diff options
author | Quincey Koziol <koziol@hdfgroup.org> | 2009-07-25 03:30:19 (GMT) |
---|---|---|
committer | Quincey Koziol <koziol@hdfgroup.org> | 2009-07-25 03:30:19 (GMT) |
commit | 21f8fa203a153bb9d3d26f73c9e56d22fd9671f2 (patch) | |
tree | 2076af8e57763501f48faaa361ba666b3444fdad /src | |
parent | acd5a4278a1e2323fede8289d9eaa567de545eac (diff) | |
download | hdf5-21f8fa203a153bb9d3d26f73c9e56d22fd9671f2.zip hdf5-21f8fa203a153bb9d3d26f73c9e56d22fd9671f2.tar.gz hdf5-21f8fa203a153bb9d3d26f73c9e56d22fd9671f2.tar.bz2 |
[svn-r17236] Description:
Add full support for any [single] dimension being unlimited when using
extensible arrays as a chunk index.
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (jam) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.7 (amazon) in debug mode
Mac OS X/32 10.5.7 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Diffstat (limited to 'src')
-rw-r--r-- | src/H5Dchunk.c | 2 | ||||
-rw-r--r-- | src/H5Dearray.c | 186 | ||||
-rw-r--r-- | src/H5Olayout.c | 8 | ||||
-rw-r--r-- | src/H5Oprivate.h | 2 | ||||
-rw-r--r-- | src/H5V.c | 69 | ||||
-rw-r--r-- | src/H5Vprivate.h | 2 |
6 files changed, 244 insertions, 25 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 794d678..f0c720e 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -513,7 +513,7 @@ H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id) if(dset->shared->layout.u.chunk.ops->init && (dset->shared->layout.u.chunk.ops->init)(&idx_info, dset->shared->space, dset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information") - /* Set the number of chunks in dataset */ + /* Set the number of chunks in dataset, etc. */ if(H5D_chunk_set_info(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set # of chunks for dataset") diff --git a/src/H5Dearray.c b/src/H5Dearray.c index f859c1c..76e0775 100644 --- a/src/H5Dearray.c +++ b/src/H5Dearray.c @@ -122,6 +122,7 @@ static herr_t H5D_earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata); static herr_t H5D_earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata); +static herr_t H5D_earray_idx_resize(H5O_layout_t *layout); static int H5D_earray_idx_iterate(const H5D_chk_idx_info_t *idx_info, H5D_chunk_cb_func_t chunk_cb, void *chunk_udata); static herr_t H5D_earray_idx_remove(const H5D_chk_idx_info_t *idx_info, @@ -155,7 +156,7 @@ const H5D_chunk_ops_t H5D_COPS_EARRAY[1] = {{ H5D_earray_idx_is_space_alloc, H5D_earray_idx_insert, H5D_earray_idx_get_addr, - NULL, + H5D_earray_idx_resize, H5D_earray_idx_iterate, H5D_earray_idx_remove, H5D_earray_idx_delete, @@ -780,7 +781,14 @@ static herr_t H5D_earray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t *space, haddr_t dset_ohdr_addr) { - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_idx_init) + hsize_t max_dims[H5O_LAYOUT_NDIMS]; /* Max. size of dataset dimensions */ + int unlim_dim; /* Rank of the dataset's unlimited dimension */ + int sndims; /* Rank of dataspace */ + unsigned ndims; /* Rank of dataspace */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_init) /* Check args */ HDassert(idx_info); @@ -790,10 +798,37 @@ H5D_earray_idx_init(const H5D_chk_idx_info_t *idx_info, const H5S_t *space, HDassert(space); HDassert(H5F_addr_defined(dset_ohdr_addr)); + /* Get the dim info for dataset */ + if((sndims = H5S_get_simple_extent_dims(space, NULL, max_dims)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace dimensions") + H5_ASSIGN_OVERFLOW(ndims, sndims, int, unsigned); + + /* Find the rank of the unlimited dimension */ + unlim_dim = (-1); + for(u = 0; u < ndims; u++) { + /* Check for unlimited dimension */ + if(H5S_UNLIMITED == max_dims[u]) { + /* Check if we've already found an unlimited dimension */ + if(unlim_dim >= 0) + HGOTO_ERROR(H5E_DATASET, H5E_ALREADYINIT, FAIL, "already found unlimited dimension") + + /* Set the unlimited dimension */ + unlim_dim = (int)u; + } /* end if */ + } /* end for */ + + /* Check if we didn't find an unlimited dimension */ + if(unlim_dim < 0) + HGOTO_ERROR(H5E_DATASET, H5E_UNINITIALIZED, FAIL, "didn't find unlimited dimension") + + /* Set the unlimited dimension for the layout's future use */ + idx_info->layout->u.chunk.u.earray.unlim_dim = (unsigned)unlim_dim; + /* Store the dataset's object header address for later */ idx_info->layout->u.chunk.u.earray.dset_ohdr_addr = dset_ohdr_addr; - FUNC_LEAVE_NOAPI(SUCCEED) +done: + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_earray_idx_init() */ @@ -947,9 +982,24 @@ H5D_earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata) /* Set convenience pointer to extensible array structure */ ea = idx_info->layout->u.chunk.u.earray.ea; - /* Calculate the index of this chunk */ - if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->common.offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + /* Check for unlimited dim. not being the slowest-changing dim. */ + if(idx_info->layout->u.chunk.u.earray.unlim_dim > 0) { + hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ + unsigned ndims = (idx_info->layout->u.chunk.ndims - 1); /* Number of dimensions */ + + /* 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.chunk.u.earray.unlim_dim); + + /* Calculate the index of this chunk */ + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.u.earray.swizzled_down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end if */ + else { + /* Calculate the index of this chunk */ + if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->common.offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end else */ /* Check for filters on chunks */ if(idx_info->pline->nused > 0) { @@ -1092,9 +1142,24 @@ H5D_earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udat /* Set convenience pointer to extensible array structure */ ea = idx_info->layout->u.chunk.u.earray.ea; - /* Calculate the index of this chunk */ - if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->common.offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + /* Check for unlimited dim. not being the slowest-changing dim. */ + if(idx_info->layout->u.chunk.u.earray.unlim_dim > 0) { + hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ + unsigned ndims = (idx_info->layout->u.chunk.ndims - 1); /* Number of dimensions */ + + /* 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.chunk.u.earray.unlim_dim); + + /* Calculate the index of this chunk */ + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.u.earray.swizzled_down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end if */ + else { + /* Calculate the index of this chunk */ + if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->common.offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end else */ /* Check for filters on chunks */ if(idx_info->pline->nused > 0) { @@ -1125,6 +1190,46 @@ done: /*------------------------------------------------------------------------- + * Function: H5D_earray_idx_resize + * + * Purpose: Calculate/setup the swizzled down chunk array, used for chunk + * index calculations. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, July 23, 2009 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_earray_idx_resize(H5O_layout_t *layout) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_earray_idx_resize) + + /* Check args */ + HDassert(layout); + + /* Set up the swizzled "down" chunk information */ + if(layout->u.chunk.u.earray.unlim_dim > 0) { + hsize_t swizzled_chunks[H5O_LAYOUT_NDIMS]; /* Swizzled form of # of chunks in each dimension */ + + HDmemcpy(swizzled_chunks, layout->u.chunk.chunks, (layout->u.chunk.ndims - 1) * sizeof(swizzled_chunks[0])); + H5V_swizzle_coords(swizzled_chunks, layout->u.chunk.u.earray.unlim_dim); + + /* Get the swizzled "down" sizes for each dimension */ + if(H5V_array_down((layout->u.chunk.ndims - 1), swizzled_chunks, layout->u.chunk.u.earray.swizzled_down_chunks) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute swizzled 'down' chunk size value") + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_earray_idx_resize() */ + + +/*------------------------------------------------------------------------- * Function: H5D_earray_idx_iterate * * Purpose: Iterate over the chunks in an index, making a callback @@ -1276,9 +1381,24 @@ H5D_earray_idx_remove(const H5D_chk_idx_info_t *idx_info, H5D_chunk_common_ud_t /* Set convenience pointer to extensible array structure */ ea = idx_info->layout->u.chunk.u.earray.ea; - /* Calculate the index of this chunk */ - if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + /* Check for unlimited dim. not being the slowest-changing dim. */ + if(idx_info->layout->u.chunk.u.earray.unlim_dim > 0) { + hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ + unsigned ndims = (idx_info->layout->u.chunk.ndims - 1); /* Number of dimensions */ + + /* 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.chunk.u.earray.unlim_dim); + + /* Calculate the index of this chunk */ + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.u.earray.swizzled_down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end if */ + else { + /* Calculate the index of this chunk */ + if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end else */ /* Check for filters on chunks */ if(idx_info->pline->nused > 0) { @@ -1640,9 +1760,24 @@ H5D_earray_idx_support(const H5D_chk_idx_info_t *idx_info, /* Set convenience pointer to extensible array structure */ ea = idx_info->layout->u.chunk.u.earray.ea; - /* Calculate the index of this chunk */ - if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + /* Check for unlimited dim. not being the slowest-changing dim. */ + if(idx_info->layout->u.chunk.u.earray.unlim_dim > 0) { + hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ + unsigned ndims = (idx_info->layout->u.chunk.ndims - 1); /* Number of dimensions */ + + /* 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.chunk.u.earray.unlim_dim); + + /* Calculate the index of this chunk */ + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.u.earray.swizzled_down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end if */ + else { + /* Calculate the index of this chunk */ + if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end else */ /* Create flush dependency between the child_entry and the piece of metadata * in the extensible array that contains the entry for this chunk. @@ -1693,9 +1828,24 @@ H5D_earray_idx_unsupport(const H5D_chk_idx_info_t *idx_info, /* Set convenience pointer to extensible array structure */ ea = idx_info->layout->u.chunk.u.earray.ea; - /* Calculate the index of this chunk */ - if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + /* Check for unlimited dim. not being the slowest-changing dim. */ + if(idx_info->layout->u.chunk.u.earray.unlim_dim > 0) { + hsize_t swizzled_coords[H5O_LAYOUT_NDIMS]; /* swizzled chunk coordinates */ + unsigned ndims = (idx_info->layout->u.chunk.ndims - 1); /* Number of dimensions */ + + /* 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.chunk.u.earray.unlim_dim); + + /* Calculate the index of this chunk */ + if(H5V_chunk_index(ndims, swizzled_coords, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.u.earray.swizzled_down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end if */ + else { + /* Calculate the index of this chunk */ + if(H5V_chunk_index((idx_info->layout->u.chunk.ndims - 1), udata->offset, idx_info->layout->u.chunk.dim, idx_info->layout->u.chunk.down_chunks, &idx) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") + } /* end else */ /* Remove flush dependency between the child_entry and the piece of metadata * in the extensible array that contains the entry for this chunk. diff --git a/src/H5Olayout.c b/src/H5Olayout.c index 1c7f3f7..96cb9b9 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -1027,12 +1027,8 @@ H5O_layout_set_latest_version(H5O_layout_t *layout, const H5S_t *space) /* If we have only 1 unlimited dimension, we can use extensible array index */ if(1 == unlim_count) { - /* Check for slowest changing dimension being unlimited */ - /* (non-slowest-changing dim. not supported yet) */ - if(max_dims[0] == H5S_UNLIMITED) { - /* Set the chunk index type */ - layout->u.chunk.idx_type = H5D_CHUNK_IDX_EARRAY; - } /* end if */ + /* Set the chunk index type */ + layout->u.chunk.idx_type = H5D_CHUNK_IDX_EARRAY; } /* end if */ /* Chunked datasets with fixed dimensions */ else if(layout->type == H5D_CHUNKED && fixed) { diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index c2b7cca..408a490 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -368,6 +368,8 @@ struct H5EA_t; /* Defined in H5EAprivate.h */ typedef struct H5O_layout_chunk_earray_t { haddr_t addr; /* File address of extensible array */ haddr_t dset_ohdr_addr; /* File address dataset's object header */ + unsigned unlim_dim; /* Rank of unlimited dimension for dataset */ + hsize_t swizzled_down_chunks[H5O_LAYOUT_NDIMS]; /* swizzled "down" size of number of chunks in each dimension */ struct H5EA_t *ea; /* Pointer to extensible array struct */ } H5O_layout_chunk_earray_t; @@ -1287,6 +1287,75 @@ 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_NOFUNC(H5V_swizzle_coords) + + /* 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_NOFUNC(H5V_unswizzle_coords) + + /* 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_memcpyvv * * Purpose: Given source and destination buffers in memory (SRC & DST) diff --git a/src/H5Vprivate.h b/src/H5Vprivate.h index e351f86..faa2505 100644 --- a/src/H5Vprivate.h +++ b/src/H5Vprivate.h @@ -89,6 +89,8 @@ 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_memcpyvv(void *_dst, size_t dst_max_nseq, size_t *dst_curr_seq, size_t dst_len_arr[], hsize_t dst_off_arr[], const void *_src, |