diff options
Diffstat (limited to 'src/H5Dcompact.c')
| -rw-r--r-- | src/H5Dcompact.c | 183 |
1 files changed, 131 insertions, 52 deletions
diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index 0458e74..d8bf8b0 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -18,7 +18,7 @@ * August 5, 2002 * * Purpose: Compact dataset I/O functions. These routines are similar - * H5D_contig_* and H5D_istore_*. + * H5D_contig_* and H5D_chunk_*. */ /****************/ @@ -38,6 +38,7 @@ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Vprivate.h" /* Vector and array functions */ @@ -57,8 +58,8 @@ /********************/ /* Layout operation callbacks */ -static herr_t H5D_compact_new(H5F_t *f, hid_t dxpl_id, H5D_t *dset, - const H5P_genplist_t *dc_plist); +static herr_t H5D_compact_construct(H5F_t *f, H5D_t *dset); +static hbool_t H5D_compact_is_space_alloc(const H5O_storage_t *storage); static herr_t H5D_compact_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *cm); @@ -68,6 +69,7 @@ static ssize_t H5D_compact_readvv(const H5D_io_info_t *io_info, static ssize_t H5D_compact_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_size_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[]); +static herr_t H5D_compact_flush(H5D_t *dset, hid_t dxpl_id); /*********************/ @@ -76,7 +78,9 @@ static ssize_t H5D_compact_writevv(const H5D_io_info_t *io_info, /* Compact storage layout I/O ops */ const H5D_layout_ops_t H5D_LOPS_COMPACT[1] = {{ - H5D_compact_new, + H5D_compact_construct, + NULL, + H5D_compact_is_space_alloc, H5D_compact_io_init, H5D_contig_read, H5D_contig_write, @@ -86,6 +90,7 @@ const H5D_layout_ops_t H5D_LOPS_COMPACT[1] = {{ #endif /* H5_HAVE_PARALLEL */ H5D_compact_readvv, H5D_compact_writevv, + H5D_compact_flush, NULL }}; @@ -123,16 +128,16 @@ H5D_compact_fill(H5D_t *dset, hid_t dxpl_id) /* Check args */ HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER)); HDassert(dset && H5D_COMPACT == dset->shared->layout.type); - HDassert(dset->shared->layout.u.compact.buf); + HDassert(dset->shared->layout.storage.u.compact.buf); HDassert(dset->shared->type); HDassert(dset->shared->space); /* Initialize the fill value buffer */ /* (use the compact dataset storage buffer as the fill value buffer) */ - if(H5D_fill_init(&fb_info, dset->shared->layout.u.compact.buf, FALSE, + if(H5D_fill_init(&fb_info, dset->shared->layout.storage.u.compact.buf, FALSE, NULL, NULL, NULL, NULL, &dset->shared->dcpl_cache.fill, dset->shared->type, - dset->shared->type_id, (size_t)0, dset->shared->layout.u.compact.size, dxpl_id) < 0) + dset->shared->type_id, (size_t)0, dset->shared->layout.storage.u.compact.size, dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info") fb_info_init = TRUE; @@ -152,7 +157,7 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_compact_new + * Function: H5D_compact_construct * * Purpose: Constructs new compact layout information for dataset * @@ -165,37 +170,60 @@ done: */ /* ARGSUSED */ static herr_t -H5D_compact_new(H5F_t *f, hid_t UNUSED dxpl_id, H5D_t *dset, - const H5P_genplist_t UNUSED *dc_plist) +H5D_compact_construct(H5F_t *f, H5D_t *dset) { hssize_t tmp_size; /* Temporary holder for raw data size */ - hsize_t comp_data_size; /* Size of compact data */ + hsize_t max_comp_data_size; /* Max. allowed size of compact data */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT(H5D_compact_new) + FUNC_ENTER_NOAPI_NOINIT(H5D_compact_construct) /* Sanity checks */ HDassert(f); HDassert(dset); - HDassert(dc_plist); /* * Compact dataset is stored in dataset object header message of * layout. */ tmp_size = H5S_GET_EXTENT_NPOINTS(dset->shared->space) * H5T_get_size(dset->shared->type); - H5_ASSIGN_OVERFLOW(dset->shared->layout.u.compact.size, tmp_size, hssize_t, size_t); + H5_ASSIGN_OVERFLOW(dset->shared->layout.storage.u.compact.size, tmp_size, hssize_t, size_t); /* Verify data size is smaller than maximum header message size * (64KB) minus other layout message fields. */ - comp_data_size = H5O_MESG_MAX_SIZE - H5O_layout_meta_size(f, &(dset->shared->layout)); - if(dset->shared->layout.u.compact.size > comp_data_size) + max_comp_data_size = H5O_MESG_MAX_SIZE - H5D_layout_meta_size(f, &(dset->shared->layout), FALSE); + if(dset->shared->layout.storage.u.compact.size > max_comp_data_size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "compact dataset size is bigger than header message maximum size") done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_compact_new() */ +} /* end H5D_compact_construct() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_compact_is_space_alloc + * + * Purpose: Query if space is allocated for layout + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, January 15, 2009 + * + *------------------------------------------------------------------------- + */ +static hbool_t +H5D_compact_is_space_alloc(const H5O_storage_t UNUSED *storage) +{ + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_compact_is_space_alloc) + + /* Sanity checks */ + HDassert(storage); + + /* Compact storage is currently always allocated */ + FUNC_LEAVE_NOAPI(TRUE) +} /* end H5D_compact_is_space_alloc() */ /*------------------------------------------------------------------------- @@ -217,8 +245,8 @@ H5D_compact_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t UNUSED * { FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_compact_io_init) - io_info->store->compact.buf = io_info->dset->shared->layout.u.compact.buf; - io_info->store->compact.dirty = &io_info->dset->shared->layout.u.compact.dirty; + io_info->store->compact.buf = io_info->dset->shared->layout.storage.u.compact.buf; + io_info->store->compact.dirty = &io_info->dset->shared->layout.storage.u.compact.dirty; FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D_compact_io_init() */ @@ -307,6 +335,40 @@ done: /*------------------------------------------------------------------------- + * Function: H5D_compact_flush + * + * Purpose: Writes dirty compact data to object header + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Monday, July 27, 2009 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_compact_flush(H5D_t *dset, hid_t dxpl_id) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_compact_flush) + + /* Sanity check */ + HDassert(dset); + + /* Check if the buffered compact information is dirty */ + if(dset->shared->layout.storage.u.compact.dirty) { + if(H5O_msg_write(&(dset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dset->shared->layout), dxpl_id) < 0) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") + dset->shared->layout.storage.u.compact.dirty = FALSE; + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_compact_flush() */ + + +/*------------------------------------------------------------------------- * Function: H5D_compact_copy * * Purpose: Copy compact storage raw data from SRC file to DST file. @@ -319,8 +381,9 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, - H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, hid_t dxpl_id) +H5D_compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src, H5F_t *f_dst, + H5O_storage_compact_t *storage_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, + hid_t dxpl_id) { hid_t tid_src = -1; /* Datatype ID for source datatype */ hid_t tid_dst = -1; /* Datatype ID for destination datatype */ @@ -334,18 +397,22 @@ H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, FUNC_ENTER_NOAPI(H5D_compact_copy, FAIL) /* Check args */ - HDassert(layout_src && H5D_COMPACT == layout_src->type); HDassert(f_src); + HDassert(storage_src); HDassert(f_dst); - HDassert(layout_dst && H5D_COMPACT == layout_dst->type); + HDassert(storage_dst); HDassert(dt_src); + /* Allocate space for destination data */ + if(NULL == (storage_dst->buf = H5MM_malloc(storage_src->size))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate memory for compact dataset") + /* Create datatype ID for src datatype, so it gets freed */ - if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype") + if((tid_src = H5I_register(H5I_DATATYPE, dt_src, FALSE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register source file datatype") /* If there's a VLEN source datatype, do type conversion information */ - if(H5T_detect_class(dt_src, H5T_VLEN) > 0) { + if(H5T_detect_class(dt_src, H5T_VLEN, FALSE) > 0) { H5T_path_t *tpath_src_mem, *tpath_mem_dst; /* Datatype conversion paths */ H5T_t *dt_dst; /* Destination datatype */ H5T_t *dt_mem; /* Memory datatype */ @@ -360,22 +427,28 @@ H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, /* create a memory copy of the variable-length datatype */ if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy") - if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0) + if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0) { + H5T_close(dt_mem); HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype") + } /* end if */ /* create variable-length datatype at the destinaton file */ if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy") - if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0) + if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0) { + H5T_close(dt_dst); HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk") - if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0) + } /* end if */ + if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst, FALSE)) < 0) { + H5T_close(dt_dst); HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype") + } /* end if */ /* Set up the conversion functions */ if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes") if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE))) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes") /* Determine largest datatype size */ if(0 == (src_dt_size = H5T_get_size(dt_src))) @@ -388,7 +461,7 @@ H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, max_dt_size = MAX(max_dt_size, tmp_dt_size); /* Set number of whole elements that fit in buffer */ - if(0 == (nelmts = layout_src->u.compact.size / src_dt_size)) + if(0 == (nelmts = storage_src->size / src_dt_size)) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "element size too large") /* Set up number of bytes to copy, and initial buffer size */ @@ -402,7 +475,7 @@ H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* Atomize */ - if((buf_sid = H5I_register(H5I_DATASPACE, buf_space)) < 0) { + if((buf_sid = H5I_register(H5I_DATASPACE, buf_space, FALSE)) < 0) { H5S_close(buf_space); HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID") } /* end if */ @@ -415,23 +488,27 @@ H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, if(NULL == (buf = H5FL_BLK_MALLOC(type_conv, buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - HDmemcpy(buf, layout_src->u.compact.buf, layout_src->u.compact.size); + HDmemcpy(buf, storage_src->buf, storage_src->size); + + /* allocate temporary bkg buff for data conversion */ + if(NULL == (bkg = H5FL_BLK_MALLOC(type_conv, buf_size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") /* Convert from source file to memory */ - if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) + if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") + /* Copy into another buffer, to reclaim memory later */ HDmemcpy(reclaim_buf, buf, buf_size); - /* allocate temporary bkg buff for data conversion */ - if(NULL == (bkg = H5FL_BLK_CALLOC(type_conv, buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") + /* Set background buffer to all zeros */ + HDmemset(bkg, 0, buf_size); /* Convert from memory to destination file */ if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") - HDmemcpy(layout_dst->u.compact.buf, buf, layout_dst->u.compact.size); + HDmemcpy(storage_dst->buf, buf, storage_dst->size); if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data") @@ -443,37 +520,39 @@ H5D_compact_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst, size_t ref_count; /* Determine # of reference elements to copy */ - ref_count = layout_src->u.compact.size / H5T_get_size(dt_src); + ref_count = storage_src->size / H5T_get_size(dt_src); /* Copy objects referenced in source buffer to destination file and set destination elements */ - if(H5O_copy_expand_ref(f_src, layout_src->u.compact.buf, dxpl_id, f_dst, - layout_dst->u.compact.buf, ref_count, H5T_get_ref_type(dt_src), cpy_info) < 0) + if(H5O_copy_expand_ref(f_src, storage_src->buf, dxpl_id, f_dst, + storage_dst->buf, ref_count, H5T_get_ref_type(dt_src), cpy_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute") } /* end if */ else /* Reset value to zero */ - HDmemset(layout_dst->u.compact.buf, 0, layout_src->u.compact.size); + HDmemset(storage_dst->buf, 0, storage_src->size); } /* end if */ else /* Type conversion not necessary */ - HDmemcpy(layout_dst->u.compact.buf, layout_src->u.compact.buf, layout_src->u.compact.size); + HDmemcpy(storage_dst->buf, storage_src->buf, storage_src->size); } /* end if */ - else + else /* Type conversion not necessary */ - HDmemcpy(layout_dst->u.compact.buf, layout_src->u.compact.buf, layout_src->u.compact.size); + HDmemcpy(storage_dst->buf, storage_src->buf, storage_src->size); + + /* Mark destination buffer as dirty */ + storage_dst->dirty = TRUE; done: - if(buf_sid > 0) - if(H5I_dec_ref(buf_sid) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID") + if(buf_sid > 0 && H5I_dec_ref(buf_sid, FALSE) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't decrement temporary dataspace ID") if(tid_src > 0) - if(H5I_dec_ref(tid_src) < 0) + if(H5I_dec_ref(tid_src, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(tid_dst > 0) - if(H5I_dec_ref(tid_dst) < 0) + if(H5I_dec_ref(tid_dst, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(tid_mem > 0) - if(H5I_dec_ref(tid_mem) < 0) + if(H5I_dec_ref(tid_mem, FALSE) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if(buf) (void)H5FL_BLK_FREE(type_conv, buf); |