diff options
Diffstat (limited to 'src/H5D.c')
| -rw-r--r-- | src/H5D.c | 226 |
1 files changed, 179 insertions, 47 deletions
@@ -50,10 +50,10 @@ * A dataset is the following struct. */ struct H5D_t { - H5G_entry_t ent; /*cached object header stuff */ - H5T_t *type; /*datatype of this dataset */ - hid_t dcpl_id; /*dataset creation property id */ - H5O_layout_t layout; /*data layout */ + H5G_entry_t ent; /* cached object header stuff */ + H5T_t *type; /* datatype of this dataset */ + hid_t dcpl_id; /* dataset creation property id */ + H5O_layout_t layout; /* data layout */ }; @@ -1500,6 +1500,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, H5D_t *new_dset = NULL; H5D_t *ret_value = NULL; int i, ndims; + hsize_t comp_data_size; unsigned u; hsize_t max_dim[H5O_LAYOUT_NDIMS]={0}; H5O_efl_t efl; @@ -1532,8 +1533,12 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter"); if(H5P_get(plist, H5D_CRT_LAYOUT_NAME, &dcpl_layout) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); + if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); if(dcpl_pline.nfilters > 0 && H5D_CHUNKED != dcpl_layout) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout"); + if(dcpl_layout==H5D_COMPACT && space_time==H5D_SPACE_ALLOC_LATE) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset doesn't support late space allocation"); /* What file is the dataset being added to? */ if (NULL==(f=H5G_insertion_file(loc, name))) @@ -1584,7 +1589,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim)); new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type); - switch (dcpl_layout) { + switch (new_dset->layout.type) { case H5D_CONTIGUOUS: /* * The maximum size of the dataset cannot exceed the storage size. @@ -1643,6 +1648,24 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, new_dset->layout.dim[u] = chunk_size[u]; break; + case H5D_COMPACT: + /* + * Compact dataset is stored in dataset object header message of + * layout. + */ + new_dset->layout.size = H5S_get_simple_extent_npoints(space) * + H5T_get_size(type); + /* Verify data size is smaller than maximum header message size + * (64KB) minus other layout message fields. + */ + comp_data_size=H5O_MAX_SIZE-H5O_layout_meta_size(f, &(new_dset->layout)); + if(new_dset->layout.size > comp_data_size) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size"); + if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim, max_dim))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize dimension size of compact dataset storage"); + /* remember to check if size is small enough to fit header message */ + break; + default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ @@ -1718,11 +1741,13 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset"); /* - * Initialize storage. We assume that external storage is already - * initialized by the caller, or at least will be before I/O is performed. + * Allocate storage. We assume that external storage is already + * allocated by the caller, or at least will be before I/O is performed. * For parallelization, space is always allocated now except using * external storage. For contiguous layout, space is allocated now if * space allocate time is early; otherwise delay allocation until H5Dwrite. + * For compact dataset, space is allocated regardless of space allocation + * time. */ #ifdef H5_HAVE_PARALLEL if (0==efl.nused) { @@ -1733,7 +1758,8 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, new_dset->layout.addr = HADDR_UNDEF; #else /*H5_HAVE_PARALLEL*/ if (0==efl.nused) { - if(dcpl_layout==H5D_CHUNKED || (dcpl_layout==H5D_CONTIGUOUS && space_time==H5D_SPACE_ALLOC_EARLY)) { + if(dcpl_layout==H5D_CHUNKED || dcpl_layout==H5D_COMPACT || + (dcpl_layout==H5D_CONTIGUOUS && space_time==H5D_SPACE_ALLOC_EARLY)) { if (H5F_arr_create(f, &(new_dset->layout))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); } /* end if */ @@ -1744,10 +1770,6 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, new_dset->layout.addr = HADDR_UNDEF; #endif /*H5_HAVE_PARALLEL*/ - /* Update layout message */ - if (H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, 0, &(new_dset->layout))<0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update layout message"); - /* Update external storage message */ if (efl.nused>0) { size_t heap_size = H5HL_ALIGN (1); @@ -1774,15 +1796,29 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, * 2. layout is contiguous, space allocation time is early, fill value * writing time is upon allocation * 3. external space is treated the same as internal except it's always - * assumed as early for space allocation time. */ + * assumed as early for space allocation time + * 4. compact dataset and fill value writing time is upon allocation + */ #ifdef H5_HAVE_PARALLEL if (H5D_init_storage(new_dset, space)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); #else /*H5_HAVE_PARALLEL*/ - if(fill_time==H5D_FILL_TIME_ALLOC && ((space_time==H5D_SPACE_ALLOC_EARLY && !efl.nused) || (efl.nused))) - if (H5D_init_storage(new_dset, space)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); + if(fill_time==H5D_FILL_TIME_ALLOC) { + if((dcpl_layout==H5D_CONTIGUOUS && space_time==H5D_SPACE_ALLOC_EARLY) + || (dcpl_layout==H5D_CHUNKED && space_time==H5D_SPACE_ALLOC_EARLY) + || dcpl_layout==H5D_COMPACT ) { + if (H5D_init_storage(new_dset, space)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); + } + } + } #endif /*H5_HAVE_PARALLEL*/ + + /* Update layout message */ + if (H5D_COMPACT != new_dset->layout.type && H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, 0, &(new_dset->layout))<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update layout"); + if (H5D_COMPACT == new_dset->layout.type) + new_dset->layout.dirty = TRUE; /* Success */ ret_value = new_dset; @@ -2048,6 +2084,12 @@ H5D_open_oid(H5G_entry_t *ent) if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->layout.dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk size"); break; + + case H5D_COMPACT: + layout = H5D_COMPACT; + if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout"); + break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ @@ -2128,6 +2170,13 @@ H5D_close(H5D_t *dataset) free_failed = (H5T_close(dataset->type) < 0 || H5I_dec_ref(dataset->dcpl_id) < 0); + /*Update header message of layout for compact dataset.*/ + if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) { + if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, &(dataset->layout))<0) + HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); + dataset->layout.dirty = FALSE; + } + /* Close the dataset object */ H5O_close(&(dataset->ent)); @@ -2307,7 +2356,10 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* If space hasn't been allocated and not using external storage, * return fill value to buffer if fill time is upon allocation, or - * do nothing if fill time is never. */ + * do nothing if fill time is never. If the dataset is compact and + * 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 && efl.nused==0 && dataset->layout.type==H5D_CONTIGUOUS && dataset->layout.addr==HADDR_UNDEF) { @@ -2373,7 +2425,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ - assert(dataset->layout.addr!=HADDR_UNDEF || efl.nused>0); + assert(dataset->layout.addr!=HADDR_UNDEF || efl.nused>0 || dataset->layout.type==H5D_COMPACT); status = (sconv->read)(dataset->ent.file, &(dataset->layout), dc_plist, H5T_get_size(dataset->type), file_space, mem_space, dxpl_id, buf/*out*/); @@ -2667,6 +2719,15 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + if (!file_space) { + if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); + file_space = free_this_space; + } /* end if */ + if (!mem_space) + mem_space = file_space; + nelmts = (*mem_space->select.get_npoints)(mem_space); + #ifdef H5_HAVE_PARALLEL /* If MPIO or MPIPOSIX is used, no VL datatype support yet. */ /* This is because they use the global heap in the file and we don't */ @@ -2687,15 +2748,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file"); - if (!file_space) { - if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); - file_space = free_this_space; - } /* end if */ - if (!mem_space) - mem_space = file_space; - nelmts = (*mem_space->select.get_npoints)(mem_space); - #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if (H5FD_MPIO==H5P_peek_hid_t(dx_plist,H5D_XFER_VFL_ID_NAME)) { @@ -2706,11 +2758,20 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, xfer_mode = dx->xfer_mode; } } /* end if */ + /* Collective access is not permissible without the MPIO or MPIPOSIX driver */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && !(IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO driver only"); + /* If dataset is compact, collective access is only allowed when file space + * selection is H5S_ALL */ + if(doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE + && dataset->layout.type==H5D_COMPACT) { + if(file_space->select.type != H5S_SEL_ALL) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access to compact dataset doesn't support partial access"); + } + /* Set the "parallel I/O possible" flag, for H5S_find() */ if (H5S_mpi_opt_types_g && IS_H5FD_MPIO(dataset->ent.file)) { /* Only collective write should call this since it eventually @@ -3211,18 +3272,27 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value"); if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); switch (dset->layout.type) { + case H5D_COMPACT: + /* + * zero set data buf. If fill value is defined, fall through + * the H5D_CONTIGUOUS case and initialize with fill value. + */ + if(!fill.buf) + HDmemset(dset->layout.buf, 0, dset->layout.size); + case H5D_CONTIGUOUS: /* * If the fill value is set then write it to the entire extent - * of the dataset. + * of the dataset. Note: library default(fill.buf is NULL) is + * not handled here. How to do it? */ snpoints = H5S_get_simple_extent_npoints(space); assert(snpoints>=0); H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); - + if (fill.buf) { /* * Fill the entire current extent with the fill value. We can do @@ -3355,22 +3425,27 @@ H5D_get_storage_size(H5D_t *dset) FUNC_ENTER_NOAPI(H5D_get_storage_size, 0); - if (H5D_CHUNKED==dset->layout.type) { - ret_value = H5F_istore_allocated(dset->ent.file, dset->layout.ndims, - dset->layout.addr); - } else { - /* Sanity Check */ - assert(dset->layout.type==H5D_CONTIGUOUS); - - /* Datasets which are not allocated yet are using no space on disk */ - if(dset->layout.addr == HADDR_UNDEF) - ret_value=0; - else { - for (u=0, ret_value=1; u<dset->layout.ndims; u++) - ret_value *= dset->layout.dim[u]; - } /* end else */ - } /* end else */ - + switch(dset->layout.type) { + case H5D_CHUNKED: + ret_value = H5F_istore_allocated(dset->ent.file, dset->layout.ndims, + dset->layout.addr); + break; + case H5D_CONTIGUOUS: + /* Datasets which are not allocated yet are using no space on disk */ + if(dset->layout.addr == HADDR_UNDEF) + ret_value=0; + else { + for (u=0, ret_value=1; u<dset->layout.ndims; u++) + ret_value *= dset->layout.dim[u]; + } /* end else */ + break; + case H5D_COMPACT: + ret_value = dset->layout.size; + break; + default: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset type"); + } + done: FUNC_LEAVE(ret_value); } @@ -4000,6 +4075,64 @@ done: /*------------------------------------------------------------------------- + * Function: H5D_flush + * + * Purpose: Flush any compact datasets cached in memory + * + * Return: Success: Non-negative + * Failure: Negative + * + * + * Programmer: Ray Lu + * + * Date: August 14, 2002 + * + * Comments: Private function + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_flush(H5F_t *f) +{ + unsigned num_dsets; /* Number of datasets in file */ + hid_t *id_list=NULL; /* list of dataset IDs */ + H5D_t *dataset=NULL; /* Dataset pointer */ + herr_t ret_value = SUCCEED; /* Return value */ + unsigned j; /* Index variable */ + + FUNC_ENTER_NOAPI(H5D_flush, FAIL); + + /* Check args */ + assert(f); + + /* Update layout message for compact dataset */ + if(H5F_get_obj_count(f, H5F_OBJ_DATASET, &num_dsets)<0) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset number"); + if(num_dsets>0) { + if(NULL==(id_list=H5MM_malloc(num_dsets*sizeof(hid_t)))) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to allocate memory for ID list"); + if(H5F_get_obj_ids(f, H5F_OBJ_DATASET, id_list)<0) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset ID list"); + for(j=0; j<num_dsets; j++) { + if(NULL==(dataset=H5I_object_verify(id_list[j], H5I_DATASET))) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset object"); + if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) + if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, &(dataset->layout))<0) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message"); + dataset->layout.dirty = FALSE; + } + } + +done: + if(id_list!=NULL) + H5MM_xfree(id_list); + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- * Function: H5Ddebug * * Purpose: Prints various information about a dataset. This function is @@ -4039,4 +4172,3 @@ H5Ddebug(hid_t dset_id, unsigned UNUSED flags) done: FUNC_LEAVE(ret_value); } - |