diff options
| -rw-r--r-- | src/H5Dearray.c | 32 | ||||
| -rw-r--r-- | src/H5Oprivate.h | 1 | ||||
| -rw-r--r-- | src/H5V.c | 69 | ||||
| -rw-r--r-- | src/H5Vprivate.h | 35 | ||||
| -rw-r--r-- | test/dsets.c | 118 |
5 files changed, 168 insertions, 87 deletions
diff --git a/src/H5Dearray.c b/src/H5Dearray.c index 72e07e0..40c5c5f 100644 --- a/src/H5Dearray.c +++ b/src/H5Dearray.c @@ -1104,10 +1104,10 @@ H5D_earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata) /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->common.offset, ndims * sizeof(udata->common.offset[0])); - H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); + H5V_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { @@ -1270,10 +1270,10 @@ H5D_earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udat /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->common.offset, ndims * sizeof(udata->common.offset[0])); - H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); + H5V_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { @@ -1333,12 +1333,18 @@ H5D_earray_idx_resize(H5O_layout_chunk_t *layout) /* Check args */ HDassert(layout); - /* Set up the swizzled "down" chunk information */ + + /* "Swizzle" constant dimensions for this dataset */ if(layout->u.earray.unlim_dim > 0) { hsize_t swizzled_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of # of chunks in each dimension */ + /* Get the swizzled chunk dimensions */ + HDmemcpy(layout->u.earray.swizzled_dim, layout->dim, (layout->ndims - 1) * sizeof(layout->dim[0])); + H5V_swizzle_coords(uint32_t, layout->u.earray.swizzled_dim, layout->u.earray.unlim_dim); + + /* Get the swizzled number of chunks in each dimension */ HDmemcpy(swizzled_chunks, layout->chunks, (layout->ndims - 1) * sizeof(swizzled_chunks[0])); - H5V_swizzle_coords(swizzled_chunks, layout->u.earray.unlim_dim); + H5V_swizzle_coords(hsize_t, swizzled_chunks, layout->u.earray.unlim_dim); /* Get the swizzled "down" sizes for each dimension */ if(H5V_array_down((layout->ndims - 1), swizzled_chunks, layout->u.earray.swizzled_down_chunks) < 0) @@ -1511,10 +1517,11 @@ H5D_earray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->offset, ndims * sizeof(udata->offset[0])); - H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); + H5V_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim); + /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { @@ -1911,10 +1918,10 @@ H5D_earray_idx_support(const H5D_chk_idx_info_t *idx_info, /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->offset, ndims * sizeof(udata->offset[0])); - H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); + H5V_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim); /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { @@ -1981,10 +1988,11 @@ H5D_earray_idx_unsupport(const H5D_chk_idx_info_t *idx_info, /* Set up the swizzled chunk coordinates */ HDmemcpy(swizzled_coords, udata->offset, ndims * sizeof(udata->offset[0])); - H5V_swizzle_coords(swizzled_coords, idx_info->layout->u.earray.unlim_dim); + H5V_swizzle_coords(hsize_t, swizzled_coords, idx_info->layout->u.earray.unlim_dim); + /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.earray.swizzled_dim, idx_info->layout->u.earray.swizzled_down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ else { diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index c05fcb4..c5074f9 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -467,6 +467,7 @@ typedef struct H5O_layout_chunk_earray_t { } cparam; unsigned unlim_dim; /* Rank of unlimited dimension for dataset */ + uint32_t swizzled_dim[H5O_LAYOUT_NDIMS]; /* swizzled chunk dimensions */ hsize_t swizzled_down_chunks[H5O_LAYOUT_NDIMS]; /* swizzled "down" size of number of chunks in each dimension */ } H5O_layout_chunk_earray_t; @@ -1295,75 +1295,6 @@ H5V_chunk_index(unsigned ndims, const hsize_t *coord, const uint32_t *chunk, /*------------------------------------------------------------------------- - * Function: H5V_swizzle_coords - * - * Purpose: Given a coordinate offset array (COORDS), move the unlimited - * dimension (UNLIM_DIM) value to offset 0, sliding any - * intermediate values down one position. - * - * Return: None - * - * Programmer: Quincey Koziol - * Tuesday, July 21, 2009 - * - *------------------------------------------------------------------------- - */ -void -H5V_swizzle_coords(hsize_t *coords, unsigned unlim_dim) -{ - FUNC_ENTER_NOAPI_NOINIT_NOERR - - /* Sanity check */ - HDassert(coords); - - /* Nothing to do when unlimited dimension is at position 0 */ - if(0 != unlim_dim) { - hsize_t tmp = coords[unlim_dim]; - - HDmemmove(&coords[1], &coords[0], sizeof(coords[0]) * unlim_dim); - coords[0] = tmp; - } /* end if */ - - FUNC_LEAVE_NOAPI_VOID -} /* end H5V_swizzle_coords() */ - - -/*------------------------------------------------------------------------- - * Function: H5V_unswizzle_coords - * - * Purpose: Given a coordinate offset array (COORDS), move the value at - * offset 0 to offset of the unlimied dimension (UNLIM_DIM), - * sliding any intermediate values up one position. Undoes the - * "swizzle_coords" operation. - * - * Return: None - * - * Programmer: Quincey Koziol - * Tuesday, July 21, 2009 - * - *------------------------------------------------------------------------- - */ -void -H5V_unswizzle_coords(hsize_t *coords, unsigned unlim_dim) -{ - FUNC_ENTER_NOAPI_NOINIT_NOERR - - /* Sanity check */ - HDassert(coords); - - /* Nothing to do when unlimited dimension is at position 0 */ - if(0 != unlim_dim) { - hsize_t tmp = coords[0]; - - HDmemmove(&coords[0], &coords[1], sizeof(coords[0]) * unlim_dim); - coords[unlim_dim] = tmp; - } /* end if */ - - FUNC_LEAVE_NOAPI_VOID -} /* end H5V_unswizzle_coords() */ - - -/*------------------------------------------------------------------------- * Function: H5V_opvv * * Purpose: Perform an operation on a source & destination sequences diff --git a/src/H5Vprivate.h b/src/H5Vprivate.h index 89e1938..c2d4e4a 100644 --- a/src/H5Vprivate.h +++ b/src/H5Vprivate.h @@ -49,6 +49,39 @@ typedef herr_t (*H5V_opvv_func_t)(hsize_t dst_off, hsize_t src_off, #define H5V_vector_zero(N,DST) HDmemset(DST,0,(N)*sizeof(*(DST))) +/* Given a coordinate offset array (COORDS) of type TYPE, move the unlimited + * dimension (UNLIM_DIM) value to offset 0, sliding any intermediate values down + * one position. */ +#define H5V_swizzle_coords(TYPE,COORDS,UNLIM_DIM) { \ + /* COORDS must be an array of type TYPE */ \ + HDassert(sizeof(COORDS[0]) == sizeof(TYPE)); \ + \ + /* Nothing to do when unlimited dimension is at position 0 */ \ + if(0 != (UNLIM_DIM)) { \ + TYPE _tmp = (COORDS)[UNLIM_DIM]; \ + \ + HDmemmove(&(COORDS)[1], &(COORDS)[0], sizeof(TYPE) * (UNLIM_DIM)); \ + (COORDS)[0] = _tmp; \ + } /* end if */ \ +} + +/* Given a coordinate offset array (COORDS) of type TYPE, move the value at + * offset 0 to offset of the unlimied dimension (UNLIM_DIM), sliding any + * intermediate values up one position. Undoes the "swizzle_coords" operation. + */ +#define H5V_unswizzle_coords(TYPE,COORDS,UNLIM_DIM) { \ + /* COORDS must be an array of type TYPE */ \ + HDassert(sizeof(COORDS[0]) == sizeof(TYPE)); \ + \ + /* Nothing to do when unlimited dimension is at position 0 */ \ + if(0 != (UNLIM_DIM)) { \ + TYPE _tmp = (COORDS)[0]; \ + \ + HDmemmove(&(COORDS)[0], &(COORDS)[1], sizeof(TYPE) * (UNLIM_DIM)); \ + (COORDS)[UNLIM_DIM] = _tmp; \ + } /* end if */ \ +} + /* A null pointer is equivalent to a zero vector */ #define H5V_ZERO NULL @@ -93,8 +126,6 @@ H5_DLL herr_t H5V_array_calc(hsize_t offset, unsigned n, const hsize_t *total_size, hsize_t *coords); H5_DLL herr_t H5V_chunk_index(unsigned ndims, const hsize_t *coord, const uint32_t *chunk, const hsize_t *down_nchunks, hsize_t *chunk_idx); -H5_DLL void H5V_swizzle_coords(hsize_t *coords, unsigned unlim_dim); -H5_DLL void H5V_unswizzle_coords(hsize_t *coords, unsigned unlim_dim); H5_DLL ssize_t H5V_opvv(size_t dst_max_nseq, size_t *dst_curr_seq, size_t dst_len_arr[], hsize_t dst_off_arr[], size_t src_max_nseq, size_t *src_curr_seq, size_t src_len_arr[], diff --git a/test/dsets.c b/test/dsets.c index a397150..898782d 100644 --- a/test/dsets.c +++ b/test/dsets.c @@ -8410,7 +8410,7 @@ test_chunk_fast(hid_t fapl) if(H5V_array_calc_pre(u, ndims, down, hs_offset) < 0) FAIL_STACK_ERROR /* Un-swizzle hyperslab offset in same way as swizzled dimensions */ - H5V_unswizzle_coords(hs_offset, unlim_dim); + H5V_unswizzle_coords(hsize_t, hs_offset, unlim_dim); /* Select a single element in the dataset */ if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0) FAIL_STACK_ERROR @@ -8460,7 +8460,7 @@ test_chunk_fast(hid_t fapl) if(H5V_array_calc(u, ndims, swizzled_dim, hs_offset) < 0) FAIL_STACK_ERROR /* Un-swizzle hyperslab offset in same way as swizzled dimensions */ - H5V_unswizzle_coords(hs_offset, unlim_dim); + H5V_unswizzle_coords(hsize_t, hs_offset, unlim_dim); /* Select a single element in the dataset */ if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0) FAIL_STACK_ERROR @@ -8524,7 +8524,7 @@ test_chunk_fast(hid_t fapl) if(H5Sget_simple_extent_dims(sid, swizzled_dim, NULL) < 0) FAIL_STACK_ERROR /* Generate the swizzled dimensions */ - H5V_swizzle_coords(swizzled_dim, unlim_dim); + H5V_swizzle_coords(hsize_t, swizzled_dim, unlim_dim); /* Compute the "down" dimension values */ if(H5V_array_down(ndims, swizzled_dim, down) < 0) FAIL_STACK_ERROR @@ -8535,7 +8535,7 @@ test_chunk_fast(hid_t fapl) if(H5V_array_calc_pre(u, ndims, down, hs_offset) < 0) FAIL_STACK_ERROR /* Unswizzle hyperslab offset in same way as swizzled dimensions */ - H5V_unswizzle_coords(hs_offset, unlim_dim); + H5V_unswizzle_coords(hsize_t, hs_offset, unlim_dim); /* Select a single element in the dataset */ if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0) FAIL_STACK_ERROR @@ -8592,6 +8592,7 @@ error: return -1; } /* end test_chunk_fast() */ + /*------------------------------------------------------------------------- * Function: test_reopen_chunk_fast * @@ -8714,6 +8715,114 @@ error: return -1; } /* end test_reopen_chunk_fast() */ + +/*------------------------------------------------------------------------- + * Function: test_chunk_fast_bug1 + * + * Purpose: Test extensible arrays where the first dimension in the + * chunk size is the same as the second dimension in the + * dataset size. This helps to confirm that all dimensions + * are being "swizzled" correctly in the earray chunk index + * code. + * + * Return: Success: 0 + * Failure: -1 + * + * Programmer: Neil Fortner + * March 22, 2012 + * + *------------------------------------------------------------------------- + */ +static herr_t +test_chunk_fast_bug1(hid_t fapl) +{ + char filename[FILENAME_BUF_SIZE]; + hid_t fid = -1; /* File ID */ + hid_t dcpl = -1; /* Dataset creation property list ID */ + hid_t sid = -1; /* Dataspace ID */ + hid_t dsid = -1; /* Dataset ID */ + hsize_t dim[2], max_dim[2], chunk_dim[2]; /* Dataset and chunk dimensions */ + H5D_alloc_time_t alloc_time; /* Storage allocation time */ + static unsigned wbuf[40][20], rbuf[40][20]; /* Element written/read */ + unsigned i, j; /* Local index variables */ + + TESTING("datasets w/extensible array chunk indexing bug"); + + h5_fixname(FILENAME[10], fapl, filename, sizeof filename); + + /* Initialize write buffer */ + for(i=0; i<40; i++) + for(j=0; j<20; j++) + wbuf[i][j] = (i * 20) + j; + + /* Create 2-D dataspace */ + dim[0] = 40; + dim[1] = 20; + max_dim[0] = 40; + max_dim[1] = H5S_UNLIMITED; + if((sid = H5Screate_simple(2, dim, max_dim)) < 0) FAIL_STACK_ERROR + + /* Loop over storage allocation time */ + for(alloc_time = H5D_ALLOC_TIME_EARLY; alloc_time <= H5D_ALLOC_TIME_INCR; alloc_time++) { + /* Create file */ + if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) FAIL_STACK_ERROR + + /* Create dataset creation property list */ + if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR + + /* Set chunking */ + chunk_dim[0] = 20; + chunk_dim[1] = 10; + if(H5Pset_chunk(dcpl, 2, chunk_dim) < 0) FAIL_STACK_ERROR + + /* Set allocation time */ + if(H5Pset_alloc_time(dcpl, alloc_time) < 0) FAIL_STACK_ERROR + + /* Create chunked dataset */ + if((dsid = H5Dcreate2(fid, "dset", H5T_NATIVE_UINT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) + FAIL_STACK_ERROR + + /* Write buffer to dataset */ + if(H5Dwrite(dsid, H5T_NATIVE_UINT, sid, sid, H5P_DEFAULT, &wbuf) < 0) + FAIL_STACK_ERROR + + /* Close everything */ + if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR + + /* Reopen the dataset */ + if((dsid = H5Dopen2(fid, "dset", H5P_DEFAULT)) < 0) FAIL_STACK_ERROR + + /* Read from dataset */ + if(H5Dread(dsid, H5T_NATIVE_UINT, sid, sid, H5P_DEFAULT, &rbuf) < 0) + FAIL_STACK_ERROR + + /* Verify read data */ + for(i=0; i<40; i++) + for(j=0; j<20; j++) + if(wbuf[i][j] != rbuf[i][j]) + FAIL_PUTS_ERROR("invalid element read"); + + if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR + if(H5Pclose(dcpl) < 0) FAIL_STACK_ERROR + if(H5Fclose(fid) < 0) FAIL_STACK_ERROR + + } /* end for */ + + if(H5Sclose(sid) < 0) FAIL_STACK_ERROR + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Pclose(dcpl); + H5Dclose(dsid); + H5Sclose(sid); + H5Fclose(fid); + } H5E_END_TRY; + return -1; +} /* end test_chunk_fast_bug1() */ + /* This message derives from H5Z */ const H5Z_class2_t H5Z_EXPAND[1] = {{ H5Z_CLASS_T_VERS, /* H5Z_class_t version */ @@ -10021,6 +10130,7 @@ main(void) nerrors += (test_big_chunks_bypass_cache(my_fapl) < 0 ? 1 : 0); nerrors += (test_chunk_fast(my_fapl) < 0 ? 1 : 0); nerrors += (test_reopen_chunk_fast(my_fapl) < 0 ? 1 : 0); + nerrors += (test_chunk_fast_bug1(my_fapl) < 0 ? 1 : 0); nerrors += (test_chunk_expand(my_fapl) < 0 ? 1 : 0); nerrors += (test_layout_extend(my_fapl) < 0 ? 1 : 0); nerrors += (test_fixed_array(my_fapl) < 0 ? 1 : 0); |