diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5D.c | 33 | ||||
| -rw-r--r-- | src/H5Distore.c | 30 | ||||
| -rw-r--r-- | src/H5Dprivate.h | 1 | ||||
| -rw-r--r-- | src/H5E.c | 2 | ||||
| -rw-r--r-- | src/H5Epublic.h | 2 | ||||
| -rw-r--r-- | src/H5Farray.c | 23 | ||||
| -rw-r--r-- | src/H5Fistore.c | 30 | ||||
| -rw-r--r-- | src/H5Fprivate.h | 14 | ||||
| -rw-r--r-- | src/H5O.c | 2 | ||||
| -rw-r--r-- | src/H5Ofill.c | 328 | ||||
| -rw-r--r-- | src/H5Omtime.c | 4 | ||||
| -rw-r--r-- | src/H5Oprivate.h | 16 | ||||
| -rw-r--r-- | src/H5P.c | 212 | ||||
| -rw-r--r-- | src/H5Ppublic.h | 2 | ||||
| -rw-r--r-- | src/H5Sall.c | 25 | ||||
| -rw-r--r-- | src/H5Shyper.c | 70 | ||||
| -rw-r--r-- | src/H5Spoint.c | 26 | ||||
| -rw-r--r-- | src/H5Sprivate.h | 2 | ||||
| -rw-r--r-- | src/H5Tconv.c | 4 | ||||
| -rw-r--r-- | src/H5V.c | 6 | ||||
| -rw-r--r-- | src/Makefile.in | 2 |
21 files changed, 735 insertions, 99 deletions
@@ -56,6 +56,9 @@ const H5D_create_t H5D_create_dflt = { 1, 1, 1, 1, 1, 1, 1, 1, /*...produce fewer, but larger I/O......*/ 1, 1, 1, 1, 1, 1, 1, 1}, /*...requests. */ + /* Fill value */ + {NULL, 0, NULL}, /* No fill value */ + /* External file list */ {H5F_ADDR_UNDEF, /* External file list heap address */ 0, /*...slots allocated */ @@ -531,6 +534,14 @@ H5Dget_create_plist(hid_t dset_id) "unable to copy the creation property list"); } + /* Copy the dataset type into the fill value message */ + if (!copied_parms->fill.type && + NULL==(copied_parms->fill.type=H5T_copy(dset->type, + H5T_COPY_TRANSIENT))) { + HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to copy dataset data type for fill value"); + } + /* Create an atom */ if ((ret_value=H5I_register ((H5I_group_t)(H5_TEMPLATE_0+ H5P_DATASET_CREATE), @@ -944,6 +955,17 @@ H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, "unable to create dataset object header"); } + /* Convert the fill value to the dataset type and write the message */ + if (H5O_fill_convert(&(new_dset->create_parms->fill), new_dset->type)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, + "unable to convert fill value to dataset type"); + } + if (H5O_modify(&(new_dset->ent), H5O_FILL, 0, H5O_FLAG_CONSTANT, + &(new_dset->create_parms->fill))<0) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, + "unable to update fill value header message"); + } + /* Update the type and space header messages */ if (H5O_modify(&(new_dset->ent), H5O_DTYPE, 0, H5O_FLAG_CONSTANT|H5O_FLAG_SHARED, new_dset->type)<0 || @@ -1105,6 +1127,14 @@ H5D_open(H5G_entry_t *loc, const char *name) "unable to read data space info from dataset header"); } + /* Get the optional fill value message */ + if (NULL==H5O_read(&(dataset->ent), H5O_FILL, 0, + &(dataset->create_parms->fill))) { + H5E_clear(); + HDmemset(&(dataset->create_parms->fill), 0, + sizeof(dataset->create_parms->fill)); + } + /* Get the optional filters message */ if (NULL==H5O_read (&(dataset->ent), H5O_PLINE, 0, &(dataset->create_parms->pline))) { @@ -1513,6 +1543,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #endif n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), + &(dataset->create_parms->fill), &(dataset->create_parms->efl), src_type_size, file_space, &file_iter, smine_nelmts, xfer_parms, tconv_buf/*out*/); @@ -1913,6 +1944,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #endif n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), + &(dataset->create_parms->fill), &(dataset->create_parms->efl), dst_type_size, file_space, &bkg_iter, smine_nelmts, xfer_parms, bkg_buf/*out*/); @@ -1955,6 +1987,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, #endif status = (sconv->f->scat)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), + &(dataset->create_parms->fill), &(dataset->create_parms->efl), dst_type_size, file_space, &file_iter, smine_nelmts, xfer_parms, tconv_buf); diff --git a/src/H5Distore.c b/src/H5Distore.c index 88399fd..ebfb004 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -1170,8 +1170,8 @@ H5F_istore_prune (H5F_t *f, size_t size) static void * H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, const double split_ratios[], const H5O_pline_t *pline, - const hssize_t offset[], hbool_t relax, - intn *idx_hint/*in,out*/) + const H5O_fill_t *fill, const hssize_t offset[], + hbool_t relax, intn *idx_hint/*in,out*/) { uintn idx; /*hash index number */ hbool_t found = FALSE; /*already in cache? */ @@ -1268,9 +1268,20 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, "data pipeline read failed"); } rdcc->nmisses++; + } else if (fill && fill->buf) { + /* + * The chunk doesn't exist in the file. Replicate the fill + * value throughout the chunk. + */ + assert(0==chunk_size % fill->size); + H5V_array_fill(chunk, fill->buf, fill->size, + chunk_size/fill->size); + rdcc->ninits++; + } else { /* - * The chunk doesn't exist in the file. Assume all zeros. + * The chunk doesn't exist in the file and no fill value was + * specified. Assume all zeros. */ HDmemset (chunk, 0, chunk_size); rdcc->ninits++; @@ -1510,8 +1521,8 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, - const H5O_pline_t *pline, const hssize_t offset_f[], - const hsize_t size[], void *buf) + const H5O_pline_t *pline, const H5O_fill_t *fill, + const hssize_t offset_f[], const hsize_t size[], void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; hsize_t size_m[H5O_LAYOUT_NDIMS]; @@ -1635,7 +1646,7 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, * the chunk. */ if (NULL==(chunk=H5F_istore_lock (f, layout, xfer->split_ratios, - pline, chunk_offset, + pline, fill, chunk_offset, FALSE, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk"); @@ -1682,8 +1693,9 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, */ herr_t H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, - const H5O_pline_t *pline, const hssize_t offset_f[], - const hsize_t size[], const void *buf) + const H5O_pline_t *pline, const H5O_fill_t *fill, + const hssize_t offset_f[], const hsize_t size[], + const void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; hsize_t size_m[H5O_LAYOUT_NDIMS]; @@ -1811,7 +1823,7 @@ H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, * chunk. */ if (NULL==(chunk=H5F_istore_lock (f, layout, xfer->split_ratios, - pline, chunk_offset, + pline, fill, chunk_offset, naccessed==chunk_size, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index c647cf0..2f65c7a 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -45,6 +45,7 @@ typedef struct H5D_create_t { H5D_layout_t layout; /*storage layout */ intn chunk_ndims; /*chunk dimensionality */ hsize_t chunk_size[32]; /*chunk size if chunked storage */ + H5O_fill_t fill; /*fill value */ H5O_efl_t efl; /*external file list */ H5O_pline_t pline; /*data filter pipeline */ } H5D_create_t; @@ -53,7 +53,7 @@ static const H5E_major_mesg_t H5E_major_mesg_g[] = { {H5E_DATASPACE, "Dataspace interface"}, {H5E_DATASET, "Dataset interface"}, {H5E_STORAGE, "Data storage layer"}, - {H5E_TEMPLATE, "Property list interface"}, + {H5E_PLIST, "Property list interface"}, {H5E_ATTR, "Attribute layer"}, {H5E_PLINE, "Data filters layer"}, {H5E_EFL, "External file list"}, diff --git a/src/H5Epublic.h b/src/H5Epublic.h index 6415b60..a31317f 100644 --- a/src/H5Epublic.h +++ b/src/H5Epublic.h @@ -70,7 +70,7 @@ typedef enum H5E_major_t { H5E_DATASPACE, /*Dataspace */ H5E_DATASET, /*Dataset */ H5E_STORAGE, /*data storage */ - H5E_TEMPLATE, /*Property lists */ + H5E_PLIST, /*Property lists */ H5E_ATTR, /*Attribute */ H5E_PLINE, /*Data filters */ H5E_EFL, /*External file list */ diff --git a/src/H5Farray.c b/src/H5Farray.c index b3ebcff..2a2cd1c 100644 --- a/src/H5Farray.c +++ b/src/H5Farray.c @@ -119,10 +119,10 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/) herr_t H5F_arr_read (H5F_t *f, const H5D_xfer_t *xfer, const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, - const hsize_t _hslab_size[], const hsize_t mem_size[], - const hssize_t mem_offset[], const hssize_t file_offset[], - void *_buf/*out*/) + const struct H5O_pline_t *pline, const H5O_fill_t *fill, + const struct H5O_efl_t *efl, const hsize_t _hslab_size[], + const hsize_t mem_size[], const hssize_t mem_offset[], + const hssize_t file_offset[], void *_buf/*out*/) { uint8 *buf = (uint8 *)_buf; /*cast for arithmetic */ hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ @@ -292,8 +292,8 @@ H5F_arr_read (H5F_t *f, const H5D_xfer_t *xfer, "unable to copy into a proper hyperslab"); } } - if (H5F_istore_read (f, xfer, layout, pline, file_offset, hslab_size, - buf)<0) { + if (H5F_istore_read (f, xfer, layout, pline, fill, file_offset, + hslab_size, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } break; @@ -344,9 +344,10 @@ herr_t H5F_arr_write (H5F_t *f, const H5D_xfer_t *xfer, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, const hsize_t _hslab_size[], - const hsize_t mem_size[], const hssize_t mem_offset[], - const hssize_t file_offset[], const void *_buf) + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, + const hsize_t _hslab_size[], const hsize_t mem_size[], + const hssize_t mem_offset[], const hssize_t file_offset[], + const void *_buf) { const uint8 *buf = (const uint8 *)_buf; /*cast for arithmetic */ hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ @@ -522,8 +523,8 @@ H5F_arr_write (H5F_t *f, const H5D_xfer_t *xfer, "unable to copy from a proper hyperslab"); } } - if (H5F_istore_write (f, xfer, layout, pline, file_offset, hslab_size, - buf)<0) { + if (H5F_istore_write (f, xfer, layout, pline, fill, file_offset, + hslab_size, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); } diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 88399fd..ebfb004 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -1170,8 +1170,8 @@ H5F_istore_prune (H5F_t *f, size_t size) static void * H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, const double split_ratios[], const H5O_pline_t *pline, - const hssize_t offset[], hbool_t relax, - intn *idx_hint/*in,out*/) + const H5O_fill_t *fill, const hssize_t offset[], + hbool_t relax, intn *idx_hint/*in,out*/) { uintn idx; /*hash index number */ hbool_t found = FALSE; /*already in cache? */ @@ -1268,9 +1268,20 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, "data pipeline read failed"); } rdcc->nmisses++; + } else if (fill && fill->buf) { + /* + * The chunk doesn't exist in the file. Replicate the fill + * value throughout the chunk. + */ + assert(0==chunk_size % fill->size); + H5V_array_fill(chunk, fill->buf, fill->size, + chunk_size/fill->size); + rdcc->ninits++; + } else { /* - * The chunk doesn't exist in the file. Assume all zeros. + * The chunk doesn't exist in the file and no fill value was + * specified. Assume all zeros. */ HDmemset (chunk, 0, chunk_size); rdcc->ninits++; @@ -1510,8 +1521,8 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, - const H5O_pline_t *pline, const hssize_t offset_f[], - const hsize_t size[], void *buf) + const H5O_pline_t *pline, const H5O_fill_t *fill, + const hssize_t offset_f[], const hsize_t size[], void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; hsize_t size_m[H5O_LAYOUT_NDIMS]; @@ -1635,7 +1646,7 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, * the chunk. */ if (NULL==(chunk=H5F_istore_lock (f, layout, xfer->split_ratios, - pline, chunk_offset, + pline, fill, chunk_offset, FALSE, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk"); @@ -1682,8 +1693,9 @@ H5F_istore_read(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, */ herr_t H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, - const H5O_pline_t *pline, const hssize_t offset_f[], - const hsize_t size[], const void *buf) + const H5O_pline_t *pline, const H5O_fill_t *fill, + const hssize_t offset_f[], const hsize_t size[], + const void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; hsize_t size_m[H5O_LAYOUT_NDIMS]; @@ -1811,7 +1823,7 @@ H5F_istore_write(H5F_t *f, const H5D_xfer_t *xfer, const H5O_layout_t *layout, * chunk. */ if (NULL==(chunk=H5F_istore_lock (f, layout, xfer->split_ratios, - pline, chunk_offset, + pline, fill, chunk_offset, naccessed==chunk_size, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 9513689..ca787f7 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -503,10 +503,12 @@ typedef struct H5F_t { case 2: UINT16DECODE(p,l); break; \ } -struct H5O_layout_t; /*forward decl for prototype arguments */ -struct H5O_efl_t; /*forward decl for prototype arguments */ -struct H5O_pline_t; /*forward decl for prototype arguments */ -struct H5D_xfer_t; /*forward decl for prototype arguments */ +/* Forward declarations for prototypes arguments */ +struct H5O_layout_t; +struct H5O_efl_t; +struct H5O_pline_t; +struct H5D_xfer_t; +struct H5O_fill_t; /* library variables */ extern const H5F_create_t H5F_create_dflt; @@ -533,12 +535,14 @@ herr_t H5F_arr_create(H5F_t *f, struct H5O_layout_t *layout /*in,out*/); herr_t H5F_arr_read (H5F_t *f, const struct H5D_xfer_t *xfer, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, const hsize_t _hslab_size[], const hsize_t mem_size[], const hssize_t mem_offset[], const hssize_t file_offset[], void *_buf/*out*/); herr_t H5F_arr_write (H5F_t *f, const struct H5D_xfer_t *xfer, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, const hsize_t _hslab_size[], const hsize_t mem_size[], const hssize_t mem_offset[], const hssize_t file_offset[], const void *_buf); @@ -552,11 +556,13 @@ herr_t H5F_istore_create(H5F_t *f, struct H5O_layout_t *layout /*in,out*/); herr_t H5F_istore_read(H5F_t *f, const struct H5D_xfer_t *xfer, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const hssize_t offset[], const hsize_t size[], void *buf /*out */ ); herr_t H5F_istore_write(H5F_t *f, const struct H5D_xfer_t *xfer, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const hssize_t offset[], const hsize_t size[], const void *buf); herr_t H5F_istore_allocate (H5F_t *f, @@ -55,7 +55,7 @@ static const H5O_class_t *const message_type_g[] = { H5O_SDSPACE, /*0x0001 Simple Dimensionality */ NULL, /*0x0002 Data space (fiber bundle?) */ H5O_DTYPE, /*0x0003 Data Type */ - NULL, /*0x0004 Not assigned */ + H5O_FILL, /*0x0004 Data storage -- fill value */ NULL, /*0x0005 Not assigned */ NULL, /*0x0006 Data storage -- compact object */ H5O_EFL, /*0x0007 Data storage -- external data files */ diff --git a/src/H5Ofill.c b/src/H5Ofill.c new file mode 100644 index 0000000..1328307 --- /dev/null +++ b/src/H5Ofill.c @@ -0,0 +1,328 @@ +/* + * Copyright (C) 1998 NCSA + * All rights reserved. + * + * Programmer: Robb Matzke <matzke@llnl.gov> + * Wednesday, September 30, 1998 + * + * Purpose: The fill message indicates a bit pattern to use for + * uninitialized data points of a dataset. + */ +#include <H5private.h> +#include <H5Eprivate.h> +#include <H5MMprivate.h> +#include <H5Oprivate.h> + +#define PABLO_MASK H5O_fill_mask + +static void *H5O_fill_decode(H5F_t *f, const uint8 *p, H5O_shared_t *sh); +static herr_t H5O_fill_encode(H5F_t *f, uint8 *p, const void *_mesg); +static void *H5O_fill_copy(const void *_mesg, void *_dest); +static size_t H5O_fill_size(H5F_t *f, const void *_mesg); +static herr_t H5O_fill_reset(void *_mesg); +static herr_t H5O_fill_debug(H5F_t *f, const void *_mesg, FILE *stream, + intn indent, intn fwidth); + +/* This message derives from H5O */ +const H5O_class_t H5O_FILL[1] = {{ + H5O_FILL_ID, /*message id number */ + "fill", /*message name for debugging */ + sizeof(H5O_fill_t), /*native message size */ + H5O_fill_decode, /*decode message */ + H5O_fill_encode, /*encode message */ + H5O_fill_copy, /*copy the native value */ + H5O_fill_size, /*raw message size */ + H5O_fill_reset, /*free internal memory */ + NULL, /*get share method */ + NULL, /*set share method */ + H5O_fill_debug, /*debug the message */ +}}; + +/* Interface initialization */ +static hbool_t interface_initialize_g = FALSE; +#define INTERFACE_INIT NULL + + +/*------------------------------------------------------------------------- + * Function: H5O_fill_decode + * + * Purpose: Decode a fill value message. + * + * Return: Success: Ptr to new message in native struct. + * + * Failure: NULL + * + * Programmer: Robb Matzke + * Wednesday, September 30, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static void * +H5O_fill_decode(H5F_t *f, const uint8 *p, H5O_shared_t *sh) +{ + H5O_fill_t *mesg=NULL; + void *ret_value = NULL; + + FUNC_ENTER(H5O_fill_decode, NULL); + assert(f); + assert(p); + assert(!sh); + + if (NULL==(mesg=H5MM_calloc(sizeof(H5O_fill_t)))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed for fill value message"); + } + UINT32DECODE(p, mesg->size); + if (NULL==(mesg->buf=H5MM_malloc(mesg->size))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed for fill value"); + } + HDmemcpy(mesg->buf, p, mesg->size); + ret_value = (void*)mesg; + + done: + if (!ret_value && mesg) { + H5MM_xfree(mesg->buf); + H5MM_xfree(mesg); + } + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- + * Function: H5O_fill_encode + * + * Purpose: Encode a fill value message. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5O_fill_encode(H5F_t *f, uint8 *p, const void *_mesg) +{ + const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg; + + FUNC_ENTER(H5O_fill_encode, FAIL); + assert(f); + assert(p); + assert(mesg && NULL==mesg->type); + + UINT32ENCODE(p, mesg->size); + HDmemcpy(p, mesg->buf, mesg->size); + + FUNC_LEAVE(SUCCEED); +} + + +/*------------------------------------------------------------------------- + * Function: H5O_fill_copy + * + * Purpose: Copies a message from _MESG to _DEST, allocating _DEST if + * necessary. + * + * Return: Success: Ptr to _DEST + * + * Failure: NULL + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static void * +H5O_fill_copy(const void *_mesg, void *_dest) +{ + const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg; + H5O_fill_t *dest = (H5O_fill_t *)_dest; + void *ret_value = NULL; + + FUNC_ENTER(H5O_fill_copy, NULL); + assert(mesg); + + if (!dest && NULL==(dest=H5MM_calloc(sizeof(H5O_fill_t)))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed for fill message"); + } + if (mesg->type && + NULL==(dest->type=H5T_copy(mesg->type, H5T_COPY_TRANSIENT))) { + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, + "unable to copy fill value data type"); + } + if (mesg->buf) { + if (NULL==(dest->buf=H5MM_malloc(mesg->size))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed for fill value"); + } + dest->size = mesg->size; + HDmemcpy(dest->buf, mesg->buf, mesg->size); + } + ret_value = dest; + + done: + if (!ret_value && dest) { + H5MM_xfree(dest->buf); + if (dest->type) H5T_close(dest->type); + if (!_dest) H5MM_xfree(dest); + } + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- + * Function: H5O_fill_size + * + * Purpose: Returns the size of the raw message in bytes not counting the + * message type or size fields, but only the data fields. This + * function doesn't take into account alignment. + * + * Return: Success: Message data size in bytes w/o alignment. + * + * Failure: 0 + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static size_t +H5O_fill_size(H5F_t *f, const void *_mesg) +{ + const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg; + + FUNC_ENTER(H5O_fill_size, 0); + assert(f); + assert(mesg); + + FUNC_LEAVE(4+mesg->size); +} + + +/*------------------------------------------------------------------------- + * Function: H5O_fill_reset + * + * Purpose: Resets a message to an initial state + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5O_fill_reset(void *_mesg) +{ + H5O_fill_t *mesg = (H5O_fill_t *)_mesg; + + FUNC_ENTER(H5O_fill_reset, FAIL); + assert(mesg); + + mesg->buf = H5MM_xfree(mesg->buf); + mesg->size = 0; + if (mesg->type) { + H5T_close(mesg->type); + mesg->type = NULL; + } + + FUNC_LEAVE(SUCCEED); +} + + +/*------------------------------------------------------------------------- + * Function: H5O_fill_debug + * + * Purpose: Prints debugging info for the message. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5O_fill_debug(H5F_t *f, const void *_mesg, FILE *stream, intn indent, + intn fwidth) +{ + const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg; + + FUNC_ENTER(H5O_fill_debug, FAIL); + assert(f); + assert(mesg); + assert(stream); + assert(indent>=0); + assert(fwidth>=0); + + HDfprintf(stream, "%*s%-*s %Zu\n", indent, "", fwidth, + "Bytes:", mesg->size); + fprintf(stream, "%*s%-*s ", indent, "", fwidth, "Data type:"); + if (mesg->type) { + H5T_debug(mesg->type, stream); + fprintf(stream, "\n"); + } else { + fprintf(stream, "<dataset type>\n"); + } + + FUNC_LEAVE(SUCCEED); +} + + +/*------------------------------------------------------------------------- + * Function: H5O_fill_convert + * + * Purpose: Convert a fill value from whatever data type it currently has + * to the specified data type. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5O_fill_convert(H5O_fill_t *fill, H5T_t *dset_type) +{ + FUNC_ENTER(H5O_fill_convert, FAIL); + assert(fill); + assert(dset_type); + + /* No-op cases */ + if (!fill->buf || !fill->type || 0==H5T_cmp(fill->type, dset_type)) { + if (fill->type) H5T_close(fill->type); + fill->type = NULL; + HRETURN(SUCCEED); + } + + + HRETURN_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, FAIL, + "fill value conversion not supported yet"); + + FUNC_LEAVE(SUCCEED); +} diff --git a/src/H5Omtime.c b/src/H5Omtime.c index f144364..8693032 100644 --- a/src/H5Omtime.c +++ b/src/H5Omtime.c @@ -18,7 +18,7 @@ static void *H5O_mtime_decode(H5F_t *f, const uint8 *p, H5O_shared_t *sh); static herr_t H5O_mtime_encode(H5F_t *f, uint8 *p, const void *_mesg); static void *H5O_mtime_copy(const void *_mesg, void *_dest); static size_t H5O_mtime_size(H5F_t *f, const void *_mesg); -static herr_t H5O_mtime_debug(H5F_t *f, const void *_mesg, FILE * stream, +static herr_t H5O_mtime_debug(H5F_t *f, const void *_mesg, FILE *stream, intn indent, intn fwidth); /* This message derives from H5O */ @@ -246,7 +246,7 @@ H5O_mtime_copy(const void *_mesg, void *_dest) * * Return: Success: Message data size in bytes w/o alignment. * - * Failure: FAIL + * Failure: 0 * * Programmer: Robb Matzke * matzke@llnl.gov diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index 748e619..adc9396 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -133,6 +133,19 @@ extern const H5O_class_t H5O_DTYPE[1]; /* operates on an H5T_t struct */ /* + * Fill Value Message. + */ +#define H5O_FILL_ID 0x0004 +extern const H5O_class_t H5O_FILL[1]; + +typedef struct H5O_fill_t { + H5T_t *type; /*type. Null implies same as dataset */ + size_t size; /*number of bytes in the fill value */ + void *buf; /*the fill value */ +} H5O_fill_t; + + +/* * External File List Message */ #define H5O_EFL_ID 0x0007 /*external file list id */ @@ -281,4 +294,7 @@ herr_t H5O_efl_read (H5F_t *f, const H5O_efl_t *efl, haddr_t *addr, herr_t H5O_efl_write (H5F_t *f, const H5O_efl_t *efl, haddr_t *addr, hsize_t size, const uint8 *buf); +/* Fill value operators */ +herr_t H5O_fill_convert(H5O_fill_t *fill, H5T_t *type); + #endif @@ -346,6 +346,7 @@ H5P_close (H5P_class_t type, void *plist) break; case H5P_DATASET_CREATE: + H5O_reset(H5O_FILL, &(dc_list->fill)); H5O_reset(H5O_EFL, &(dc_list->efl)); H5O_reset(H5O_PLINE, &(dc_list->pline)); break; @@ -2086,15 +2087,16 @@ H5Pget_buffer(hid_t plist_id, void **tconv/*out*/, void **bkg/*out*/) /*------------------------------------------------------------------------- * Function: H5Pset_hyper_cache * - * Purpose: Given a dataset transfer property list, indicate whether to cache - * the hyperslab blocks during the I/O (which speeds things up) and the - * maximum size of the hyperslab block to cache. If a block is smaller - * than to limit, it may still not be cached if no memory is available. - * Setting the limit to 0 indicates no limitation on the size of block - * to attempt to cache. + * Purpose: Given a dataset transfer property list, indicate whether to + * cache the hyperslab blocks during the I/O (which speeds + * things up) and the maximum size of the hyperslab block to + * cache. If a block is smaller than to limit, it may still not + * be cached if no memory is available. Setting the limit to 0 + * indicates no limitation on the size of block to attempt to + * cache. * - * The default is to cache blocks with no limit on block size for serial - * I/O and to not cache blocks for parallel I/O + * The default is to cache blocks with no limit on block size + * for serial I/O and to not cache blocks for parallel I/O * * Return: Success: SUCCEED * @@ -2147,7 +2149,8 @@ H5Pset_hyper_cache(hid_t plist_id, unsigned cache, unsigned limit) *------------------------------------------------------------------------- */ herr_t -H5Pget_hyper_cache(hid_t plist_id, unsigned *cache/*out*/, unsigned *limit/*out*/) +H5Pget_hyper_cache(hid_t plist_id, unsigned *cache/*out*/, + unsigned *limit/*out*/) { H5D_xfer_t *plist = NULL; @@ -2594,7 +2597,6 @@ herr_t H5Pset_btree_ratios(hid_t plist_id, double left, double middle, double right) { - H5D_xfer_t *plist = NULL; FUNC_ENTER(H5Pget_btree_ratios, FAIL); @@ -2621,6 +2623,186 @@ H5Pset_btree_ratios(hid_t plist_id, double left, double middle, } +/*------------------------------------------------------------------------- + * Function: H5Pset_fill_value + * + * Purpose: Set the fill value for a dataset creation property list. The + * VALUE is interpretted as being of type TYPE, which need not + * be the same type as the dataset but the library must be able + * to convert VALUE to the dataset type when the dataset is + * created. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Pset_fill_value(hid_t plist_id, hid_t type_id, const void *value) +{ + H5D_create_t *plist = NULL; + H5T_t *type = NULL; + + FUNC_ENTER(H5Pset_fill_value, FAIL); + H5TRACE3("e","iix",plist_id,type_id,value); + + /* Check arguments */ + if (H5P_DATASET_CREATE!=H5P_get_class(plist_id) || + NULL==(plist=H5I_object(plist_id))) { + HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, + "not a dataset creation property list"); + } + if (H5_DATATYPE!=H5I_group(type_id) || + NULL==(type=H5I_object(type_id))) { + HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); + } + if (!value) { + HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no fill value specified"); + } + + /* Set the fill value */ + H5O_reset(H5O_FILL, &(plist->fill)); + if (NULL==(plist->fill.type=H5T_copy(type, H5T_COPY_TRANSIENT))) { + HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, + "unable to copy data type"); + } + plist->fill.size = H5T_get_size(type); + if (NULL==(plist->fill.buf=H5MM_malloc(plist->fill.size))) { + HRETURN_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, + "memory allocation failed for fill value"); + } + HDmemcpy(plist->fill.buf, value, plist->fill.size); + + FUNC_LEAVE(SUCCEED); +} + + +/*------------------------------------------------------------------------- + * Function: H5Pget_fill_value + * + * Purpose: Queries the fill value property of a dataset creation + * property list. The fill value is returned through the VALUE + * pointer and the memory is allocated by the caller. The fill + * value will be converted from its current data type to the + * specified TYPE. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Robb Matzke + * Thursday, October 1, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Pget_fill_value(hid_t plist_id, hid_t type_id, void *value/*out*/) +{ + H5D_create_t *plist = NULL; + H5T_t *type = NULL; + H5T_cdata_t *cdata = NULL; /*conversion data */ + H5T_conv_t cfunc = NULL; /*conversion function */ + void *buf = NULL; /*conversion buffer */ + void *bkg = NULL; /*conversion buffer */ + H5_timer_t timer; /*conversion timer */ + hid_t src_id = -1; /*source data type id */ + herr_t status; + herr_t ret_value = FAIL; + + FUNC_ENTER(H5Pget_fill_value, FAIL); + H5TRACE3("e","iix",plist_id,type_id,value); + + /* Check arguments */ + if (H5P_DATASET_CREATE!=H5P_get_class(plist_id) || + NULL==(plist=H5I_object(plist_id))) { + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, + "not a dataset creation proprety list"); + } + if (H5_DATATYPE!=H5I_group(type_id) || + NULL==(type=H5I_object(type_id))) { + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); + } + if (!value) { + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "no fill value output buffer"); + } + + /* + * If no fill value is defined then return an error. We can't even + * return zero because we don't know the data type of the dataset and + * data type conversion might not have resulted in zero. + */ + if (NULL==plist->fill.buf) { + HGOTO_ERROR(H5E_PLIST, H5E_NOTFOUND, FAIL, "no fill value defined"); + } + + /* + * Can we convert between the source and destination data types? + */ + if (NULL==(cfunc=H5T_find(plist->fill.type, type, H5T_BKG_NO, &cdata))) { + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, + "unable to convert between src and dst data types"); + } + src_id = H5I_register(H5_DATATYPE, + H5T_copy (plist->fill.type, H5T_COPY_TRANSIENT)); + if (src_id<0) { + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, + "unable to copy/register data type"); + } + + /* + * Data type conversions are always done in place, so we need a buffer + * other than the fill value buffer that is large enough for both source + * and destination. The app-supplied buffer might do okay. + */ + if (H5T_get_size(type)>=H5T_get_size(plist->fill.type)) { + buf = value; + if (cdata->need_bkg>=H5T_BKG_TEMP && + NULL==(bkg=H5MM_malloc(H5T_get_size(type)))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for type conversion"); + } + } else { + if (NULL==(buf=H5MM_malloc(H5T_get_size(plist->fill.type)))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for type conversion"); + } + if (cdata->need_bkg>=H5T_BKG_TEMP) bkg = value; + } + HDmemcpy(buf, plist->fill.buf, H5T_get_size(plist->fill.type)); + + /* Do the conversion */ +#ifdef H5T_DEBUG + H5T_timer_begin(&timer, cdata); +#endif + cdata->command = H5T_CONV_CONV; + status = (cfunc)(src_id, type_id, cdata, 1, buf, bkg); +#ifdef H5T_DEBUG + H5T_timer_end(&timer, cdata, 1); +#endif + if (status<0) { + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, + "data type conversion failed"); + } + if (buf!=value) HDmemcpy(value, buf, H5T_get_size(type)); + ret_value = SUCCEED; + + done: + if (buf!=value) H5MM_xfree(buf); + if (bkg!=value) H5MM_xfree(bkg); + if (src_id>=0) H5I_dec_ref(src_id); + FUNC_LEAVE(ret_value); +} + + #ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5Pset_mpi @@ -3015,16 +3197,22 @@ H5P_copy (H5P_class_t type, const void *src) dc_src = (const H5D_create_t*)src; dc_dst = (H5D_create_t*)dst; + /* Copy the fill value */ + if (NULL==H5O_copy(H5O_FILL, &(dc_src->fill), &(dc_dst->fill))) { + HRETURN_ERROR(H5E_PLIST, H5E_CANTINIT, NULL, + "unabe to copy fill value message"); + } + /* Copy the external file list */ HDmemset(&(dc_dst->efl), 0, sizeof(dc_dst->efl)); if (NULL==H5O_copy(H5O_EFL, &(dc_src->efl), &(dc_dst->efl))) { - HRETURN_ERROR(H5E_TEMPLATE, H5E_CANTINIT, NULL, + HRETURN_ERROR(H5E_PLIST, H5E_CANTINIT, NULL, "unable to copy external file list message"); } /* Copy the filter pipeline */ if (NULL==H5O_copy(H5O_PLINE, &(dc_src->pline), &(dc_dst->pline))) { - HRETURN_ERROR(H5E_TEMPLATE, H5E_CANTINIT, NULL, + HRETURN_ERROR(H5E_PLIST, H5E_CANTINIT, NULL, "unable to copy filter pipeline message"); } diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h index cc6c4e3..cccd4fd 100644 --- a/src/H5Ppublic.h +++ b/src/H5Ppublic.h @@ -112,6 +112,8 @@ herr_t H5Pset_btree_ratios(hid_t plist_id, double left, double middle, double right); herr_t H5Pget_btree_ratios(hid_t plist_id, double *left/*out*/, double *middle/*out*/, double *right/*out*/); +herr_t H5Pset_fill_value(hid_t plist_id, hid_t type_id, const void *value); +herr_t H5Pget_fill_value(hid_t plist_id, hid_t type_id, void *value/*out*/); #ifdef HAVE_PARALLEL herr_t H5Pset_mpi (hid_t plist_id, MPI_Comm comm, MPI_Info info); diff --git a/src/H5Sall.c b/src/H5Sall.c index e3ea157..c798a61 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -24,12 +24,14 @@ static size_t H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *iter, size_t max); static size_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_xfer_t *xfer_parms, void *buf/*out*/); static herr_t H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, @@ -167,9 +169,10 @@ H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *sel_iter, size_t max) static size_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, const H5D_xfer_t *xfer_parms, void *_buf/*out*/) + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, + size_t elmt_size, const H5S_t *file_space, + H5S_sel_iter_t *file_iter, size_t nelmts, + const H5D_xfer_t *xfer_parms, void *_buf/*out*/) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -222,8 +225,8 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, /* * Gather from file. */ - if (H5F_arr_read (f, xfer_parms, layout, pline, efl, hsize, hsize, zero, - file_offset, buf/*out*/)<0) { + if (H5F_arr_read (f, xfer_parms, layout, pline, fill, efl, hsize, hsize, + zero, file_offset, buf/*out*/)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } @@ -256,10 +259,10 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, */ static herr_t H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, - H5S_sel_iter_t *file_iter, size_t nelmts, - const H5D_xfer_t *xfer_parms, const void *_buf) + const struct H5O_pline_t *pline, const struct H5O_fill_t *fill, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + size_t nelmts, const H5D_xfer_t *xfer_parms, const void *_buf) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of hyperslab */ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -308,8 +311,8 @@ H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, /* * Scatter to file. */ - if (H5F_arr_write (f, xfer_parms, layout, pline, efl, hsize, hsize, zero, - file_offset, buf)<0) { + if (H5F_arr_write (f, xfer_parms, layout, pline, fill, efl, hsize, hsize, + zero, file_offset, buf)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); } diff --git a/src/H5Shyper.c b/src/H5Shyper.c index 54ee1bd..c27d068 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -26,6 +26,7 @@ typedef struct { H5F_t *f; const struct H5O_layout_t *layout; const struct H5O_pline_t *pline; + const struct H5O_fill_t *fill; const struct H5O_efl_t *efl; size_t elmt_size; const H5S_t *space; @@ -55,12 +56,14 @@ static size_t H5S_hyper_favail (const H5S_t *space, const H5S_sel_iter_t *iter, size_t max); static size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_xfer_t *xfer_parms, void *buf/*out*/); static herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, @@ -425,7 +428,8 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, *------------------------------------------------------------------------- */ static herr_t -H5S_hyper_block_cache (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_info, uintn block_read) +H5S_hyper_block_cache (H5S_hyper_node_t *node, + H5S_hyper_fhyper_info_t *fhyper_info, uintn block_read) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -454,8 +458,8 @@ H5S_hyper_block_cache (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_i if (H5F_arr_read (fhyper_info->f, fhyper_info->xfer_parms, fhyper_info->layout, fhyper_info->pline, - fhyper_info->efl, hsize, hsize, zero, file_offset, - node->cinfo.block/*out*/)<0) + fhyper_info->fill, fhyper_info->efl, hsize, hsize, + zero, file_offset, node->cinfo.block/*out*/)<0) HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, FAIL, "read error"); } /* end if */ else { @@ -501,9 +505,14 @@ H5S_hyper_block_read (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_in !! NOTE !! This will need to be changed for different dimension permutations from the standard 'C' ordering! */ - HDmemcpy(fhyper_info->dst,node->cinfo.pos,region_size*fhyper_info->elmt_size); + HDmemcpy(fhyper_info->dst, + node->cinfo.pos, + region_size*fhyper_info->elmt_size); - /* Decrement the number of elements left in block to read & move the offset */ + /* + * Decrement the number of elements left in block to read & move the + * offset + */ node->cinfo.pos+=region_size*fhyper_info->elmt_size; node->cinfo.left-=region_size; @@ -536,7 +545,9 @@ H5S_hyper_block_read (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_in *------------------------------------------------------------------------- */ static herr_t -H5S_hyper_block_write (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_info, hsize_t region_size) +H5S_hyper_block_write (H5S_hyper_node_t *node, + H5S_hyper_fhyper_info_t *fhyper_info, + hsize_t region_size) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -552,16 +563,24 @@ H5S_hyper_block_write (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_i !! NOTE !! This will need to be changed for different dimension permutations from the standard 'C' ordering! */ - HDmemcpy(node->cinfo.pos,fhyper_info->src,region_size*fhyper_info->elmt_size); + HDmemcpy(node->cinfo.pos, + fhyper_info->src, + region_size*fhyper_info->elmt_size); - /* Decrement the number of elements left in block to read & move the offset */ + /* + * Decrement the number of elements left in block to read & move the + * offset + */ node->cinfo.pos+=region_size*fhyper_info->elmt_size; node->cinfo.left-=region_size; /* If we've read in all the elements from the block, throw it away */ if(node->cinfo.left==0) { /* Copy the location of the region in the file */ - HDmemcpy(file_offset,node->start,(fhyper_info->space->extent.u.simple.rank * sizeof(hssize_t))); + HDmemcpy(file_offset, + node->start, + (fhyper_info->space->extent.u.simple.rank * + sizeof(hssize_t))); file_offset[fhyper_info->space->extent.u.simple.rank]=0; /* Set the hyperslab size to write */ @@ -571,8 +590,8 @@ H5S_hyper_block_write (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_i if (H5F_arr_write (fhyper_info->f, fhyper_info->xfer_parms, fhyper_info->layout, fhyper_info->pline, - fhyper_info->efl, hsize, hsize, zero, file_offset, - node->cinfo.block/*out*/)<0) + fhyper_info->fill, fhyper_info->efl, hsize, hsize, + zero, file_offset, node->cinfo.block/*out*/)<0) HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); /* Release the temporary buffer */ @@ -650,10 +669,14 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* perform I/O on data from regions */ for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { /* Compute the size of the region to read */ - region_size=MIN(fhyper_info->nelmts, (regions[i].end-regions[i].start)+1); + region_size=MIN(fhyper_info->nelmts, + (regions[i].end-regions[i].start)+1); /* Check if this hyperslab block is cached or could be cached */ - if(!regions[i].node->cinfo.cached && (fhyper_info->xfer_parms->cache_hyper && (fhyper_info->xfer_parms->block_limit==0 || fhyper_info->xfer_parms->block_limit>=(regions[i].node->cinfo.size*fhyper_info->elmt_size)))) { + if(!regions[i].node->cinfo.cached && + (fhyper_info->xfer_parms->cache_hyper && + (fhyper_info->xfer_parms->block_limit==0 || + fhyper_info->xfer_parms->block_limit>=(regions[i].node->cinfo.size*fhyper_info->elmt_size)))) { /* if we aren't cached, attempt to cache the block */ H5S_hyper_block_cache(regions[i].node,fhyper_info,1); } /* end if */ @@ -691,17 +714,17 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) */ if (H5F_arr_read (fhyper_info->f, fhyper_info->xfer_parms, fhyper_info->layout, fhyper_info->pline, - fhyper_info->efl, hsize, hsize, zero, - file_offset, + fhyper_info->fill, fhyper_info->efl, + hsize, hsize, zero, file_offset, fhyper_info->dst/*out*/)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } #ifdef QAK - printf("%s: check 2.3, region #%d\n",FUNC,(int)i); - for(j=0; j<fhyper_info->space->extent.u.simple.rank; j++) - printf("%s: %d - pos=%d\n", - FUNC,j,(int)fhyper_info->iter->hyp.pos[j]); + printf("%s: check 2.3, region #%d\n",FUNC,(int)i); + for(j=0; j<fhyper_info->space->extent.u.simple.rank; j++) + printf("%s: %d - pos=%d\n", + FUNC,j,(int)fhyper_info->iter->hyp.pos[j]); #endif /* QAK */ } /* end else */ @@ -789,6 +812,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) static size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_xfer_t *xfer_parms, @@ -833,6 +857,7 @@ H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, fhyper_info.f=f; fhyper_info.layout=layout; fhyper_info.pline=pline; + fhyper_info.fill=fill; fhyper_info.efl=efl; fhyper_info.elmt_size=elmt_size; fhyper_info.space=file_space; @@ -961,8 +986,9 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) */ if (H5F_arr_write (fhyper_info->f, fhyper_info->xfer_parms, fhyper_info->layout, fhyper_info->pline, - fhyper_info->efl, hsize, hsize, zero, - file_offset, fhyper_info->src)<0) { + fhyper_info->fill, fhyper_info->efl, + hsize, hsize, zero, file_offset, + fhyper_info->src)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); } @@ -1049,6 +1075,7 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) static herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_xfer_t *xfer_parms, @@ -1094,6 +1121,7 @@ H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, fhyper_info.f=f; fhyper_info.layout=layout; fhyper_info.pline=pline; + fhyper_info.fill=fill; fhyper_info.efl=efl; fhyper_info.elmt_size=elmt_size; fhyper_info.space=file_space; diff --git a/src/H5Spoint.c b/src/H5Spoint.c index d532fcf..11aa324 100644 --- a/src/H5Spoint.c +++ b/src/H5Spoint.c @@ -25,6 +25,7 @@ static size_t H5S_point_favail (const H5S_t *space, const H5S_sel_iter_t *iter, size_t max); static size_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, @@ -32,6 +33,7 @@ static size_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, void *buf/*out*/); static herr_t H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, @@ -265,10 +267,10 @@ H5S_point_favail (const H5S_t __unused__ *space, static size_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, const H5D_xfer_t *xfer_parms, - void *_buf/*out*/) + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, + size_t elmt_size, const H5S_t *file_space, + H5S_sel_iter_t *file_iter, size_t nelmts, + const H5D_xfer_t *xfer_parms, void *_buf/*out*/) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -317,8 +319,8 @@ H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, file_offset[i] += file_space->select.offset[i]; /* Go read the point */ - if (H5F_arr_read (f, xfer_parms, layout, pline, efl, hsize, hsize, - zero, file_offset, buf/*out*/)<0) { + if (H5F_arr_read (f, xfer_parms, layout, pline, fill, efl, hsize, + hsize, zero, file_offset, buf/*out*/)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } @@ -374,10 +376,10 @@ H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, static herr_t H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, - const struct H5O_efl_t *efl, size_t elmt_size, - const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, const H5D_xfer_t *xfer_parms, - const void *_buf) + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, + size_t elmt_size, const H5S_t *file_space, + H5S_sel_iter_t *file_iter, size_t nelmts, + const H5D_xfer_t *xfer_parms, const void *_buf) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of hyperslab */ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ @@ -445,8 +447,8 @@ H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, } #endif /* QAK */ /* Go write the point */ - if (H5F_arr_write (f, xfer_parms, layout, pline, efl, hsize, hsize, - zero, file_offset, buf)<0) { + if (H5F_arr_write (f, xfer_parms, layout, pline, fill, efl, hsize, + hsize, zero, file_offset, buf)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); } diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index c870a29..c434690 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -191,6 +191,7 @@ typedef struct H5S_fconv_t { /* Gather elements from disk to type conversion buffer */ size_t (*gath)(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const struct H5D_xfer_t *xfer_parms, @@ -199,6 +200,7 @@ typedef struct H5S_fconv_t { /* Scatter elements from type conversion buffer to disk */ herr_t (*scat)(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, + const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const struct H5D_xfer_t *xfer_parms, diff --git a/src/H5Tconv.c b/src/H5Tconv.c index 0f1d120..76d92c9 100644 --- a/src/H5Tconv.c +++ b/src/H5Tconv.c @@ -517,16 +517,18 @@ H5T_conv_struct(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, if (src2dst[i]<0) continue; src_memb = src->u.compnd.memb + i; dst_memb = dst->u.compnd.memb + src2dst[i]; - offset -= dst_memb->size; if (dst_memb->size > src_memb->size) { H5T_conv_t tconv_func = priv->memb_conv[src2dst[i]]; H5T_cdata_t *memb_cdata = priv->memb_cdata[src2dst[i]]; + offset -= src_memb->size; memb_cdata->command = H5T_CONV_CONV; (tconv_func)(priv->src_memb_id[src2dst[i]], priv->dst_memb_id[src2dst[i]], memb_cdata, priv->memb_nelmts[i], buf+offset, bkg+dst_memb->offset); + } else { + offset -= dst_memb->size; } HDmemmove (bkg+dst_memb->offset, buf+offset, dst_memb->size); } @@ -643,9 +643,9 @@ H5V_stride_copy2(hsize_t nelmts, hsize_t elmt_size, /*------------------------------------------------------------------------- * Function: H5V_array_fill * - * Purpose: Fills all bytes of an array with the same value using memset(). - * Increases amount copied by power of two until the halfway point is - * crossed, then copies the rest in one swoop. + * Purpose: Fills all bytes of an array with the same value using + * memset(). Increases amount copied by power of two until the + * halfway point is crossed, then copies the rest in one swoop. * * Return: Success: SUCCEED * diff --git a/src/Makefile.in b/src/Makefile.in index 158b452..750a200 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -17,7 +17,7 @@ LIB=libhdf5.a LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5D.c H5E.c H5F.c H5Farray.c H5Fcore.c \ H5Ffamily.c H5Fistore.c H5Flow.c H5Fmpio.c H5Fsec2.c H5Fsplit.c \ H5Fstdio.c H5G.c H5Gent.c H5Gnode.c H5Gstab.c H5HG.c H5HL.c H5I.c H5MF.c \ - H5MM.c H5O.c H5Oattr.c H5Ocomp.c H5Ocont.c H5Odtype.c H5Oefl.c \ + H5MM.c H5O.c H5Oattr.c H5Ocomp.c H5Ocont.c H5Odtype.c H5Oefl.c H5Ofill.c \ H5Olayout.c H5Omtime.c H5Oname.c H5Onull.c H5Osdspace.c H5Oshared.c \ H5Ostab.c H5P.c H5R.c H5S.c H5Sall.c H5Shyper.c H5Smpio.c H5Spoint.c \ H5Sselect.c H5T.c H5Tbit.c H5Tconv.c H5Tinit.c H5TB.c H5V.c H5Z.c |