diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 92 |
1 files changed, 51 insertions, 41 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 985089e..a465413 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -63,6 +63,7 @@ typedef struct fm_map { H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */ unsigned m_ndims; /* Number of dimensions for memory dataspace */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */ + hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ H5O_layout_t *layout; /* Dataset layout information*/ H5S_sel_type msel_type; /* Selection type in memory */ @@ -694,8 +695,9 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, * fill time is NEVER, there is no way to tell whether part of data * has been overwritten. So just proceed in reading. */ - if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT - && dataset->layout.addr==HADDR_UNDEF) { + if(nelmts > 0 && dataset->efl.nused==0 && + ((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr)))) { H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ /* Retrieve dataset's fill-value properties */ @@ -912,13 +914,14 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* <none needed currently> */ /* Allocate data space and initialize it if it hasn't been. */ - if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT - && dataset->layout.addr==HADDR_UNDEF) { + if(nelmts > 0 && dataset->efl.nused==0 && + ((dataset->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->layout.u.chunk.addr)))) { hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ hbool_t full_overwrite; /* Whether we are over-writing all the elements */ /* Get the number of elements in file dataset's dataspace */ - if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0) + if((file_nelmts=H5S_GET_SIMPLE_EXTENT_NPOINTS(file_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset") /* Always allow fill values to be written if the dataset has a VL datatype */ @@ -1081,7 +1084,9 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || H5S_NULL == H5S_GET_SIMPLE_EXTENT_TYPE(file_space) || dataset->layout.type==H5D_COMPACT); H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t); @@ -1178,7 +1183,9 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, H5_timer_begin(&timer); #endif /* Sanity check that space is allocated, then read data from it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), file_space, @@ -1580,8 +1587,9 @@ UNUSED H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || - dataset->layout.type==H5D_COMPACT); + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); /* Get first node in chunk tree */ chunk_node=H5TB_first(fm.fsel->root); @@ -1709,8 +1717,9 @@ UNUSED H5_timer_begin(&timer); #endif /* Sanity check that space is allocated, then read data from it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || - dataset->layout.type==H5D_COMPACT); + assert(((dataset->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->layout.u.contig.addr)) + || (dataset->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->layout.u.chunk.addr))) + || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), &dataset->dcpl_cache, &store, chunk_info->fspace, &file_iter, smine_nelmts, dxpl_cache, dxpl_id, tconv_buf/*out*/); @@ -2324,16 +2333,16 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp hsize_t dims[H5O_LAYOUT_NDIMS]; /* Temporary dimension information */ /* Set up "equivalent" n-dimensional dataspace with size '1' in each dimension */ - for(u=0; u<dataset->layout.ndims-1; u++) + for(u=0; u<dataset->layout.u.chunk.ndims-1; u++) dims[u]=1; - if((equiv_mspace = H5S_create_simple(dataset->layout.ndims-1,dims,NULL))==NULL) + if((equiv_mspace = H5S_create_simple(dataset->layout.u.chunk.ndims-1,dims,NULL))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create equivalent dataspace for scalar space") /* Indicate that this space needs to be released */ equiv_mspace_init=1; /* Set the number of dimensions for the memory dataspace */ - fm->m_ndims=dataset->layout.ndims-1; + fm->m_ndims=dataset->layout.u.chunk.ndims-1; } /* end else */ else { equiv_mspace=(H5S_t *)mem_space; /* Casting away 'const' OK... */ @@ -2343,7 +2352,7 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp } /* end else */ /* Get dim number and dimensionality for each dataspace */ - fm->f_ndims=f_ndims=dataset->layout.ndims-1; + fm->f_ndims=f_ndims=dataset->layout.u.chunk.ndims-1; if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality") @@ -2352,8 +2361,11 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp last_nchunks=0; nchunks=1; for(u=0; u<f_ndims; u++) { + /* Keep the size of the chunk dimensions as hsize_t for various routines */ + fm->chunk_dim[u]=fm->layout->u.chunk.dim[u]; + /* Round up to the next integer # of chunks, to accomodate partial chunks */ - fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u]; + fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.u.chunk.dim[u])-1) / dataset->layout.u.chunk.dim[u]; /* Track total number of chunks in dataset */ nchunks *= fm->chunks[u]; @@ -2653,7 +2665,6 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) hssize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ hssize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ - hsize_t count[H5O_LAYOUT_NDIMS]; /* Hyperslab count information */ hssize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ hsize_t chunk_index; /* Index of chunk */ int curr_dim; /* Current dimension to increment */ @@ -2675,21 +2686,21 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) /* Set initial chunk location & hyperslab size */ for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t); - start_coords[u]=(sel_start[u]/(hssize_t)fm->layout->dim[u])*(hssize_t)fm->layout->dim[u]; + H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t); + start_coords[u]=(sel_start[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u]; coords[u]=start_coords[u]; - count[u]=fm->layout->dim[u]; - end[u]=(coords[u]+count[u])-1; + end[u]=(coords[u]+fm->chunk_dim[u])-1; } /* end for */ /* Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Iterate through each chunk in the dataset */ while(sel_points) { /* Check for intersection of temporary chunk and file selection */ - if(H5S_hyper_intersect_block(fm->file_space,coords,end)==TRUE) { + /* (Casting away const OK - QAK) */ + if(H5S_hyper_intersect_block((H5S_t *)fm->file_space,coords,end)==TRUE) { H5S_t *tmp_fchunk; /* Temporary file dataspace */ H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */ hssize_t schunk_points; /* Number of elements in chunk selection */ @@ -2707,13 +2718,13 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") /* "AND" temporary chunk and current chunk */ - if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,count,NULL)<0) { + if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection") } /* end if */ /* Resize chunk's dataspace dimensions to size of chunk */ - if(H5S_set_extent_real(tmp_fchunk,count)<0) { + if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions") } /* end if */ @@ -2775,9 +2786,9 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) curr_dim=(int)fm->f_ndims-1; /* Increment chunk location in fastest changing dimension */ - H5_CHECK_OVERFLOW(count[curr_dim],hsize_t,hssize_t); - coords[curr_dim]+=(hssize_t)count[curr_dim]; - end[curr_dim]+=(hssize_t)count[curr_dim]; + H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t); + coords[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim]; + end[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim]; /* Bring chunk location back into bounds, if necessary */ if(coords[curr_dim]>sel_end[curr_dim]) { @@ -2789,12 +2800,12 @@ H5D_create_chunk_file_map_hyper(fm_map *fm) curr_dim--; /* Increment chunk location in current dimension */ - coords[curr_dim]+=(hssize_t)count[curr_dim]; - end[curr_dim]=(coords[curr_dim]+(hssize_t)count[curr_dim])-1; + coords[curr_dim]+=(hssize_t)fm->chunk_dim[curr_dim]; + end[curr_dim]=(coords[curr_dim]+(hssize_t)fm->chunk_dim[curr_dim])-1; } while(coords[curr_dim]>sel_end[curr_dim]); /* Re-Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ } /* end while */ @@ -2871,7 +2882,8 @@ H5D_create_chunk_mem_map_hyper(const fm_map *fm) } /* end if */ else { /* Just point at the memory dataspace & selection */ - chunk_info->mspace=fm->mem_space; + /* (Casting away const OK -QAK) */ + chunk_info->mspace=(H5S_t *)fm->mem_space; /* Indicate that the chunk's memory space is shared */ chunk_info->mspace_shared=1; @@ -2931,10 +2943,8 @@ H5D_create_chunk_mem_map_hyper(const fm_map *fm) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection") /* Compensate for the chunk offset */ - for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t); + for(u=0; u<fm->f_ndims; u++) chunk_adjust[u]=adjust[u]-chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */ - } /* end for */ #ifdef QAK { int mpi_rank; @@ -3016,7 +3026,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb) /* Calculate the index of this chunk */ - if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory TBBTs */ @@ -3047,7 +3057,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize new_chunk_info->index=chunk_index; /* Create a dataspace for the chunk */ - if((fspace = H5S_create_simple(fm->f_ndims,fm->layout->dim,NULL))==NULL) { + if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) { H5FL_FREE(H5D_chunk_info_t,new_chunk_info); HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk") } /* end if */ @@ -3071,8 +3081,8 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize /* Compute the chunk's coordinates */ for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t); - new_chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->dim[u])*(hssize_t)fm->layout->dim[u]; + H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t); + new_chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u]; } /* end for */ new_chunk_info->coords[fm->f_ndims]=0; @@ -3096,7 +3106,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize /* Get the coordinates of the element in the chunk */ for(u=0; u<fm->f_ndims; u++) - coords_in_chunk[u]=coords[u]%fm->layout->dim[u]; + coords_in_chunk[u]=coords[u]%fm->layout->u.chunk.dim[u]; /* Add point to file selection for chunk */ if(H5S_select_elements(chunk_info->fspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_chunk)<0) @@ -3140,7 +3150,7 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb) /* Calculate the index of this chunk */ - if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->down_chunks,&chunk_index)<0) + if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory TBBTs */ |