diff options
Diffstat (limited to 'src/H5Dchunk.c')
| -rw-r--r-- | src/H5Dchunk.c | 122 |
1 files changed, 77 insertions, 45 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 5664d84..ab621ca 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -60,7 +60,7 @@ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5MFprivate.h" /* File memory management */ -#include "H5VMprivate.h" /* Vector and array functions */ +#include "H5VMprivate.h" /* Vector and array functions */ /****************/ @@ -408,7 +408,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, /* Set the chunk's filter mask to the new settings */ udata.filter_mask = filters; - if((layout->storage.u.chunk.ops->insert)(&idx_info, &udata) < 0) + if((layout->storage.u.chunk.ops->insert)(&idx_info, &udata, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") } /* end if */ @@ -1648,7 +1648,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static herr_t H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, unsigned ndims, const hsize_t *coords, void *_fm) { @@ -2090,7 +2089,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, } /* end if */ else { if(need_insert && io_info->dset->shared->layout.storage.u.chunk.ops->insert) - if((io_info->dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata) < 0) + if((io_info->dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") } /* end else */ @@ -2226,7 +2225,7 @@ H5D__chunk_dest(H5D_t *dset, hid_t dxpl_id) FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL) - /* Sanity check */ + /* Sanity checks */ HDassert(dset); /* Fill the DXPL cache values for later use */ @@ -2630,7 +2629,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t 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; @@ -2714,7 +2713,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t /* Insert the chunk record into the index */ if(need_insert && dset->shared->layout.storage.u.chunk.ops->insert) - if((dset->shared->layout.storage.u.chunk.ops->insert)(&idx_info, &udata) < 0) + 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") /* Cache the chunk's info, in case it's accessed again shortly */ @@ -3309,7 +3308,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static int H5D__chunk_allocated_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { @@ -3690,7 +3688,7 @@ H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, * serial operation. -QAK */ if(need_insert && ops->insert) - if((ops->insert)(&idx_info, &udata) < 0) + if((ops->insert)(&idx_info, &udata, dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk addr into index") /* Increment indices and adjust the edge chunk state */ @@ -4120,9 +4118,9 @@ done: herr_t H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) { - hsize_t min_mod_chunk_off[H5O_LAYOUT_NDIMS]; /* Scaled offset of first chunk to modify in each dimension */ - hsize_t max_mod_chunk_off[H5O_LAYOUT_NDIMS]; /* Scaled offset of last chunk to modify in each dimension */ - hssize_t max_fill_chunk_off[H5O_LAYOUT_NDIMS]; /* Scaled offset of last chunk that might be filled in each dimension */ + hsize_t min_mod_chunk_sc[H5O_LAYOUT_NDIMS]; /* Scaled offset of first chunk to modify in each dimension */ + hsize_t max_mod_chunk_sc[H5O_LAYOUT_NDIMS]; /* Scaled offset of last chunk to modify in each dimension */ + hssize_t max_fill_chunk_sc[H5O_LAYOUT_NDIMS]; /* Scaled offset of last chunk that might be filled in each dimension */ hbool_t fill_dim[H5O_LAYOUT_NDIMS]; /* Whether the plane of edge chunks in this dimension needs to be filled */ H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_io_info_t chk_io_info; /* Chunked I/O info object */ @@ -4226,19 +4224,19 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) /* * Determine the chunks which need to be filled or removed */ - HDmemset(min_mod_chunk_off, 0, sizeof(min_mod_chunk_off)); - HDmemset(max_mod_chunk_off, 0, sizeof(max_mod_chunk_off)); + HDmemset(min_mod_chunk_sc, 0, sizeof(min_mod_chunk_sc)); + HDmemset(max_mod_chunk_sc, 0, sizeof(max_mod_chunk_sc)); for(op_dim = 0; op_dim < (unsigned)space_ndims; op_dim++) { /* Calculate the largest offset of chunks that might need to be * modified in this dimension */ - max_mod_chunk_off[op_dim] = (old_dim[op_dim] - 1) / chunk_dim[op_dim]; + max_mod_chunk_sc[op_dim] = (old_dim[op_dim] - 1) / chunk_dim[op_dim]; /* Calculate the largest offset of chunks that might need to be * filled in this dimension */ if(0 == space_dim[op_dim]) - max_fill_chunk_off[op_dim] = -1; + max_fill_chunk_sc[op_dim] = -1; else - max_fill_chunk_off[op_dim] = (hssize_t)(((MIN(space_dim[op_dim], old_dim[op_dim]) - 1) + max_fill_chunk_sc[op_dim] = (hssize_t)(((MIN(space_dim[op_dim], old_dim[op_dim]) - 1) / chunk_dim[op_dim])); if(shrunk_dim[op_dim]) { @@ -4246,10 +4244,10 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) * modified in this dimension. Note that this array contains * garbage for all dimensions which are not shrunk. These locations * must not be read from! */ - min_mod_chunk_off[op_dim] = space_dim[op_dim] / chunk_dim[op_dim]; + min_mod_chunk_sc[op_dim] = space_dim[op_dim] / chunk_dim[op_dim]; /* Determine if we need to fill chunks in this dimension */ - if((hssize_t)min_mod_chunk_off[op_dim] == max_fill_chunk_off[op_dim]) + if((hssize_t)min_mod_chunk_sc[op_dim] == max_fill_chunk_sc[op_dim]) fill_dim[op_dim] = TRUE; else fill_dim[op_dim] = FALSE; @@ -4268,22 +4266,22 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) if(!shrunk_dim[op_dim]) continue; else { - HDassert(max_mod_chunk_off[op_dim] >= min_mod_chunk_off[op_dim]); + HDassert(max_mod_chunk_sc[op_dim] >= min_mod_chunk_sc[op_dim]); /* Reset the chunk offset indices */ HDmemset(scaled, 0, (space_ndims * sizeof(scaled[0]))); - scaled[op_dim] = min_mod_chunk_off[op_dim]; + scaled[op_dim] = min_mod_chunk_sc[op_dim]; /* Initialize "dims_outside_fill" array */ ndims_outside_fill = 0; for(u = 0; u < space_ndims; u++) - if((hssize_t)scaled[u] > max_fill_chunk_off[u]) { + if((hssize_t)scaled[u] > max_fill_chunk_sc[u]) { dims_outside_fill[u] = TRUE; ndims_outside_fill++; } /* end if */ else dims_outside_fill[u] = FALSE; - } /* end if */ + } /* end if */ carry = FALSE; while(!carry) { @@ -4291,7 +4289,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) if(0 == ndims_outside_fill) { HDassert(fill_dim[op_dim]); - HDassert(scaled[op_dim] == min_mod_chunk_off[op_dim]); + HDassert(scaled[op_dim] == min_mod_chunk_sc[op_dim]); /* Fill the unused parts of the chunk */ if(H5D__chunk_prune_fill(&udata) < 0) @@ -4339,11 +4337,11 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) carry = TRUE; for(i = (int)(space_ndims - 1); i >= 0; --i) { scaled[i]++; - if(scaled[i] > max_mod_chunk_off[i]) { + if(scaled[i] > max_mod_chunk_sc[i]) { /* Left maximum dimensions, "wrap around" and check if this * dimension is no longer outside the fill dimension */ if((unsigned)i == op_dim) { - scaled[i] = min_mod_chunk_off[i]; + scaled[i] = min_mod_chunk_sc[i]; if(dims_outside_fill[i] && fill_dim[i]) { dims_outside_fill[i] = FALSE; ndims_outside_fill--; @@ -4351,7 +4349,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) } /* end if */ else { scaled[i] = 0; - if(dims_outside_fill[i] && max_fill_chunk_off[i] >= 0) { + if(dims_outside_fill[i] && max_fill_chunk_sc[i] >= 0) { dims_outside_fill[i] = FALSE; ndims_outside_fill--; } /* end if */ @@ -4359,7 +4357,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) } /* end if */ else { /* Check if we just went outside the fill dimension */ - if(!dims_outside_fill[i] && (hssize_t)scaled[i] > max_fill_chunk_off[i]) { + if(!dims_outside_fill[i] && (hssize_t)scaled[i] > max_fill_chunk_sc[i]) { dims_outside_fill[i] = TRUE; ndims_outside_fill++; } /* end if */ @@ -4371,13 +4369,13 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) } /* end for */ } /* end while(!carry) */ - /* Adjust max_mod_chunk_off so we don't modify the same chunk twice. + /* Adjust max_mod_chunk_sc so we don't modify the same chunk twice. * Also check if this dimension started from 0 (and hence removed all * of the chunks). */ - if(min_mod_chunk_off[op_dim] == 0) + if(min_mod_chunk_sc[op_dim] == 0) break; else - max_mod_chunk_off[op_dim] = min_mod_chunk_off[op_dim] - 1; + max_mod_chunk_sc[op_dim] = min_mod_chunk_sc[op_dim] - 1; } /* end for(op_dim=0...) */ /* Reset any cached chunk info for this dataset */ @@ -4677,7 +4675,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) const H5O_pline_t *pline = udata->pline; /* I/O pipeline for applying filters */ /* needed for commpressed variable length data */ - hbool_t has_filters = FALSE; /* Whether chunk has filters */ + hbool_t must_filter = FALSE; /* Whether chunk must be filtered during copy */ size_t nbytes; /* Size of chunk in file (in bytes) */ H5Z_cb_t cb_struct; /* Filter failure callback struct */ @@ -4699,8 +4697,8 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) } /* end if */ /* Check for filtered chunks */ - if(pline && pline->nused) { - has_filters = TRUE; + if((is_vlen || fix_ref) && pline && pline->nused) { + must_filter = TRUE; cb_struct.func = NULL; /* no callback function when failed */ } /* end if */ @@ -4731,7 +4729,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) HGOTO_ERROR(H5E_IO, H5E_READERROR, H5_ITER_ERROR, "unable to read raw data chunk") /* Need to uncompress variable-length & reference data elements */ - if(has_filters && (is_vlen || fix_ref)) { + if(must_filter) { unsigned filter_mask = chunk_rec->filter_mask; if(H5Z_pipeline(pline, H5Z_FLAG_REVERSE, &filter_mask, H5Z_NO_EDC, cb_struct, &nbytes, &buf_size, &buf) < 0) @@ -4795,7 +4793,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) udata_dst.filter_mask = chunk_rec->filter_mask; /* Need to compress variable-length & reference data elements before writing to file */ - if(has_filters && (is_vlen || fix_ref)) { + if(must_filter) { 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 @@ -4822,7 +4820,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) /* Insert chunk record into index */ if(need_insert && udata->idx_info_dst->storage->ops->insert) - if((udata->idx_info_dst->storage->ops->insert)(udata->idx_info_dst, &udata_dst) < 0) + if((udata->idx_info_dst->storage->ops->insert)(udata->idx_info_dst, &udata_dst, NULL) < 0) HGOTO_ERROR_TAG(H5E_DATASET, H5E_CANTINSERT, H5_ITER_ERROR, "unable to insert chunk addr into index") /* Reset metadata tag in dxpl_id */ @@ -5104,32 +5102,67 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__chunk_bh_info(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout, - const H5O_pline_t *pline, hsize_t *index_size) +H5D__chunk_bh_info(const H5O_loc_t *loc, hid_t dxpl_id, H5O_t *oh, H5O_layout_t *layout, + hsize_t *index_size) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ + H5S_t *space = NULL; /* Dataset's dataspace */ + H5O_pline_t pline; /* I/O pipeline message */ + htri_t exists; /* Flag if header message of interest exists */ + hbool_t idx_info_init = FALSE; /* Whether the chunk index info has been initialized */ + hbool_t pline_read = FALSE; /* Whether the I/O pipeline message was read */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ - HDassert(f); + HDassert(loc); + HDassert(loc->file); + HDassert(H5F_addr_defined(loc->addr)); HDassert(layout); - HDassert(pline); HDassert(index_size); + /* Check for I/O pipeline message */ + if((exists = H5O_msg_exists_oh(oh, H5O_PLINE_ID)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header") + else if(exists) { + if(NULL == H5O_msg_read_oh(loc->file, dxpl_id, oh, H5O_PLINE_ID, &pline)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't find I/O pipeline message") + pline_read = TRUE; + } /* end else if */ + else + HDmemset(&pline, 0, sizeof(pline)); + /* Compose chunked index info struct */ - idx_info.f = f; + idx_info.f = loc->file; idx_info.dxpl_id = dxpl_id; - idx_info.pline = pline; + idx_info.pline = &pline; idx_info.layout = &layout->u.chunk; idx_info.storage = &layout->storage.u.chunk; + /* Get the dataspace for the dataset */ + if(NULL == (space = H5S_read(loc, dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") + + /* Allocate any indexing structures */ + if(layout->storage.u.chunk.ops->init && (layout->storage.u.chunk.ops->init)(&idx_info, space, loc->addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information") + idx_info_init = TRUE; + /* Get size of index structure */ - if((layout->storage.u.chunk.ops->size)(&idx_info, index_size) < 0) + if(layout->storage.u.chunk.ops->size && (layout->storage.u.chunk.ops->size)(&idx_info, index_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve chunk index info") done: + /* Free resources, if they've been initialized */ + if(idx_info_init && layout->storage.u.chunk.ops->dest && + (layout->storage.u.chunk.ops->dest)(&idx_info) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") + if(pline_read && H5O_msg_reset(H5O_PLINE_ID, &pline) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset I/O pipeline message") + if(space && H5S_close(space) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_bh_info() */ @@ -5149,7 +5182,6 @@ done: * *------------------------------------------------------------------------- */ -/* ARGSUSED */ static int H5D__chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) { |