summaryrefslogtreecommitdiffstats
path: root/src/H5Dchunk.c
diff options
context:
space:
mode:
authorVailin Choi <vchoi@hdfgroup.org>2017-04-26 19:04:24 (GMT)
committerVailin Choi <vchoi@hdfgroup.org>2017-04-26 19:04:24 (GMT)
commit2d535d8c88181aeb9d778b3b13f92a8d8518586e (patch)
treea31b12a27ae32d351a2a2bca9be5dfbcf45a0346 /src/H5Dchunk.c
parent9c30b393163cfaf069aa166ce261034b3010394d (diff)
parentbacb45b38ae8513024baf2dfe08c8918625489e2 (diff)
downloadhdf5-2d535d8c88181aeb9d778b3b13f92a8d8518586e.zip
hdf5-2d535d8c88181aeb9d778b3b13f92a8d8518586e.tar.gz
hdf5-2d535d8c88181aeb9d778b3b13f92a8d8518586e.tar.bz2
Merge pull request #473 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop
* commit 'bacb45b38ae8513024baf2dfe08c8918625489e2': Modifications based on pull request review. Made couple changes based on the review comments. Incorporate patch from GE Healthcare (HDFFV-9934) This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
Diffstat (limited to 'src/H5Dchunk.c')
-rw-r--r--src/H5Dchunk.c282
1 files changed, 261 insertions, 21 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index ce684a0..4905a70 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -303,6 +303,9 @@ static herr_t H5D__chunk_collective_fill(const H5D_t *dset, hid_t dxpl_id,
H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, const void *fill_buf);
#endif /* H5_HAVE_PARALLEL */
+static int
+H5D__chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
+
/*********************/
/* Package Variables */
/*********************/
@@ -369,8 +372,7 @@ H5FL_EXTERN(H5S_sel_iter_t);
/*-------------------------------------------------------------------------
* Function: H5D__chunk_direct_write
*
- * Purpose: Internal routine to write a chunk
- * directly into the file.
+ * Purpose: Internal routine to write a chunk directly into the file.
*
* Return: Non-negative on success/Negative on failure
*
@@ -408,7 +410,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
/* Allocate dataspace and initialize it if it hasn't been. */
if(!(*layout->ops->is_space_alloc)(&layout->storage)) {
- /* Allocate storage */
+ /* Allocate storage */
if(H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, FALSE, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
}
@@ -465,7 +467,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], FALSE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
} /* end if */
/* Write the data to the file */
@@ -491,6 +493,244 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_direct_read
+ *
+ * Purpose: Internal routine to read a chunk directly from the file.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 14 February 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__chunk_direct_read(const H5D_t *dset, hid_t dxpl_id, hsize_t *offset,
+ uint32_t* filters, void *buf)
+{
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
+ H5D_chunk_ud_t udata; /* User data for querying chunk info */
+ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */
+ H5D_io_info_t io_info; /* to hold the dset and two dxpls (meta and raw data) */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ hbool_t md_dxpl_generated = FALSE; /* bool to indicate whether we should free the md_dxpl_id at exit */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(offset);
+ HDassert(filters);
+ HDassert(buf);
+
+ io_info.dset = dset;
+ io_info.raw_dxpl_id = dxpl_id;
+ io_info.md_dxpl_id = dxpl_id;
+
+ /* set the dxpl IO type for sanity checking at the FD layer */
+#ifdef H5_DEBUG_BUILD
+ if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls")
+ md_dxpl_generated = TRUE;
+#endif /* H5_DEBUG_BUILD */
+
+ /* Allocate dataspace and initialize it if it hasn't been. */
+ if(!(*layout->ops->is_space_alloc)(&layout->storage))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "storage is not initialized")
+
+ /* Calculate the index of this chunk */
+ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled);
+ scaled[dset->shared->ndims] = 0;
+
+ /* Reset fields about the chunk we are looking for */
+ udata.filter_mask = 0;
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Find out the file address of the chunk */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+
+ /* Sanity check */
+ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) ||
+ (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0));
+
+ /* Check if the requested chunk exists in the chunk cache */
+ if(UINT_MAX != udata.idx_hint) {
+ H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint];
+
+ /* Sanity checks */
+ HDassert(udata.idx_hint < rdcc->nslots);
+ HDassert(rdcc->slot[udata.idx_hint]);
+
+ /* If the cached chunk is dirty, it must be flushed to get accurate size */
+ if( ent->dirty == TRUE ) {
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D__get_dxpl_cache(io_info.raw_dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Flush the chunk to disk and clear the cache entry */
+ if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+
+ /* Reset fields about the chunk we are looking for */
+ udata.filter_mask = 0;
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Get the new file address / chunk size after flushing */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+ }
+ }
+
+ /* Make sure the address of the chunk is returned. */
+ if(!H5F_addr_defined(udata.chunk_block.offset))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
+
+ /* Read the chunk data into the supplied buffer */
+ if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, udata.chunk_block.offset, udata.chunk_block.length, io_info.raw_dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+
+ /* Return the filter mask */
+ *filters = udata.filter_mask;
+
+done:
+#ifdef H5_DEBUG_BUILD
+ if(md_dxpl_generated && H5I_dec_ref(io_info.md_dxpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close metadata dxpl")
+#endif /* H5_DEBUG_BUILD */
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_direct_read() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_chunk_storage_size
+ *
+ * Purpose: Internal routine to read the storage size of a chunk on disk.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 20 October 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__get_chunk_storage_size(H5D_t *dset, hid_t dxpl_id, const hsize_t *offset, hsize_t *storage_size)
+{
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
+ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */
+ H5D_io_info_t io_info; /* to hold the dset and two dxpls (meta and raw data) */
+ H5D_chunk_ud_t udata; /* User data for querying chunk info */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ hbool_t md_dxpl_generated = FALSE; /* bool to indicate whether we should free the md_dxpl_id at exit */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(offset);
+ HDassert(storage_size);
+
+ io_info.dset = dset;
+ io_info.raw_dxpl_id = dxpl_id;
+ io_info.md_dxpl_id = dxpl_id;
+
+ /* set the dxpl IO type for sanity checking at the FD layer */
+#ifdef H5_DEBUG_BUILD
+ if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls")
+ md_dxpl_generated = TRUE;
+#endif /* H5_DEBUG_BUILD */
+
+ /* Allocate dataspace and initialize it if it hasn't been. */
+ if(!(*layout->ops->is_space_alloc)(&layout->storage)) {
+ *storage_size = 0;
+ HGOTO_DONE(SUCCEED)
+ }
+
+ /* Calculate the index of this chunk */
+ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled);
+ scaled[dset->shared->ndims] = 0;
+
+ /* Reset fields about the chunk we are looking for */
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Find out the file address of the chunk */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+
+ /* Sanity check */
+ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) ||
+ (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0));
+
+ /* The requested chunk is not in cache or on disk */
+ if(!H5F_addr_defined(udata.chunk_block.offset) && UINT_MAX == udata.idx_hint)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk storage is not allocated")
+
+ /* Check if there are filters registered to the dataset */
+ if( dset->shared->dcpl_cache.pline.nused > 0 ) {
+ /* Check if the requested chunk exists in the chunk cache */
+ if(UINT_MAX != udata.idx_hint) {
+ /* Sanity checks */
+ HDassert(udata.idx_hint < rdcc->nslots);
+ HDassert(rdcc->slot[udata.idx_hint]);
+ H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint];
+
+ /* If the cached chunk is dirty, it must be flushed to get accurate size */
+ if( ent->dirty == TRUE ) {
+ /* Fill the DXPL cache values for later use */
+ if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Flush the chunk to disk and clear the cache entry */
+ if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+
+ /* Reset fields about the chunk we are looking for */
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Get the new file address / chunk size after flushing */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+ }
+ }
+
+ /* Make sure the address of the chunk is returned. */
+ if(!H5F_addr_defined(udata.chunk_block.offset))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
+
+ /* Return the chunk size on disk */
+ *storage_size = udata.chunk_block.length;
+ }
+ /* There are no filters registered, return the chunk size from the storage layout */
+ else
+ *storage_size = dset->shared->layout.u.chunk.size;
+
+done:
+#ifdef H5_DEBUG_BUILD
+ if(md_dxpl_generated && H5I_dec_ref(io_info.md_dxpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close metadata dxpl")
+#endif /* H5_DEBUG_BUILD */
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__get_chunk_storage_size */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D__chunk_set_info_real
*
* Purpose: Internal routine to set the information about chunks for a dataset
@@ -519,22 +759,22 @@ H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims,
/* Compute the # of chunks in dataset dimensions */
for(u = 0, layout->nchunks = 1, layout->max_nchunks = 1; u < ndims; u++) {
/* Round up to the next integer # of chunks, to accomodate partial chunks */
- layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
+ layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
if(H5S_UNLIMITED == max_dims[u])
layout->max_chunks[u] = H5S_UNLIMITED;
else
layout->max_chunks[u] = ((max_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
/* Accumulate the # of chunks */
- layout->nchunks *= layout->chunks[u];
- layout->max_nchunks *= layout->max_chunks[u];
+ layout->nchunks *= layout->chunks[u];
+ layout->max_nchunks *= layout->max_chunks[u];
} /* end for */
/* Get the "down" sizes for each dimension */
if(H5VM_array_down(ndims, layout->chunks, layout->down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
if(H5VM_array_down(ndims, layout->max_chunks, layout->max_down_chunks) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -2383,14 +2623,14 @@ H5D__chunk_dest(H5D_t *dset, hid_t dxpl_id)
/* Flush all the cached chunks */
for(ent = rdcc->head; ent; ent = next) {
- next = ent->next;
- if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
- nerrors++;
+ next = ent->next;
+ if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ nerrors++;
} /* end for */
/* Continue even if there are failures. */
if(nerrors)
- HDONE_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
+ HDONE_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
/* Release cache structures */
if(rdcc->slot)
@@ -2997,27 +3237,27 @@ H5D__chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t
HDassert(ent->idx < rdcc->nslots);
if(flush) {
- /* Flush */
- if(H5D__chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
- HDONE_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+ /* Flush */
+ if(H5D__chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ HDONE_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end if */
else {
/* Don't flush, just free chunk */
- if(ent->chunk != NULL)
- ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk,
+ if(ent->chunk != NULL)
+ ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk,
((ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS) ? NULL
: &(dset->shared->dcpl_cache.pline)));
} /* end else */
/* Unlink from list */
if(ent->prev)
- ent->prev->next = ent->next;
+ ent->prev->next = ent->next;
else
- rdcc->head = ent->next;
+ rdcc->head = ent->next;
if(ent->next)
- ent->next->prev = ent->prev;
+ ent->next->prev = ent->prev;
else
- rdcc->tail = ent->prev;
+ rdcc->tail = ent->prev;
ent->prev = ent->next = NULL;
/* Unlink from temporary list */