERROR, "chunk too large for 32-bit length")
#endif /* H5_SIZEOF_SIZE_T > 4 */
H5_CHECKED_ASSIGN(udata_dst.chunk_block.length, uint32_t, nbytes, size_t);
- udata->buf = buf;
- udata->buf_size = buf_size;
+ udata->buf = buf;
+ udata->buf_size = buf_size;
} /* end if */
+ udata->chunk_in_cache = FALSE;
+
udata_dst.chunk_idx = H5VM_array_offset_pre(udata_dst.common.layout->ndims - 1,
- udata_dst.common.layout->max_down_chunks, udata_dst.common.scaled);
+ udata_dst.common.layout->max_down_chunks, udata_dst.common.scaled);
/* Allocate chunk in the file */
if(H5D__chunk_file_alloc(udata->idx_info_dst, NULL, &udata_dst.chunk_block, &need_insert, udata_dst.common.scaled) < 0)
@@ -6047,11 +6090,35 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src,
udata.dset_ndims = (unsigned)sndims;
udata.dset_dims = curr_dims;
udata.cpy_info = cpy_info;
+ udata.chunk_in_cache = FALSE;
+ udata.chunk = NULL;
/* Iterate over chunks to copy data */
if((storage_src->ops->iterate)(&idx_info_src, H5D__chunk_copy_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to copy data")
+ /* Iterate over the chunk cache to copy data for chunks with undefined address */
+ if(udata.cpy_info->shared_fo) {
+ H5D_rdcc_ent_t *ent, *next;
+ H5D_chunk_rec_t chunk_rec;
+ H5D_shared_t *shared_fo = (H5D_shared_t *)udata.cpy_info->shared_fo;
+
+ chunk_rec.nbytes = layout_src->size;
+ chunk_rec.filter_mask = 0;
+ chunk_rec.chunk_addr = HADDR_UNDEF;
+
+ for(ent = shared_fo->cache.chunk.head; ent; ent = next) {
+ if(!H5F_addr_defined(ent->chunk_block.offset)) {
+ HDmemcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled));
+ udata.chunk = ent->chunk;
+ udata.chunk_in_cache = TRUE;
+ if(H5D__chunk_copy_cb(&chunk_rec, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy chunk data in cache")
+ }
+ next = ent->next;
+ } /* end for */
+ }
+
/* I/O buffers may have been re-allocated */
buf = udata.buf;
bkg = udata.bkg;
generated by cgit v0.12 at 2024-08-28 08:18:05 (GMT)