diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5D.c | 568 | ||||
| -rw-r--r-- | src/H5Dcompact.c | 10 | ||||
| -rw-r--r-- | src/H5Dcontig.c | 193 | ||||
| -rw-r--r-- | src/H5Distore.c | 78 | ||||
| -rw-r--r-- | src/H5Dprivate.h | 2 | ||||
| -rw-r--r-- | src/H5Dpublic.h | 6 | ||||
| -rw-r--r-- | src/H5FDmpio.h | 9 | ||||
| -rw-r--r-- | src/H5FDmpiposix.h | 4 | ||||
| -rw-r--r-- | src/H5Farray.c | 64 | ||||
| -rw-r--r-- | src/H5Fcompact.c | 10 | ||||
| -rw-r--r-- | src/H5Fcontig.c | 193 | ||||
| -rw-r--r-- | src/H5Fistore.c | 78 | ||||
| -rw-r--r-- | src/H5Fpkg.h | 2 | ||||
| -rw-r--r-- | src/H5Fprivate.h | 9 | ||||
| -rw-r--r-- | src/H5Oefl.c | 2 | ||||
| -rw-r--r-- | src/H5Olayout.c | 1 | ||||
| -rw-r--r-- | src/H5S.c | 22 | ||||
| -rw-r--r-- | src/H5Smpio.c | 2 | ||||
| -rw-r--r-- | src/H5Sprivate.h | 10 | ||||
| -rw-r--r-- | src/H5Sselect.c | 4 |
20 files changed, 857 insertions, 410 deletions
@@ -22,6 +22,7 @@ #include "H5Gprivate.h" /* Group headers */ #include "H5HLprivate.h" /* Name heap */ #include "H5Iprivate.h" /* IDs */ +#include "H5MFprivate.h" /* File space management */ #include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ @@ -44,8 +45,11 @@ # include "H5Rpublic.h" #endif /*H5_HAVE_PARALLEL*/ +/* Pablo information */ #define PABLO_MASK H5D_mask +/* Local typedefs */ + /* * A dataset is the following struct. */ @@ -56,11 +60,22 @@ struct H5D_t { H5O_layout_t layout; /* data layout */ }; +/* Enumerated type for allocating dataset's storage */ +typedef enum { + H5D_ALLOC_CREATE, /* Dataset is being created */ + H5D_ALLOC_OPEN, /* Dataset is being opened */ + H5D_ALLOC_EXTEND, /* Dataset's dataspace is being extended */ + H5D_ALLOC_WRITE /* Dataset is being extended */ +} H5D_alloc_time_t; +/* Interface initialization */ static int interface_initialize_g = 0; #define INTERFACE_INIT H5D_init_interface + +/* Local functions */ static herr_t H5D_init_interface(void); -static herr_t H5D_init_storage(H5D_t *dataset, const H5S_t *space); +static herr_t H5D_alloc_storage (H5F_t *f, H5D_t *dset,H5D_alloc_time_t alloc_time); +static herr_t H5D_init_storage(H5D_t *dataset); H5D_t * H5D_new(hid_t dcpl_id); static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space); @@ -70,7 +85,7 @@ static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation); H5FL_DEFINE_STATIC(H5D_t); /* Declare a free list to manage blocks of type conversion data */ -H5FL_BLK_DEFINE_STATIC(type_conv); +H5FL_BLK_DEFINE(type_conv); /* Declare a free list to manage blocks of single datatype element data */ H5FL_BLK_DEFINE(type_elem); @@ -1533,22 +1548,46 @@ 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) + 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"); + + /* Check if the space_time is the default and set it accordingly */ + if(space_time==H5D_SPACE_ALLOC_DEFAULT) { + switch(dcpl_layout) { + case H5D_COMPACT: + space_time=H5D_SPACE_ALLOC_EARLY; + break; + + case H5D_CONTIGUOUS: + space_time=H5D_SPACE_ALLOC_LATE; + break; + + case H5D_CHUNKED: + space_time=H5D_SPACE_ALLOC_INCR; + break; + + default: + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); + } /* end switch */ + } /* end if */ + + /* Don't allow compact datasets to allocate space later */ + if(dcpl_layout==H5D_COMPACT && space_time!=H5D_SPACE_ALLOC_EARLY) 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))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to locate insertion point"); -#ifdef H5_HAVE_PARALLEL /* If MPIO or MPIPOSIX is used, no filter support yet. */ if((IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) && dcpl_pline.nfilters > 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet"); -#endif /*H5_HAVE_PARALLEL*/ + + /* Check if this dataset is going into a parallel file and set space allocation time */ + if(IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) + space_time=H5D_SPACE_ALLOC_EARLY; if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill time"); @@ -1576,6 +1615,10 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, if (NULL == (new_plist = H5I_object(new_dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); + /* Set the space_time for the dataset, in case the default was used */ + if(H5P_set(new_plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, NULL, "can't set allocation time"); + if(H5P_get(new_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); @@ -1588,6 +1631,7 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, new_dset->layout.ndims = H5S_get_simple_extent_ndims(space) + 1; 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); + new_dset->layout.addr = HADDR_UNDEF; /* Initialize to no address */ switch (new_dset->layout.type) { case H5D_CONTIGUOUS: @@ -1741,34 +1785,11 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset"); /* - * 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. + * Allocate storage if space allocate time is early; otherwise delay allocation until later. */ -#ifdef H5_HAVE_PARALLEL - if (0==efl.nused) { - if(H5F_arr_create(f, &(new_dset->layout))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); - } /* end if */ - else - new_dset->layout.addr = HADDR_UNDEF; -#else /*H5_HAVE_PARALLEL*/ - if (0==efl.nused) { - 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 */ - else - new_dset->layout.addr = HADDR_UNDEF; - } /* end if */ - else - new_dset->layout.addr = HADDR_UNDEF; -#endif /*H5_HAVE_PARALLEL*/ + if(space_time==H5D_SPACE_ALLOC_EARLY) + if (H5D_alloc_storage(f, new_dset,H5D_ALLOC_CREATE)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); /* Update external storage message */ if (efl.nused>0) { @@ -1791,34 +1812,9 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update external file list message"); } /* end if */ - /* Initialize the raw data when it's - * 1. Parallel I/O - * 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 - * 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) { - 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; @@ -1969,7 +1965,6 @@ H5D_open_oid(H5G_entry_t *ent) { H5D_t *dataset = NULL; /*new dataset struct */ H5D_t *ret_value = NULL; /*return value */ - H5S_t *space = NULL; /*data space */ H5O_fill_new_t fill = {NULL, 0, NULL, H5D_SPACE_ALLOC_LATE, H5D_FILL_TIME_ALLOC, TRUE}; H5O_fill_t fill_prop = {NULL, 0, NULL}; H5O_pline_t pline; /* I/O pipeline information */ @@ -1997,47 +1992,11 @@ H5D_open_oid(H5G_entry_t *ent) /* Get the type and space */ if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load type info from dataset header"); - if (NULL==(space=H5S_read (&(dataset->ent)))) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to read data space info from dataset header"); /* Get dataset creation property list object */ if (NULL == (plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); - /* Retrieve & release the previous fill-value settings */ - if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't get fill value"); - H5O_reset(H5O_FILL, &fill_prop); - - /* Get the new fill value message */ - if(NULL == H5O_read(&(dataset->ent), H5O_FILL_NEW, 0, &fill)) { - H5E_clear(); - HDmemset(&fill, 0, sizeof(fill)); - } - if(fill.fill_defined) { - if(NULL==H5O_copy(H5O_FILL, &fill, &fill_prop)) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy fill value"); - } else { - /* For compatibility with v1.4. Retrieve the old fill value message. - * If size is 0, make it -1 for undefined. */ - if(NULL == H5O_read(&(dataset->ent), H5O_FILL, 0, &fill_prop)) { - H5E_clear(); - HDmemset(&fill_prop, 0, sizeof(fill_prop)); - } - if(fill_prop.size == 0) { - fill_prop.type = fill_prop.buf = NULL; - fill_prop.size = (size_t)-1; - } - } /* end else */ - - /* Set fill value properties */ - if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); - if(H5P_set(plist, H5D_CRT_SPACE_TIME_NAME, &fill.space_time) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); - if(H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill.fill_time) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); - /* Get the optional filters message */ HDmemset(&pline,0,sizeof(H5O_pline_t)); if(NULL == H5O_read(&(dataset->ent), H5O_PLINE, 0, &pline)) { @@ -2047,11 +2006,9 @@ H5D_open_oid(H5G_entry_t *ent) if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set pipeline"); -#ifdef H5_HAVE_PARALLEL /* If MPIO or MPIPOSIX is used, no filter support yet. */ if((IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file)) && pline.nfilters > 0) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel IO does not support filters yet"); -#endif /*H5_HAVE_PARALLEL*/ /* * Get the raw data layout info. It's actually stored in two locations: @@ -2094,6 +2051,58 @@ H5D_open_oid(H5G_entry_t *ent) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ + /* Retrieve & release the previous fill-value settings */ + if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't get fill value"); + H5O_reset(H5O_FILL, &fill_prop); + + /* Get the new fill value message */ + if(NULL == H5O_read(&(dataset->ent), H5O_FILL_NEW, 0, &fill)) { + H5E_clear(); + HDmemset(&fill, 0, sizeof(fill)); + + /* Set the space allocation time appropriately, based on the type of dataset storage */ + switch (dataset->layout.type) { + case H5D_COMPACT: + fill.space_time=H5D_SPACE_ALLOC_EARLY; + break; + + case H5D_CONTIGUOUS: + fill.space_time=H5D_SPACE_ALLOC_LATE; + break; + + case H5D_CHUNKED: + fill.space_time=H5D_SPACE_ALLOC_INCR; + break; + + default: + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); + } /* end switch */ + } /* end if */ + if(fill.fill_defined) { + if(NULL==H5O_copy(H5O_FILL, &fill, &fill_prop)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy fill value"); + } else { + /* For compatibility with v1.4. Retrieve the old fill value message. + * If size is 0, make it -1 for undefined. */ + if(NULL == H5O_read(&(dataset->ent), H5O_FILL, 0, &fill_prop)) { + H5E_clear(); + HDmemset(&fill_prop, 0, sizeof(fill_prop)); + } + if(fill_prop.size == 0) { + fill_prop.type = fill_prop.buf = NULL; + fill_prop.size = (size_t)-1; + } + } /* end else */ + + /* Set fill value properties */ + if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); + if(H5P_set(plist, H5D_CRT_SPACE_TIME_NAME, &fill.space_time) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); + if(H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill.fill_time) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); + /* Get the external file list message, which might not exist. Space is * also undefined when space allocate time is H5D_SPACE_ALLOC_LATE. */ if( !H5F_addr_defined(dataset->layout.addr)) { @@ -2103,12 +2112,14 @@ H5D_open_oid(H5G_entry_t *ent) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set external file list"); } /* - * Make sure all storage is properly initialized for chunked datasets. - * This is especially important for parallel I/O where the B-tree must - * be fully populated before I/O can happen. + * Make sure all storage is properly initialized. + * This is important only for parallel I/O where the space must + * be fully allocated before I/O can happen. */ - if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) && H5D_CHUNKED==dataset->layout.type) { - if (H5D_init_storage(dataset, space)<0) + if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) + && (dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) + && (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file))) { + if (H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_OPEN)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize file storage"); } @@ -2116,8 +2127,6 @@ H5D_open_oid(H5G_entry_t *ent) ret_value = dataset; done: - if (space) - H5S_close(space); if (ret_value==NULL && dataset) { if (H5F_addr_defined(dataset->ent.header)) H5O_close(&(dataset->ent)); @@ -2360,7 +2369,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, * 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 + if(nelmts > 0 && efl.nused==0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { /* Should be impossible, but check anyway... */ @@ -2695,6 +2704,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5O_efl_t efl; /* External File List info */ H5O_fill_t fill; /* Fill value info */ H5D_fill_time_t fill_time; /* When to write the fill values */ + H5D_space_time_t space_time; /* When to allocate raw data space */ H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ unsigned sconv_flags=0; /* Flags for the space conversion */ @@ -2728,14 +2738,11 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *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 */ /* support parallel access of that yet */ if ( (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file)) && H5T_get_class(mem_type)==H5T_VLEN) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet"); -#endif /*H5_HAVE_PARALLEL*/ -#ifdef H5_HAVE_PARALLEL /* If MPIO or MPIPOSIX is used, no dataset region reference datatype support yet. */ /* This is because they use the global heap in the file and we don't */ /* support parallel access of that yet */ @@ -2743,7 +2750,6 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5T_get_class(mem_type)==H5T_REFERENCE && H5T_get_ref_type(mem_type)==H5R_DATASET_REGION) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet"); -#endif /*H5_HAVE_PARALLEL*/ if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file"); @@ -2794,24 +2800,15 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill time"); if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); + if(H5P_get(dc_plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); - /* Allocate data space and initialize it if it hasn't been. Also modify - * header message for layout(this is only for forward compatibility). */ - if(nelmts > 0 && efl.nused==0 && dataset->layout.type==H5D_CONTIGUOUS && + /* Allocate data space and initialize it if it hasn't been. */ + if(nelmts > 0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { /* Allocate storage */ - if(H5F_arr_create(dataset->ent.file, &(dataset->layout))<0) + if(H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_WRITE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); - - /* Initialize raw data */ - if(fill_time==H5D_FILL_TIME_ALLOC) - if(H5D_init_storage(dataset, file_space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); - - /* Update layout message */ - if (H5O_modify (&(dataset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, - &(dataset->layout)) < 0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); } /* end if */ /* @@ -3084,10 +3081,11 @@ done: herr_t H5D_extend (H5D_t *dataset, const hsize_t *size) { - herr_t changed, ret_value=SUCCEED; - H5S_t *space = NULL; - H5O_fill_t fill; - H5P_genplist_t *plist; /* Property list */ + int changed; /* Flag to indicate that the dataspace was successfully extended */ + H5S_t *space = NULL; /* Dataset's dataspace */ + H5D_space_time_t space_time; /* When to allocate raw data space */ + H5P_genplist_t *plist; /* Property list */ + herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_extend, FAIL); @@ -3095,6 +3093,12 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) assert (dataset); assert (size); + /* Get the dataset creation property list */ + if (NULL == (plist = H5I_object(dataset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + 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"); + /* * NOTE: Restrictions on extensions were checked when the dataset was * created. All extensions are allowed here since none should be @@ -3112,26 +3116,10 @@ H5D_extend (H5D_t *dataset, const hsize_t *size) if (H5S_modify (&(dataset->ent), space)<0) HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); - /* Initialize the new parts of the dataset */ -#ifdef LATER - if (H5S_select_all(space)<0 || - H5S_select_hyperslab(space, H5S_SELECT_DIFF, zero, NULL, old_dims, NULL)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to select new extents for fill value"); -#else - /* - * We don't have the H5S_SELECT_DIFF operator yet. We really only - * need it for contiguous datasets because the chunked datasets will - * either fill on demand during I/O or attempt a fill of all chunks. - */ - if (NULL == (plist = H5I_object(dataset->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); - if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value"); - if(H5D_CONTIGUOUS == dataset->layout.type && fill.buf) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to select fill value region"); -#endif - if (H5D_init_storage(dataset, space)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); + /* Allocate space for the new parts of the dataset, if appropriate */ + if(space_time==H5D_SPACE_ALLOC_EARLY) + if (H5D_alloc_storage(dataset->ent.file, dataset, H5D_ALLOC_EXTEND)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); } /* end if */ done: @@ -3226,6 +3214,128 @@ H5D_get_file (const H5D_t *dset) /*------------------------------------------------------------------------- + * Function: H5D_alloc_storage + * + * Purpose: Allocate storage for the raw data of a dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Friday, January 16, 1998 + * + * Modifications: + * Quincey Koziol + * Thursday, August 22, 2002 + * Moved here from H5F_arr_create and moved more logic into + * this function from places where it was being called. + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_alloc_time_t alloc_time) +{ + H5P_genplist_t *plist; /* Dataset's creation property list */ + H5O_efl_t efl; /* External File List info */ + H5D_fill_time_t fill_time; /* When to write fill values */ + H5D_space_time_t space_time; /* When to allocate raw data space */ + struct H5O_layout_t *layout; /* The dataset's layout information */ + hsize_t nbytes; /* The number of bytes in the dataset */ + unsigned space_allocated=0; /* Flag to indicate that space was allocated */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOINIT(H5D_alloc_storage); + + /* check args */ + assert (f); + assert (dset); + + /* Get external file list properties */ + if (NULL == (plist = H5I_object(dset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); + + /* If the data is stored in external files, don't set an address for the layout + * We assume that external storage is already + * allocated by the caller, or at least will be before I/O is performed. + */ + if(efl.nused==0) { + /* Get properties needed */ + if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time"); + 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"); + + /* Get a pointer to the dataset's layout information */ + layout=&(dset->layout); + + switch (layout->type) { + case H5D_CONTIGUOUS: + if(layout->addr==HADDR_UNDEF) { + /* Reserve space in the file for the entire array */ + for (u=0, nbytes=1; u<layout->ndims; u++) + nbytes *= layout->dim[u]; + assert (nbytes>0); + if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, nbytes))) + HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); + + /* Indicate that we allocated space */ + space_allocated=1; + } /* end if */ + break; + + case H5D_CHUNKED: + if(layout->addr==HADDR_UNDEF) { + /* Create the root of the B-tree that describes chunked storage */ + if (H5F_istore_create (f, layout/*out*/)<0) + HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage"); + + /* Indicate that we allocated space */ + space_allocated=1; + } /* end if */ + break; + + case H5D_COMPACT: + /* Check if space is already allocated */ + if(layout->buf==NULL) { + /* Reserve space in layout header message for the entire array. */ + assert(layout->size>0); + if (NULL==(layout->buf=H5MM_malloc(layout->size))) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate memory for compact dataset"); + layout->dirty = TRUE; + + /* Indicate that we allocated space */ + space_allocated=1; + } /* end if */ + break; + + default: + assert ("not implemented yet" && 0); + HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout"); + } /* end switch */ + + /* If we are filling the dataset on allocation, do that now */ + if(fill_time==H5D_FILL_TIME_ALLOC + && !(space_time==H5D_SPACE_ALLOC_INCR && alloc_time==H5D_ALLOC_WRITE)) { + if(H5D_init_storage(dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); + } /* end if */ + + /* Also update header message for layout with new address + * (this is only for forward compatibility). + */ + if(space_allocated && alloc_time!=H5D_ALLOC_CREATE) + if (H5O_modify (&(dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, &(dset->layout)) < 0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); + } /* end if */ + +done: + FUNC_LEAVE (ret_value); +} /* end H5D_alloc_storage() */ + + +/*------------------------------------------------------------------------- * Function: H5D_init_storage * * Purpose: Initialize the data for a new dataset. If a selection is @@ -3247,32 +3357,31 @@ H5D_get_file (const H5D_t *dset) *------------------------------------------------------------------------- */ static herr_t -H5D_init_storage(H5D_t *dset, const H5S_t *space) +H5D_init_storage(H5D_t *dset) { hssize_t snpoints; /* Number of points in space (for error checking) */ size_t npoints; /* Number of points in space */ - size_t ptsperbuf; /* Maximum # of points which fit in the buffer */ - size_t bufsize=64*1024; /* Size of buffer to write */ - size_t size; /* Current # of points to write */ - hsize_t addr; /* Offset in dataset */ - void *buf = NULL; /* Buffer for fill value writing */ + H5S_t *space = NULL; /* Dataset's dataspace */ H5O_fill_t fill; /* Fill value information */ - H5D_space_time_t space_time; /* When to allocate space */ + H5O_efl_t efl; /* External File List info */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_init_storage); assert(dset); - assert(space); /* Get fill value, external file list, and data pipeline properties */ if (NULL == (plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); 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, FAIL, "can't retrieve space allocation time"); + if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); + + /* Get the dataset's dataspace */ + if (NULL==(space=H5S_read (&(dset->ent)))) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); /* Get the number of elements in the dataset's dataspace */ snpoints = H5S_get_simple_extent_npoints(space); @@ -3290,54 +3399,17 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) break; case H5D_CONTIGUOUS: - /* If fill value is library default, get the dataset's type's size */ - if(!fill.buf) { - fill.size=H5T_get_size(dset->type); - assert(fill.size); - } /* end if */ - - /* - * Fill the entire current extent with the fill value. We can do - * this quite efficiently by making sure we copy the fill value - * in relatively large pieces. - */ - ptsperbuf = MAX(1, bufsize/fill.size); - bufsize = ptsperbuf*fill.size; - - /* Allocate temporary buffer */ - if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); - - /* Fill the buffer with the user's fill value */ - if(fill.buf) - H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf); - else /* Fill the buffer with the default fill value */ - HDmemset(buf,0,bufsize); - - /* Start at the beginning of the dataset */ - addr = 0; - - /* Loop through writing the fill value to the dataset */ - while (npoints>0) { - size = MIN(ptsperbuf, npoints) * fill.size; - if (H5F_seq_write(dset->ent.file, H5P_DATASET_XFER_DEFAULT, - &(dset->layout), plist, space, fill.size, size, addr, buf)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); - npoints -= MIN(ptsperbuf, npoints); - addr += size; - } /* end while */ + if (H5F_contig_fill(dset->ent.file, H5P_DATASET_XFER_DEFAULT, + &(dset->layout), plist, space, H5T_get_size(dset->type))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); break; case H5D_CHUNKED: /* - * If the dataset is accessed via parallel I/O, allocate file space + * Allocate file space * for all chunks now and initialize each chunk with the fill value. */ - if (space_time==H5D_SPACE_ALLOC_EARLY -#ifdef H5_HAVE_PARALLEL - || (IS_H5FD_MPIO(dset->ent.file) || IS_H5FD_MPIPOSIX(dset->ent.file)) -#endif /*H5_HAVE_PARALLEL*/ - ) { + { /* We only handle simple data spaces so far */ int ndims; hsize_t dim[H5O_LAYOUT_NDIMS]; @@ -3345,7 +3417,6 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info"); dim[ndims] = dset->layout.dim[ndims]; - ndims++; if (H5F_istore_allocate(dset->ent.file, H5P_DATASET_XFER_DEFAULT, &(dset->layout), dim, plist)<0) @@ -3355,8 +3426,8 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) } /* end switch */ done: - if (buf) - H5FL_BLK_FREE(type_conv,buf); + if (space) + H5S_close(space); FUNC_LEAVE(ret_value); } @@ -3430,23 +3501,29 @@ H5D_get_storage_size(H5D_t *dset) switch(dset->layout.type) { case H5D_CHUNKED: - ret_value = H5F_istore_allocated(dset->ent.file, dset->layout.ndims, + if(dset->layout.addr == HADDR_UNDEF) + ret_value=0; + else + 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; + 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"); + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type"); } done: @@ -4001,8 +4078,11 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size) herr_t ret_value = SUCCEED; /* Return value */ H5S_t *space = NULL; H5P_genplist_t *plist; + H5D_space_time_t space_time; /* When to allocate raw data space */ int u; - int shrink = 0; + unsigned shrink = 0; /* Flag to indicate a dimension has shrank */ + unsigned expand = 0; /* Flag to indicate a dimension has grown */ + int changed = 0; FUNC_ENTER_NOAPI(H5D_set_extent, FAIL); @@ -4018,56 +4098,62 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space info from dset header"); /*------------------------------------------------------------------------- - * Check if we are shrinking in any of the dimensions + * Check if we are shrinking or expanding any of the dimensions *------------------------------------------------------------------------- */ if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions"); for(u = 0; u < rank; u++) { - if(size[u] < curr_dims[u]) { + if(size[u] < curr_dims[u]) shrink = 1; - break; - } + if(size[u] > curr_dims[u]) + expand = 1; } /*------------------------------------------------------------------------- * Modify the size of the data space *------------------------------------------------------------------------- */ - if(H5S_set_extent(space, size) < 0) + if((changed=H5S_set_extent(space, size)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space"); - /*------------------------------------------------------------------------- - * Modify the dataset storage - *------------------------------------------------------------------------- - */ - /* Save the new dataspace in the file if necessary */ - if(H5S_modify(&(dset->ent), space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); - - /* Initialize the new parts of the dset */ - if(H5D_init_storage(dset, space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage"); - - - /*------------------------------------------------------------------------- - * Remove chunk information in the case of chunked datasets - * This removal takes place only in case we are shrinking the dateset - *------------------------------------------------------------------------- - */ - if(shrink && H5D_CHUNKED == dset->layout.type) { - /* Remove excess chunks */ - if(H5F_istore_prune_by_extent(dset->ent.file, &dset->layout, space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks "); - + /* Don't bother updating things, unless they've changed */ + if(changed) { /* Get the dataset creation property list */ - if(NULL == (plist = H5I_object(dset->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list"); - - /* Reset the elements outsize the new dimensions, but in existing chunks */ - if(H5F_istore_initialize_by_extent(dset->ent.file, &dset->layout, plist, space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks "); + if(NULL == (plist = H5I_object(dset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list"); + 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"); + + /*------------------------------------------------------------------------- + * Modify the dataset storage + *------------------------------------------------------------------------- + */ + /* Save the new dataspace in the file if necessary */ + if(H5S_modify(&(dset->ent), space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); + + /* Allocate space for the new parts of the dataset, if appropriate */ + if(expand && space_time==H5D_SPACE_ALLOC_EARLY) + if(H5D_alloc_storage(dset->ent.file, dset, H5D_ALLOC_EXTEND) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage"); + + + /*------------------------------------------------------------------------- + * Remove chunk information in the case of chunked datasets + * This removal takes place only in case we are shrinking the dateset + *------------------------------------------------------------------------- + */ + if(shrink && H5D_CHUNKED == dset->layout.type) { + /* Remove excess chunks */ + if(H5F_istore_prune_by_extent(dset->ent.file, &dset->layout, space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks "); + + /* Reset the elements outsize the new dimensions, but in existing chunks */ + if(H5F_istore_initialize_by_extent(dset->ent.file, &dset->layout, plist, space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks "); + } /* end if */ } /* end if */ done: diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index 3a36edb..0a21211 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -44,9 +44,9 @@ static int interface_initialize_g = 0; *------------------------------------------------------------------------- */ herr_t -H5F_compact_readv(H5F_t *f, const H5O_layout_t *layout, size_t nseq, +H5F_compact_readv(H5F_t UNUSED *f, const H5O_layout_t *layout, size_t nseq, size_t size_arr[], hsize_t offset_arr[], - hid_t dxpl_id, void *_buf/*out*/) + hid_t UNUSED dxpl_id, void *_buf/*out*/) { unsigned char *buf=(unsigned char *)_buf; size_t size; @@ -93,11 +93,11 @@ done: *------------------------------------------------------------------------- */ herr_t -H5F_compact_writev(H5F_t *f, H5O_layout_t *layout, size_t nseq, +H5F_compact_writev(H5F_t UNUSED *f, H5O_layout_t *layout, size_t nseq, size_t size_arr[], hsize_t offset_arr[], - hid_t dxpl_id, const void *_buf) + hid_t UNUSED dxpl_id, const void *_buf) { - unsigned char *buf=(unsigned char *)_buf; + const unsigned char *buf=(const unsigned char *)_buf; size_t size; haddr_t offset; unsigned u; diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 89f9fc5..fce1ba9 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -14,11 +14,19 @@ #define H5F_PACKAGE /*suppress error about including H5Fpkg */ -#include "H5private.h" -#include "H5Eprivate.h" +#include "H5private.h" /* Generic Functions */ +#include "H5Dprivate.h" /* Dataset functions */ +#include "H5Eprivate.h" /* Error handling */ #include "H5Fpkg.h" #include "H5FDprivate.h" /*file driver */ #include "H5FLprivate.h" /*Free Lists */ +#include "H5Oprivate.h" /* Object headers */ +#include "H5Pprivate.h" /* Property lists */ +#include "H5Vprivate.h" /* Vector and array functions */ + +/* MPIO & MPIPOSIX drivers needed for special checks */ +#include "H5FDmpio.h" +#include "H5FDmpiposix.h" /* Interface initialization */ #define PABLO_MASK H5Fcontig_mask @@ -28,6 +36,187 @@ static int interface_initialize_g = 0; /* Declare a PQ free list to manage the sieve buffer information */ H5FL_BLK_DEFINE(sieve_buf); +/* Extern the free list to manage blocks of type conversion data */ +H5FL_BLK_EXTERN(type_conv); + + +/*------------------------------------------------------------------------- + * Function: H5F_contig_fill + * + * Purpose: Write fill values to a contiguously stored dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * August 22, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, + struct H5P_genplist_t *dc_plist, const struct H5S_t *space, + size_t elmt_size) +{ + H5O_fill_t fill; /* Fill value information */ + H5O_efl_t efl; /* External File List info */ + hssize_t snpoints; /* Number of points in space (for error checking) */ + size_t npoints; /* Number of points in space */ + size_t ptsperbuf; /* Maximum # of points which fit in the buffer */ + size_t bufsize=64*1024; /* Size of buffer to write */ + size_t size; /* Current # of points to write */ + hsize_t addr; /* Offset in dataset */ + void *buf = NULL; /* Buffer for fill value writing */ +#ifdef H5_HAVE_PARALLEL + MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ + int mpi_rank=(-1); /* This process's rank */ + int mpi_size=(-1); /* Total # of processes */ + int mpi_round=0; /* Current process responsible for I/O */ + int mpi_code; /* MPI return code */ + unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */ + unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ +#endif /* H5_HAVE_PARALLEL */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5F_contig_fill, FAIL); + + /* Check args */ + assert(f); + assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); + assert(layout && H5D_CONTIGUOUS==layout->type); + assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->addr)); + assert(dc_plist!=NULL); + assert(space); + assert(elmt_size>0); + + /* Get necessary properties from dataset creation property list */ + if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get fill value"); + if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); + +#ifdef H5_HAVE_PARALLEL + /* Retrieve up MPI parameters */ + if(IS_H5FD_MPIO(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ + if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); + if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + else { + if(IS_H5FD_MPIPOSIX(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ + if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); + if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + + /* Get the number of elements in the dataset's dataspace */ + snpoints = H5S_get_simple_extent_npoints(space); + assert(snpoints>=0); + H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); + + /* Don't write default fill-values to external files */ + if(efl.nused>0 && !fill.buf) + HGOTO_DONE(SUCCEED); + + /* If fill value is library default, use the element size */ + if(!fill.buf) + fill.size=elmt_size; + + /* + * Fill the entire current extent with the fill value. We can do + * this quite efficiently by making sure we copy the fill value + * in relatively large pieces. + */ + ptsperbuf = MAX(1, bufsize/fill.size); + bufsize = ptsperbuf*fill.size; + + /* Allocate temporary buffer */ + if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); + + /* Fill the buffer with the user's fill value */ + if(fill.buf) + H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf); + else /* Fill the buffer with the default fill value */ + HDmemset(buf,0,bufsize); + + /* Start at the beginning of the dataset */ + addr = 0; + + /* Loop through writing the fill value to the dataset */ + while (npoints>0) { + size = MIN(ptsperbuf, npoints) * fill.size; + +#ifdef H5_HAVE_PARALLEL + /* Check if this file is accessed with an MPI-capable file driver */ + if(using_mpi) { + /* Round-robin write the chunks out from only one process */ + if(mpi_round==mpi_rank) { + if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space, + fill.size, size, addr, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); + } /* end if */ + mpi_round=(++mpi_round)%mpi_size; + + /* Indicate that blocks are being written */ + blocks_written=1; + } /* end if */ + else { +#endif /* H5_HAVE_PARALLEL */ + if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space, + fill.size, size, addr, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); +#ifdef H5_HAVE_PARALLEL + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + + npoints -= MIN(ptsperbuf, npoints); + addr += size; + } /* end while */ + +#ifdef H5_HAVE_PARALLEL + /* Only need to block at the barrier if we actually wrote fill values */ + /* And if we are using an MPI-capable file driver */ + if(using_mpi && blocks_written) { + /* Wait at barrier to avoid race conditions where some processes are + * still writing out fill values and other processes race ahead to data + * in, getting bogus data. + */ + if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ + +done: + /* Free the buffer for fill values */ + if (buf) + H5FL_BLK_FREE(type_conv,buf); + + FUNC_LEAVE(ret_value); +} + /*------------------------------------------------------------------------- * Function: H5F_contig_read diff --git a/src/H5Distore.c b/src/H5Distore.c index 0bba74e..f36b6200 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -1758,7 +1758,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 && chunk_addr!=HADDR_UNDEF) -#ifdef H5_HAVE_PARALLEL /* * If MPIO or MPIPOSIX is used and file can be written to, we must bypass the * chunk-cache scheme because other MPI processes could be writing to @@ -1766,7 +1765,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Do a direct write-through of only the elements requested. */ || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags)) -#endif /* H5_HAVE_PARALLEL */ ) { H5O_layout_t l; /* temporary layout */ @@ -1942,14 +1940,12 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 && chunk_addr!=HADDR_UNDEF) -#ifdef H5_HAVE_PARALLEL /* * If MPIO or MPIPOSIX is used, must bypass the chunk-cache scheme because other * MPI processes could be writing to other elements in the same chunk. * Do a direct write-through of only the elements requested. */ || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags)) -#endif /* H5_HAVE_PARALLEL */ ) { H5O_layout_t l; /* temporary layout */ @@ -2334,6 +2330,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, H5P_genplist_t *dx_plist; /* Data xfer property list */ double split_ratios[3];/* B-tree node splitting ratios */ #ifdef H5_HAVE_PARALLEL + MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ int mpi_rank=(-1); /* This process's rank */ int mpi_size=(-1); /* Total # of processes */ int mpi_round=0; /* Current process responsible for I/O */ @@ -2342,6 +2339,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ #endif /* H5_HAVE_PARALLEL */ int carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ + unsigned chunk_exists; /* Flag to indicate whether a chunk exists already */ int i; /* Local index variable */ unsigned u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ @@ -2374,6 +2372,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, #ifdef H5_HAVE_PARALLEL /* Retrieve up MPI parameters */ if(IS_H5FD_MPIO(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0) @@ -2384,6 +2387,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end if */ else { if(IS_H5FD_MPIPOSIX(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + /* Get the MPI rank & size */ if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); @@ -2396,12 +2403,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end else */ #endif /* H5_HAVE_PARALLEL */ -#ifdef H5_HAVE_PARALLEL - /* Can't use data I/O pipeline in parallel (yet) */ - if (using_mpi && pline.nfilters>0) - HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, FAIL, "can't use data pipeline in parallel"); -#endif /* H5_HAVE_PARALLEL */ - /* * Setup indice to go through all chunks. (Future improvement * should allocate only chunks that have no file space assigned yet. @@ -2450,8 +2451,32 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, /* Loop over all chunks */ carry=0; while (carry==0) { - /* Check if the chunk exists yet */ + /* Check if the chunk exists yet on disk */ + chunk_exists=1; if(H5F_istore_get_addr(f,layout,chunk_offset)==HADDR_UNDEF) { + H5F_rdcc_t *rdcc = &(f->shared->rdcc); /*raw data chunk cache */ + H5F_rdcc_ent_t *ent = NULL; /*cache entry */ + + /* Didn't find the chunk on disk */ + chunk_exists = 0; + + /* Look for chunk in cache */ + for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) { + /* Make certain we are dealing with the correct B-tree, etc */ + if (layout->ndims==ent->layout->ndims && + H5F_addr_eq(layout->addr, ent->layout->addr)) { + + /* Assume a match */ + chunk_exists = 1; + for(u = 0; u < layout->ndims && chunk_exists; u++) { + if(ent->offset[u] != chunk_offset[u]) + chunk_exists = 0; /* Reset if no match */ + } /* end for */ + } /* end if */ + } /* end for */ + } /* end if */ + + if(!chunk_exists) { /* Initialize the chunk information */ udata.mesg = *layout; udata.key.filter_mask = 0; @@ -2507,17 +2532,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * still writing out chunks and other processes race ahead to read * them in, getting bogus data. */ - if(IS_H5FD_MPIO(f)) { - if (MPI_SUCCESS != (mpi_code=MPI_Barrier(H5FD_mpio_communicator(f->shared->lf)))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); - } /* end if */ - else { - /* Sanity Check */ - assert(IS_H5FD_MPIPOSIX(f)); - - if (MPI_SUCCESS!=(mpi_code=MPI_Barrier(H5FD_mpiposix_communicator(f->shared->lf)))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); - } /* end else */ + if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); } /* end if */ #endif /* H5_HAVE_PARALLEL */ @@ -2662,13 +2678,17 @@ H5F_istore_prune_by_extent(H5F_t *f, const H5O_layout_t *layout, const H5S_t * s for(ent = rdcc->head; ent; ent = next) { next = ent->next; - found = 0; - for(u = 0; u < ent->layout->ndims - 1; u++) { - if((hsize_t)ent->offset[u] > curr_dims[u]) { - found = 1; - break; - } - } + /* Make certain we are dealing with the correct B-tree, etc */ + if (layout->ndims==ent->layout->ndims && + H5F_addr_eq(layout->addr, ent->layout->addr)) { + found = 0; + for(u = 0; u < ent->layout->ndims - 1; u++) { + if((hsize_t)ent->offset[u] > curr_dims[u]) { + found = 1; + break; + } + } + } /* end if */ if(found) { #if defined (H5F_ISTORE_DEBUG) diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index a60c041..d1d0a02 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -63,7 +63,7 @@ /* Definitions for space allocation time */ #define H5D_CRT_SPACE_TIME_NAME "space_time" #define H5D_CRT_SPACE_TIME_SIZE sizeof(H5D_space_time_t) -#define H5D_CRT_SPACE_TIME_DEF H5D_SPACE_ALLOC_LATE +#define H5D_CRT_SPACE_TIME_DEF H5D_SPACE_ALLOC_DEFAULT /* Definitions for time of fill value writing */ #define H5D_CRT_FILL_TIME_NAME "fill_time" #define H5D_CRT_FILL_TIME_SIZE sizeof(H5D_fill_time_t) diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index 855f05f..3cad621 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -33,8 +33,10 @@ typedef enum H5D_layout_t { /* Values for the space allocation time property */ typedef enum H5D_space_time_t { H5D_SPACE_ALLOC_ERROR =-1, - H5D_SPACE_ALLOC_LATE =0, - H5D_SPACE_ALLOC_EARLY =1 + H5D_SPACE_ALLOC_DEFAULT =0, + H5D_SPACE_ALLOC_EARLY =1, + H5D_SPACE_ALLOC_LATE =2, + H5D_SPACE_ALLOC_INCR =3 } H5D_space_time_t; /* Values for the status of space allocation */ diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h index c5133f3..f1dd6f7 100644 --- a/src/H5FDmpio.h +++ b/src/H5FDmpio.h @@ -34,8 +34,12 @@ typedef struct H5FD_mpio_dxpl_t { H5FD_mpio_xfer_t xfer_mode; /*collective or independent I/O */ } H5FD_mpio_dxpl_t; -#ifdef H5_HAVE_PARALLEL /* Macros */ + +#define IS_H5FD_MPIO(f) /* (H5F_t *f) */ \ + (H5FD_MPIO==H5F_get_driver_id(f)) + +#ifdef H5_HAVE_PARALLEL /*Turn on H5FDmpio_debug if H5F_DEBUG is on */ #ifdef H5F_DEBUG #ifndef H5FDmpio_DEBUG @@ -43,9 +47,6 @@ typedef struct H5FD_mpio_dxpl_t { #endif #endif -#define IS_H5FD_MPIO(f) /* (H5F_t *f) */ \ - (H5FD_MPIO==H5F_get_driver_id(f)) - /* Function prototypes */ #ifdef __cplusplus extern "C" { diff --git a/src/H5FDmpiposix.h b/src/H5FDmpiposix.h index 81d05d4..3f262e1 100644 --- a/src/H5FDmpiposix.h +++ b/src/H5FDmpiposix.h @@ -31,13 +31,13 @@ # define H5FD_MPIPOSIX (-1) #endif -#ifdef H5_HAVE_PARALLEL - /* Macros */ #define IS_H5FD_MPIPOSIX(f) /* (H5F_t *f) */ \ (H5FD_MPIPOSIX==H5F_get_driver_id(f)) +#ifdef H5_HAVE_PARALLEL + /* Function prototypes */ #ifdef __cplusplus extern "C" { diff --git a/src/H5Farray.c b/src/H5Farray.c index e3657d0..8e01099 100644 --- a/src/H5Farray.c +++ b/src/H5Farray.c @@ -20,7 +20,6 @@ #include "H5Fpkg.h" #include "H5FDprivate.h" /*file driver */ #include "H5Iprivate.h" -#include "H5MFprivate.h" #include "H5MMprivate.h" /*memory management */ #include "H5Oprivate.h" #include "H5Pprivate.h" @@ -37,69 +36,6 @@ static int interface_initialize_g = 0; /*------------------------------------------------------------------------- - * Function: H5F_arr_create - * - * Purpose: Creates an array of bytes. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Friday, January 16, 1998 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/) -{ - unsigned u; - hsize_t nbytes; - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5F_arr_create, FAIL); - - /* check args */ - assert (f); - assert (layout); - layout->addr = HADDR_UNDEF; /*just in case we fail*/ - - switch (layout->type) { - case H5D_CONTIGUOUS: - /* Reserve space in the file for the entire array */ - for (u=0, nbytes=1; u<layout->ndims; u++) - nbytes *= layout->dim[u]; - assert (nbytes>0); - if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, nbytes))) - HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); - break; - - case H5D_CHUNKED: - /* Create the root of the B-tree that describes chunked storage */ - if (H5F_istore_create (f, layout/*out*/)<0) - HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage"); - break; - - case H5D_COMPACT: - /* Reserve space in layout header message for the entire array. */ - assert(layout->size>0); - if (NULL==(layout->buf=H5MM_malloc(layout->size))) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "unable to allocate memory for compact dataset"); - layout->dirty = TRUE; - break; - - default: - assert ("not implemented yet" && 0); - HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, - "unsupported storage layout"); - } /* end switch */ - -done: - FUNC_LEAVE (ret_value); -} - - -/*------------------------------------------------------------------------- * Function: H5F_arr_read * * Purpose: Reads a hyperslab of a file byte array into a hyperslab of diff --git a/src/H5Fcompact.c b/src/H5Fcompact.c index 3a36edb..0a21211 100644 --- a/src/H5Fcompact.c +++ b/src/H5Fcompact.c @@ -44,9 +44,9 @@ static int interface_initialize_g = 0; *------------------------------------------------------------------------- */ herr_t -H5F_compact_readv(H5F_t *f, const H5O_layout_t *layout, size_t nseq, +H5F_compact_readv(H5F_t UNUSED *f, const H5O_layout_t *layout, size_t nseq, size_t size_arr[], hsize_t offset_arr[], - hid_t dxpl_id, void *_buf/*out*/) + hid_t UNUSED dxpl_id, void *_buf/*out*/) { unsigned char *buf=(unsigned char *)_buf; size_t size; @@ -93,11 +93,11 @@ done: *------------------------------------------------------------------------- */ herr_t -H5F_compact_writev(H5F_t *f, H5O_layout_t *layout, size_t nseq, +H5F_compact_writev(H5F_t UNUSED *f, H5O_layout_t *layout, size_t nseq, size_t size_arr[], hsize_t offset_arr[], - hid_t dxpl_id, const void *_buf) + hid_t UNUSED dxpl_id, const void *_buf) { - unsigned char *buf=(unsigned char *)_buf; + const unsigned char *buf=(const unsigned char *)_buf; size_t size; haddr_t offset; unsigned u; diff --git a/src/H5Fcontig.c b/src/H5Fcontig.c index 89f9fc5..fce1ba9 100644 --- a/src/H5Fcontig.c +++ b/src/H5Fcontig.c @@ -14,11 +14,19 @@ #define H5F_PACKAGE /*suppress error about including H5Fpkg */ -#include "H5private.h" -#include "H5Eprivate.h" +#include "H5private.h" /* Generic Functions */ +#include "H5Dprivate.h" /* Dataset functions */ +#include "H5Eprivate.h" /* Error handling */ #include "H5Fpkg.h" #include "H5FDprivate.h" /*file driver */ #include "H5FLprivate.h" /*Free Lists */ +#include "H5Oprivate.h" /* Object headers */ +#include "H5Pprivate.h" /* Property lists */ +#include "H5Vprivate.h" /* Vector and array functions */ + +/* MPIO & MPIPOSIX drivers needed for special checks */ +#include "H5FDmpio.h" +#include "H5FDmpiposix.h" /* Interface initialization */ #define PABLO_MASK H5Fcontig_mask @@ -28,6 +36,187 @@ static int interface_initialize_g = 0; /* Declare a PQ free list to manage the sieve buffer information */ H5FL_BLK_DEFINE(sieve_buf); +/* Extern the free list to manage blocks of type conversion data */ +H5FL_BLK_EXTERN(type_conv); + + +/*------------------------------------------------------------------------- + * Function: H5F_contig_fill + * + * Purpose: Write fill values to a contiguously stored dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * August 22, 2002 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5F_contig_fill(H5F_t *f, hid_t dxpl_id, struct H5O_layout_t *layout, + struct H5P_genplist_t *dc_plist, const struct H5S_t *space, + size_t elmt_size) +{ + H5O_fill_t fill; /* Fill value information */ + H5O_efl_t efl; /* External File List info */ + hssize_t snpoints; /* Number of points in space (for error checking) */ + size_t npoints; /* Number of points in space */ + size_t ptsperbuf; /* Maximum # of points which fit in the buffer */ + size_t bufsize=64*1024; /* Size of buffer to write */ + size_t size; /* Current # of points to write */ + hsize_t addr; /* Offset in dataset */ + void *buf = NULL; /* Buffer for fill value writing */ +#ifdef H5_HAVE_PARALLEL + MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ + int mpi_rank=(-1); /* This process's rank */ + int mpi_size=(-1); /* Total # of processes */ + int mpi_round=0; /* Current process responsible for I/O */ + int mpi_code; /* MPI return code */ + unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */ + unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ +#endif /* H5_HAVE_PARALLEL */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5F_contig_fill, FAIL); + + /* Check args */ + assert(f); + assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); + assert(layout && H5D_CONTIGUOUS==layout->type); + assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); + assert(H5F_addr_defined(layout->addr)); + assert(dc_plist!=NULL); + assert(space); + assert(elmt_size>0); + + /* Get necessary properties from dataset creation property list */ + if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get fill value"); + if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); + +#ifdef H5_HAVE_PARALLEL + /* Retrieve up MPI parameters */ + if(IS_H5FD_MPIO(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ + if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); + if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + else { + if(IS_H5FD_MPIPOSIX(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ + if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); + if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + + /* Get the number of elements in the dataset's dataspace */ + snpoints = H5S_get_simple_extent_npoints(space); + assert(snpoints>=0); + H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); + + /* Don't write default fill-values to external files */ + if(efl.nused>0 && !fill.buf) + HGOTO_DONE(SUCCEED); + + /* If fill value is library default, use the element size */ + if(!fill.buf) + fill.size=elmt_size; + + /* + * Fill the entire current extent with the fill value. We can do + * this quite efficiently by making sure we copy the fill value + * in relatively large pieces. + */ + ptsperbuf = MAX(1, bufsize/fill.size); + bufsize = ptsperbuf*fill.size; + + /* Allocate temporary buffer */ + if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); + + /* Fill the buffer with the user's fill value */ + if(fill.buf) + H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf); + else /* Fill the buffer with the default fill value */ + HDmemset(buf,0,bufsize); + + /* Start at the beginning of the dataset */ + addr = 0; + + /* Loop through writing the fill value to the dataset */ + while (npoints>0) { + size = MIN(ptsperbuf, npoints) * fill.size; + +#ifdef H5_HAVE_PARALLEL + /* Check if this file is accessed with an MPI-capable file driver */ + if(using_mpi) { + /* Round-robin write the chunks out from only one process */ + if(mpi_round==mpi_rank) { + if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space, + fill.size, size, addr, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); + } /* end if */ + mpi_round=(++mpi_round)%mpi_size; + + /* Indicate that blocks are being written */ + blocks_written=1; + } /* end if */ + else { +#endif /* H5_HAVE_PARALLEL */ + if (H5F_seq_write(f, dxpl_id, layout, dc_plist, space, + fill.size, size, addr, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); +#ifdef H5_HAVE_PARALLEL + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + + npoints -= MIN(ptsperbuf, npoints); + addr += size; + } /* end while */ + +#ifdef H5_HAVE_PARALLEL + /* Only need to block at the barrier if we actually wrote fill values */ + /* And if we are using an MPI-capable file driver */ + if(using_mpi && blocks_written) { + /* Wait at barrier to avoid race conditions where some processes are + * still writing out fill values and other processes race ahead to data + * in, getting bogus data. + */ + if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ + +done: + /* Free the buffer for fill values */ + if (buf) + H5FL_BLK_FREE(type_conv,buf); + + FUNC_LEAVE(ret_value); +} + /*------------------------------------------------------------------------- * Function: H5F_contig_read diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 0bba74e..f36b6200 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -1758,7 +1758,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 && chunk_addr!=HADDR_UNDEF) -#ifdef H5_HAVE_PARALLEL /* * If MPIO or MPIPOSIX is used and file can be written to, we must bypass the * chunk-cache scheme because other MPI processes could be writing to @@ -1766,7 +1765,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * Do a direct write-through of only the elements requested. */ || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags)) -#endif /* H5_HAVE_PARALLEL */ ) { H5O_layout_t l; /* temporary layout */ @@ -1942,14 +1940,12 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 && chunk_addr!=HADDR_UNDEF) -#ifdef H5_HAVE_PARALLEL /* * If MPIO or MPIPOSIX is used, must bypass the chunk-cache scheme because other * MPI processes could be writing to other elements in the same chunk. * Do a direct write-through of only the elements requested. */ || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags)) -#endif /* H5_HAVE_PARALLEL */ ) { H5O_layout_t l; /* temporary layout */ @@ -2334,6 +2330,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, H5P_genplist_t *dx_plist; /* Data xfer property list */ double split_ratios[3];/* B-tree node splitting ratios */ #ifdef H5_HAVE_PARALLEL + MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ int mpi_rank=(-1); /* This process's rank */ int mpi_size=(-1); /* Total # of processes */ int mpi_round=0; /* Current process responsible for I/O */ @@ -2342,6 +2339,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ #endif /* H5_HAVE_PARALLEL */ int carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */ + unsigned chunk_exists; /* Flag to indicate whether a chunk exists already */ int i; /* Local index variable */ unsigned u; /* Local index variable */ herr_t ret_value=SUCCEED; /* Return value */ @@ -2374,6 +2372,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, #ifdef H5_HAVE_PARALLEL /* Retrieve up MPI parameters */ if(IS_H5FD_MPIO(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + + /* Get the MPI rank & size */ if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0) @@ -2384,6 +2387,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end if */ else { if(IS_H5FD_MPIPOSIX(f)) { + /* Get the MPI communicator */ + if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf))) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); + /* Get the MPI rank & size */ if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); @@ -2396,12 +2403,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end else */ #endif /* H5_HAVE_PARALLEL */ -#ifdef H5_HAVE_PARALLEL - /* Can't use data I/O pipeline in parallel (yet) */ - if (using_mpi && pline.nfilters>0) - HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, FAIL, "can't use data pipeline in parallel"); -#endif /* H5_HAVE_PARALLEL */ - /* * Setup indice to go through all chunks. (Future improvement * should allocate only chunks that have no file space assigned yet. @@ -2450,8 +2451,32 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, /* Loop over all chunks */ carry=0; while (carry==0) { - /* Check if the chunk exists yet */ + /* Check if the chunk exists yet on disk */ + chunk_exists=1; if(H5F_istore_get_addr(f,layout,chunk_offset)==HADDR_UNDEF) { + H5F_rdcc_t *rdcc = &(f->shared->rdcc); /*raw data chunk cache */ + H5F_rdcc_ent_t *ent = NULL; /*cache entry */ + + /* Didn't find the chunk on disk */ + chunk_exists = 0; + + /* Look for chunk in cache */ + for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) { + /* Make certain we are dealing with the correct B-tree, etc */ + if (layout->ndims==ent->layout->ndims && + H5F_addr_eq(layout->addr, ent->layout->addr)) { + + /* Assume a match */ + chunk_exists = 1; + for(u = 0; u < layout->ndims && chunk_exists; u++) { + if(ent->offset[u] != chunk_offset[u]) + chunk_exists = 0; /* Reset if no match */ + } /* end for */ + } /* end if */ + } /* end for */ + } /* end if */ + + if(!chunk_exists) { /* Initialize the chunk information */ udata.mesg = *layout; udata.key.filter_mask = 0; @@ -2507,17 +2532,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, * still writing out chunks and other processes race ahead to read * them in, getting bogus data. */ - if(IS_H5FD_MPIO(f)) { - if (MPI_SUCCESS != (mpi_code=MPI_Barrier(H5FD_mpio_communicator(f->shared->lf)))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); - } /* end if */ - else { - /* Sanity Check */ - assert(IS_H5FD_MPIPOSIX(f)); - - if (MPI_SUCCESS!=(mpi_code=MPI_Barrier(H5FD_mpiposix_communicator(f->shared->lf)))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); - } /* end else */ + if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); } /* end if */ #endif /* H5_HAVE_PARALLEL */ @@ -2662,13 +2678,17 @@ H5F_istore_prune_by_extent(H5F_t *f, const H5O_layout_t *layout, const H5S_t * s for(ent = rdcc->head; ent; ent = next) { next = ent->next; - found = 0; - for(u = 0; u < ent->layout->ndims - 1; u++) { - if((hsize_t)ent->offset[u] > curr_dims[u]) { - found = 1; - break; - } - } + /* Make certain we are dealing with the correct B-tree, etc */ + if (layout->ndims==ent->layout->ndims && + H5F_addr_eq(layout->addr, ent->layout->addr)) { + found = 0; + for(u = 0; u < ent->layout->ndims - 1; u++) { + if((hsize_t)ent->offset[u] > curr_dims[u]) { + found = 1; + break; + } + } + } /* end if */ if(found) { #if defined (H5F_ISTORE_DEBUG) diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h index 92e6a5b..fb2c58d 100644 --- a/src/H5Fpkg.h +++ b/src/H5Fpkg.h @@ -183,8 +183,6 @@ __DLL__ herr_t H5F_istore_init (H5F_t *f); __DLL__ herr_t H5F_istore_flush (H5F_t *f, hbool_t preempt); __DLL__ herr_t H5F_istore_dest (H5F_t *f); __DLL__ herr_t H5F_istore_stats (H5F_t *f, hbool_t headers); -__DLL__ herr_t H5F_istore_create(H5F_t *f, - struct H5O_layout_t *layout/*in,out*/); __DLL__ herr_t H5F_istore_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, struct H5P_genplist_t *dc_plist, diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 15ef548..b3a48f3 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -345,8 +345,6 @@ __DLL__ herr_t H5F_get_obj_count(H5F_t *f, unsigned types, __DLL__ herr_t H5F_get_obj_ids(H5F_t *f, unsigned types, hid_t *obj_id_list); /* Functions that operate on array storage */ -__DLL__ herr_t H5F_arr_create(H5F_t *f, - struct H5O_layout_t *layout /*in,out*/); __DLL__ herr_t H5F_arr_read (H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, struct H5P_genplist_t *dc_plist, @@ -393,7 +391,14 @@ __DLL__ herr_t H5F_seq_writev(H5F_t *f, hid_t dxpl_id, size_t seq_len[], hsize_t file_offset[], const void *_buf); +/* Functions that operate on contiguous storage */ +__DLL__ herr_t H5F_contig_fill(H5F_t *f, hid_t dxpl_id, + struct H5O_layout_t *layout, struct H5P_genplist_t *dc_plist, + const struct H5S_t *space, size_t elmt_size); + /* Functions that operate on indexed storage */ +__DLL__ herr_t H5F_istore_create(H5F_t *f, + struct H5O_layout_t *layout/*in,out*/); __DLL__ herr_t H5F_istore_allocate (H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, const hsize_t *space_dim, diff --git a/src/H5Oefl.c b/src/H5Oefl.c index eacdeb3..388aa4a 100644 --- a/src/H5Oefl.c +++ b/src/H5Oefl.c @@ -532,7 +532,7 @@ H5O_efl_write (H5F_t UNUSED *f, const H5O_efl_t *efl, haddr_t addr, HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "write past logical end of file"); if (H5F_OVERFLOW_HSIZET2OFFT (efl->slot[i].offset+skip)) HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed"); - if ((fd=HDopen (efl->slot[i].name, O_RDWR, 0))<0) { + if ((fd=HDopen (efl->slot[i].name, O_CREAT|O_RDWR, 0666))<0) { if (HDaccess (efl->slot[i].name, F_OK)<0) { HGOTO_ERROR (H5E_EFL, H5E_CANTOPENFILE, FAIL, "external raw data file does not exist"); } else { diff --git a/src/H5Olayout.c b/src/H5Olayout.c index 65f4cdb..33797c6 100644 --- a/src/H5Olayout.c +++ b/src/H5Olayout.c @@ -211,7 +211,6 @@ H5O_layout_encode(H5F_t *f, uint8_t *p, const void *_mesg) if(mesg->type==H5D_COMPACT) { UINT32ENCODE(p, mesg->size); if(mesg->size>0 && mesg->buf) { - H5_CHECK_OVERFLOW(mesg->size,ssize_t,size_t); HDmemcpy(p, mesg->buf, mesg->size); p += mesg->size; } @@ -1899,11 +1899,11 @@ done: * *------------------------------------------------------------------------- */ -herr_t +int H5S_set_extent( H5S_t *space, const hsize_t *size ) { unsigned u; - herr_t ret_value=SUCCEED; + herr_t ret_value=0; FUNC_ENTER_NOAPI( H5S_set_extent, FAIL ); @@ -1911,19 +1911,21 @@ H5S_set_extent( H5S_t *space, const hsize_t *size ) assert( space && H5S_SIMPLE==space->extent.type ); assert( size); - /* Check for changing dimensions of a scalar dataspace */ - if(space->extent.u.simple.rank==0) - /* Verify that the dimensions being changed are allowed to change */ - for ( u = 0; u < space->extent.u.simple.rank; u++ ) + for ( u = 0; u < space->extent.u.simple.rank; u++ ) { if ( space->extent.u.simple.max && H5S_UNLIMITED != space->extent.u.simple.max[u] && - space->extent.u.simple.max[u]<size[u] ) + space->extent.u.simple.max[u]!=size[u] ) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,"dimension cannot be modified"); + ret_value++; + } /* end for */ - /* Update dimensions with new values */ - for ( u = 0; u < space->extent.u.simple.rank; u++ ) - space->extent.u.simple.size[u] = size[u]; + /* Update */ + if (ret_value) { + /* Update dimensions with new values */ + for ( u = 0; u < space->extent.u.simple.rank; u++ ) + space->extent.u.simple.size[u] = size[u]; + } /* end if */ done: FUNC_LEAVE( ret_value ); diff --git a/src/H5Smpio.c b/src/H5Smpio.c index 61297bb..125c946 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -915,7 +915,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5S_mpio_spaces_write(H5F_t *f, const H5O_layout_t *layout, +H5S_mpio_spaces_write(H5F_t *f, H5O_layout_t *layout, H5P_genplist_t UNUSED *dc_plist, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, const void *buf) diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 393f6bb..083847e 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -109,7 +109,7 @@ typedef struct H5S_conv_t { /* Write directly from app buffer to file */ - herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout, + herr_t (*write)(H5F_t *f, struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, const void *buf); @@ -156,7 +156,7 @@ __DLL__ int H5S_cmp(const H5S_t *ds1, const H5S_t *ds2); __DLL__ htri_t H5S_is_simple(const H5S_t *sdim); __DLL__ herr_t H5S_extent_release(H5S_t *space); __DLL__ int H5S_extend(H5S_t *space, const hsize_t *size); -__DLL__ herr_t H5S_set_extent(H5S_t *space, const hsize_t *size); +__DLL__ int H5S_set_extent(H5S_t *space, const hsize_t *size); __DLL__ herr_t H5S_debug(H5F_t *f, const void *_mesg, FILE *stream, int indent, int fwidth); @@ -168,7 +168,7 @@ __DLL__ herr_t H5S_select_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, void *operator_data); __DLL__ herr_t H5S_select_fill(void *fill, size_t fill_size, const H5S_t *space, void *buf); -__DLL__ herr_t H5S_select_fscat (H5F_t *f, const struct H5O_layout_t *layout, +__DLL__ herr_t H5S_select_fscat (H5F_t *f, struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, const void *_buf); @@ -185,7 +185,7 @@ __DLL__ hsize_t H5S_select_mgath (const void *_buf, size_t elmt_size, __DLL__ herr_t H5S_select_read(H5F_t *f, const struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/); -__DLL__ herr_t H5S_select_write(H5F_t *f, const struct H5O_layout_t *layout, +__DLL__ herr_t H5S_select_write(H5F_t *f, struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, const void *buf/*out*/); @@ -206,7 +206,7 @@ __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f, /* MPI-IO function to write directly from app buffer to file rky980813 */ __DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f, - const struct H5O_layout_t *layout, + struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, diff --git a/src/H5Sselect.c b/src/H5Sselect.c index 10ece00..70888e8 100644 --- a/src/H5Sselect.c +++ b/src/H5Sselect.c @@ -777,7 +777,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5S_select_fscat (H5F_t *f, const struct H5O_layout_t *layout, +H5S_select_fscat (H5F_t *f, struct H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *space, H5S_sel_iter_t *iter, hsize_t nelmts, hid_t dxpl_id, const void *_buf) @@ -1365,7 +1365,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5S_select_write(H5F_t *f, const H5O_layout_t *layout, H5P_genplist_t *dc_plist, +H5S_select_write(H5F_t *f, H5O_layout_t *layout, H5P_genplist_t *dc_plist, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, const void *_buf/*out*/) { |