diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5D.c | 12 | ||||
| -rw-r--r-- | src/H5Distore.c | 58 | ||||
| -rw-r--r-- | src/H5Fistore.c | 58 | ||||
| -rw-r--r-- | src/H5Olayout.c | 5 | ||||
| -rw-r--r-- | src/H5Oprivate.h | 1 |
5 files changed, 55 insertions, 79 deletions
@@ -1845,7 +1845,6 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space const H5T_t *type; /* Datatype for dataset */ H5D_t *new_dset = NULL; int i, ndims; - hsize_t comp_data_size; unsigned u; hsize_t max_dim[H5O_LAYOUT_NDIMS]={0}; H5F_t *file=NULL; @@ -2041,11 +2040,16 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space /* Set the dataset's chunk sizes from the property list's chunk sizes */ for (u=0; u<new_dset->layout.ndims-1; u++) new_dset->layout.dim[u] = chunk_size[u]; + + /* Compute the total size of a chunk */ + for (u=0, new_dset->layout.chunk_size=1; u<new_dset->layout.ndims; u++) + new_dset->layout.chunk_size *= new_dset->layout.dim[u]; break; case H5D_COMPACT: { hssize_t tmp_size; /* Temporary holder for raw data size */ + hsize_t comp_data_size; /* * Compact dataset is stored in dataset object header message of @@ -2060,10 +2064,8 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space comp_data_size=H5O_MAX_SIZE-H5O_layout_meta_size(file, &(new_dset->layout)); if(new_dset->layout.size > comp_data_size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size") - if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim, max_dim))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize dimension size of compact dataset storage") - /* remember to check if size is small enough to fit header message */ - + if (H5S_get_simple_extent_dims(space, new_dset->layout.dim, NULL)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize dimension size of compact dataset storage"); } break; diff --git a/src/H5Distore.c b/src/H5Distore.c index 95876e9..3efc914 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -212,8 +212,8 @@ H5B_class_t H5B_ISTORE[1] = {{ /* Declare a free list to manage H5F_rdcc_ent_t objects */ H5FL_DEFINE_STATIC(H5F_rdcc_ent_t); -/* Declare a PQ free list to manage the H5F_rdcc_ent_ptr_t array information */ -H5FL_ARR_DEFINE_STATIC(H5F_rdcc_ent_ptr_t,-1); +/* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */ +H5FL_SEQ_DEFINE_STATIC(H5F_rdcc_ent_ptr_t); /*------------------------------------------------------------------------- @@ -882,7 +882,7 @@ H5F_istore_init (H5F_t *f) HDmemset (rdcc, 0, sizeof(H5F_rdcc_t)); if (f->shared->rdcc_nbytes>0 && f->shared->rdcc_nelmts>0) { rdcc->nslots = f->shared->rdcc_nelmts; - rdcc->slot = H5FL_ARR_CALLOC (H5F_rdcc_ent_ptr_t,rdcc->nslots); + rdcc->slot = H5FL_SEQ_CALLOC (H5F_rdcc_ent_ptr_t,rdcc->nslots); if (NULL==rdcc->slot) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); } @@ -1183,7 +1183,7 @@ H5F_istore_dest (H5F_t *f, hid_t dxpl_id) if (nerrors) HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks"); - H5FL_ARR_FREE (H5F_rdcc_ent_ptr_t,rdcc->slot); + H5FL_SEQ_FREE (H5F_rdcc_ent_ptr_t,rdcc->slot); HDmemset (rdcc, 0, sizeof(H5F_rdcc_t)); done: @@ -1357,7 +1357,6 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con unsigned u; /*counters */ H5F_istore_ud1_t udata; /*B-tree pass-through */ size_t chunk_size=0; /*size of a chunk */ - hsize_t tempchunk_size; herr_t status; /*func return status */ void *chunk=NULL; /*the file chunk */ void *ret_value; /*return value */ @@ -1405,9 +1404,8 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con HDfflush(stderr); #endif rdcc->nhits++; - for (u=0, tempchunk_size=1; u<layout->ndims; u++) - tempchunk_size *= layout->dim[u]; - H5_ASSIGN_OVERFLOW(chunk_size,tempchunk_size,hsize_t,size_t); + assert(layout->chunk_size>0); + H5_ASSIGN_OVERFLOW(chunk_size,layout->chunk_size,hsize_t,size_t); if (NULL==(chunk=H5MM_malloc (chunk_size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk"); @@ -1417,11 +1415,10 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con * Not in the cache. Read it from the file and count this as a miss * if it's in the file or an init if it isn't. */ - for (u=0, tempchunk_size=1; u<layout->ndims; u++) { + for (u=0; u<layout->ndims; u++) udata.key.offset[u] = offset[u]; - tempchunk_size *= layout->dim[u]; - } - H5_ASSIGN_OVERFLOW(chunk_size,tempchunk_size,hsize_t,size_t); + assert(layout->chunk_size>0); + H5_ASSIGN_OVERFLOW(chunk_size,layout->chunk_size,hsize_t,size_t); udata.mesg = *layout; udata.addr = HADDR_UNDEF; status = H5B_find (f, dxpl_id, H5B_ISTORE, layout->addr, &udata); @@ -1637,17 +1634,15 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, */ if (dirty) { H5F_rdcc_ent_t x; - hsize_t tempchunk_size; HDmemset (&x, 0, sizeof x); x.dirty = TRUE; x.layout = H5O_copy (H5O_LAYOUT_ID, layout, NULL); x.pline = H5O_copy (H5O_PLINE_ID, pline, NULL); - for (u=0, tempchunk_size=1; u<layout->ndims; u++) { + for (u=0; u<layout->ndims; u++) x.offset[u] = offset[u]; - tempchunk_size *= layout->dim[u]; - } - H5_ASSIGN_OVERFLOW(x.chunk_size,tempchunk_size,hsize_t,size_t); + assert(layout->chunk_size>0); + H5_ASSIGN_OVERFLOW(x.chunk_size,layout->chunk_size,hsize_t,size_t); x.alloc_size = x.chunk_size; x.chunk = chunk; @@ -1699,7 +1694,6 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], void *buf) { - hsize_t chunk_size; /* Chunk size, in bytes */ haddr_t chunk_addr; /* Chunk address on disk */ hssize_t chunk_coords_in_elmts[H5O_LAYOUT_NDIMS]; size_t u; /* Local index variables */ @@ -1719,10 +1713,6 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp assert(mem_offset_arr); assert(buf); - /* Compute chunk size */ - for (u=0, chunk_size=1; u<layout->ndims; u++) - chunk_size *= layout->dim[u]; - #ifndef NDEBUG for (u=0; u<layout->ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ @@ -1739,7 +1729,7 @@ for(u=0; u<layout->ndims; u++) #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords_in_elmts); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]); @@ -1752,9 +1742,9 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * for the chunk has been defined, then don't load the chunk into the * cache, just write the data to it directly. */ - if (chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && + if (layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) { - if ((ret_value=H5F_contig_readvv(f, chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_readvv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file"); } /* end if */ else { @@ -1811,7 +1801,6 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], const void *buf) { - hsize_t chunk_size; /* Chunk size, in bytes */ haddr_t chunk_addr; /* Chunk address on disk */ hssize_t chunk_coords_in_elmts[H5O_LAYOUT_NDIMS]; size_t u; /* Local index variables */ @@ -1831,10 +1820,6 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, assert(mem_offset_arr); assert(buf); - /* Compute chunk size */ - for (u=0, chunk_size=1; u<layout->ndims; u++) - chunk_size *= layout->dim[u]; - #ifndef NDEBUG for (u=0; u<layout->ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ @@ -1851,7 +1836,7 @@ for(u=0; u<layout->ndims; u++) #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords_in_elmts); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]); @@ -1869,14 +1854,14 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * writing to other elements in the same chunk. Do a direct * write-through of only the elements requested. */ - if ((chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) + if ((layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) || (IS_H5FD_MPI(f) && (H5F_ACC_RDWR & f->shared->flags))) { #ifdef H5_HAVE_PARALLEL /* Additional sanity check when operating in parallel */ if (chunk_addr==HADDR_UNDEF || dcpl_cache->pline.nused>0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk"); #endif /* H5_HAVE_PARALLEL */ - if ((ret_value=H5F_contig_writevv(f, chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_writevv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); } /* end if */ else { @@ -1889,7 +1874,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if(chunk_max_nseq==1 && chunk_len_arr[0] == chunk_size) + if(chunk_max_nseq==1 && chunk_len_arr[0] == layout->chunk_size) relax = TRUE; else relax = FALSE; @@ -2177,10 +2162,9 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Setup indice to go through all chunks. (Future improvement * should allocate only chunks that have no file space assigned yet. */ - for (u=0, chunk_size=1; u<layout->ndims; u++) { + for (u=0; u<layout->ndims; u++) chunk_offset[u] = 0; - chunk_size *= layout->dim[u]; - } /* end for */ + chunk_size = layout->chunk_size; /* Check the dataset's fill-value status */ if (H5P_is_fill_value_defined(&fill, &fill_status) < 0) diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 95876e9..3efc914 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -212,8 +212,8 @@ H5B_class_t H5B_ISTORE[1] = {{ /* Declare a free list to manage H5F_rdcc_ent_t objects */ H5FL_DEFINE_STATIC(H5F_rdcc_ent_t); -/* Declare a PQ free list to manage the H5F_rdcc_ent_ptr_t array information */ -H5FL_ARR_DEFINE_STATIC(H5F_rdcc_ent_ptr_t,-1); +/* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */ +H5FL_SEQ_DEFINE_STATIC(H5F_rdcc_ent_ptr_t); /*------------------------------------------------------------------------- @@ -882,7 +882,7 @@ H5F_istore_init (H5F_t *f) HDmemset (rdcc, 0, sizeof(H5F_rdcc_t)); if (f->shared->rdcc_nbytes>0 && f->shared->rdcc_nelmts>0) { rdcc->nslots = f->shared->rdcc_nelmts; - rdcc->slot = H5FL_ARR_CALLOC (H5F_rdcc_ent_ptr_t,rdcc->nslots); + rdcc->slot = H5FL_SEQ_CALLOC (H5F_rdcc_ent_ptr_t,rdcc->nslots); if (NULL==rdcc->slot) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); } @@ -1183,7 +1183,7 @@ H5F_istore_dest (H5F_t *f, hid_t dxpl_id) if (nerrors) HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks"); - H5FL_ARR_FREE (H5F_rdcc_ent_ptr_t,rdcc->slot); + H5FL_SEQ_FREE (H5F_rdcc_ent_ptr_t,rdcc->slot); HDmemset (rdcc, 0, sizeof(H5F_rdcc_t)); done: @@ -1357,7 +1357,6 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con unsigned u; /*counters */ H5F_istore_ud1_t udata; /*B-tree pass-through */ size_t chunk_size=0; /*size of a chunk */ - hsize_t tempchunk_size; herr_t status; /*func return status */ void *chunk=NULL; /*the file chunk */ void *ret_value; /*return value */ @@ -1405,9 +1404,8 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con HDfflush(stderr); #endif rdcc->nhits++; - for (u=0, tempchunk_size=1; u<layout->ndims; u++) - tempchunk_size *= layout->dim[u]; - H5_ASSIGN_OVERFLOW(chunk_size,tempchunk_size,hsize_t,size_t); + assert(layout->chunk_size>0); + H5_ASSIGN_OVERFLOW(chunk_size,layout->chunk_size,hsize_t,size_t); if (NULL==(chunk=H5MM_malloc (chunk_size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk"); @@ -1417,11 +1415,10 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con * Not in the cache. Read it from the file and count this as a miss * if it's in the file or an init if it isn't. */ - for (u=0, tempchunk_size=1; u<layout->ndims; u++) { + for (u=0; u<layout->ndims; u++) udata.key.offset[u] = offset[u]; - tempchunk_size *= layout->dim[u]; - } - H5_ASSIGN_OVERFLOW(chunk_size,tempchunk_size,hsize_t,size_t); + assert(layout->chunk_size>0); + H5_ASSIGN_OVERFLOW(chunk_size,layout->chunk_size,hsize_t,size_t); udata.mesg = *layout; udata.addr = HADDR_UNDEF; status = H5B_find (f, dxpl_id, H5B_ISTORE, layout->addr, &udata); @@ -1637,17 +1634,15 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, */ if (dirty) { H5F_rdcc_ent_t x; - hsize_t tempchunk_size; HDmemset (&x, 0, sizeof x); x.dirty = TRUE; x.layout = H5O_copy (H5O_LAYOUT_ID, layout, NULL); x.pline = H5O_copy (H5O_PLINE_ID, pline, NULL); - for (u=0, tempchunk_size=1; u<layout->ndims; u++) { + for (u=0; u<layout->ndims; u++) x.offset[u] = offset[u]; - tempchunk_size *= layout->dim[u]; - } - H5_ASSIGN_OVERFLOW(x.chunk_size,tempchunk_size,hsize_t,size_t); + assert(layout->chunk_size>0); + H5_ASSIGN_OVERFLOW(x.chunk_size,layout->chunk_size,hsize_t,size_t); x.alloc_size = x.chunk_size; x.chunk = chunk; @@ -1699,7 +1694,6 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], void *buf) { - hsize_t chunk_size; /* Chunk size, in bytes */ haddr_t chunk_addr; /* Chunk address on disk */ hssize_t chunk_coords_in_elmts[H5O_LAYOUT_NDIMS]; size_t u; /* Local index variables */ @@ -1719,10 +1713,6 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp assert(mem_offset_arr); assert(buf); - /* Compute chunk size */ - for (u=0, chunk_size=1; u<layout->ndims; u++) - chunk_size *= layout->dim[u]; - #ifndef NDEBUG for (u=0; u<layout->ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ @@ -1739,7 +1729,7 @@ for(u=0; u<layout->ndims; u++) #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords_in_elmts); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]); @@ -1752,9 +1742,9 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * for the chunk has been defined, then don't load the chunk into the * cache, just write the data to it directly. */ - if (chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && + if (layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) { - if ((ret_value=H5F_contig_readvv(f, chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_readvv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file"); } /* end if */ else { @@ -1811,7 +1801,6 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], const void *buf) { - hsize_t chunk_size; /* Chunk size, in bytes */ haddr_t chunk_addr; /* Chunk address on disk */ hssize_t chunk_coords_in_elmts[H5O_LAYOUT_NDIMS]; size_t u; /* Local index variables */ @@ -1831,10 +1820,6 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, assert(mem_offset_arr); assert(buf); - /* Compute chunk size */ - for (u=0, chunk_size=1; u<layout->ndims; u++) - chunk_size *= layout->dim[u]; - #ifndef NDEBUG for (u=0; u<layout->ndims; u++) assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */ @@ -1851,7 +1836,7 @@ for(u=0; u<layout->ndims; u++) #endif /* QAK */ chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords_in_elmts); #ifdef QAK -HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,chunk_size); +HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->chunk_size); HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: chunk_offset_arr[%Zu]=%Hu\n",FUNC,*chunk_curr_seq,chunk_offset_arr[*chunk_curr_seq]); HDfprintf(stderr,"%s: mem_len_arr[%Zu]=%Zu\n",FUNC,*mem_curr_seq,mem_len_arr[*mem_curr_seq]); @@ -1869,14 +1854,14 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * writing to other elements in the same chunk. Do a direct * write-through of only the elements requested. */ - if ((chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) + if ((layout->chunk_size>f->shared->rdcc_nbytes && dcpl_cache->pline.nused==0 && chunk_addr!=HADDR_UNDEF) || (IS_H5FD_MPI(f) && (H5F_ACC_RDWR & f->shared->flags))) { #ifdef H5_HAVE_PARALLEL /* Additional sanity check when operating in parallel */ if (chunk_addr==HADDR_UNDEF || dcpl_cache->pline.nused>0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk"); #endif /* H5_HAVE_PARALLEL */ - if ((ret_value=H5F_contig_writevv(f, chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) + if ((ret_value=H5F_contig_writevv(f, layout->chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); } /* end if */ else { @@ -1889,7 +1874,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if(chunk_max_nseq==1 && chunk_len_arr[0] == chunk_size) + if(chunk_max_nseq==1 && chunk_len_arr[0] == layout->chunk_size) relax = TRUE; else relax = FALSE; @@ -2177,10 +2162,9 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Setup indice to go through all chunks. (Future improvement * should allocate only chunks that have no file space assigned yet. */ - for (u=0, chunk_size=1; u<layout->ndims; u++) { + for (u=0; u<layout->ndims; u++) chunk_offset[u] = 0; - chunk_size *= layout->dim[u]; - } /* end for */ + chunk_size = layout->chunk_size; /* Check the dataset's fill-value status */ if (H5P_is_fill_value_defined(&fill, &fill_status) < 0) diff --git a/src/H5Olayout.c b/src/H5Olayout.c index b9a41ec..9e92c3f 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -147,6 +147,11 @@ H5O_layout_decode(H5F_t *f, hid_t UNUSED dxpl_id, const uint8_t *p, H5O_shared_t p += mesg->size; } } + else if(mesg->type == H5D_CHUNKED) { + /* Compute chunk size */ + for (u=0, mesg->chunk_size=1; u<mesg->ndims; u++) + mesg->chunk_size *= mesg->dim[u]; + } /* end if */ /* Set return value */ ret_value=mesg; diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index 70362ad..49cb08e 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -129,6 +129,7 @@ typedef struct H5O_layout_t { haddr_t addr; /*file address of data or B-tree */ unsigned ndims; /*num dimensions in stored data */ hsize_t dim[H5O_LAYOUT_NDIMS]; /*size of data or chunk in bytes */ + hsize_t chunk_size; /*size of chunk in bytes */ hbool_t dirty; /*dirty flag for compact dataset */ size_t size; /*size of compact dataset in bytes */ void *buf; /*buffer for compact dataset */ |