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[svn-r13167] Description:

Browse Source 
Get rid of two different types of fill value struct (merge H5O_fill_t
and H5O_fill_new_t) and clean up & simplify dataset initialization code.
        (In preparation for shared object header message method call
refactoring).

Tested on:
        FreeBSD/32 6.2 (duty)
        Mac OS X/32 10.4.8 (amazon)
This commit is contained in:
Quincey Koziol 2007-01-22 16:07:54 -05:00
parent 681d9231cf
commit dc41c73711
15 changed files with 1290 additions and 1627 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1161
src/H5D.c
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File diff suppressed because it is too large Load Diff

87
src/H5Dcontig.c
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@ -141,20 +141,20 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank=(-1); /* This process's rank */
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 */
hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */
hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
#endif /* H5_HAVE_PARALLEL */
int non_zero_fill_f=(-1); /* Indicate that a non-zero fill-value was used */
herr_t ret_value=SUCCEED; /* Return value */
int non_zero_fill_f = (-1); /* Indicate that a non-zero fill-value was used */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_contig_fill, FAIL)
/* Check args */
assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));
assert(dset && H5D_CONTIGUOUS==dset->shared->layout.type);
assert(H5F_addr_defined(dset->shared->layout.u.contig.addr));
assert(dset->shared->layout.u.contig.size>0);
assert(dset->shared->space);
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
HDassert(dset && H5D_CONTIGUOUS == dset->shared->layout.type);
HDassert(H5F_addr_defined(dset->shared->layout.u.contig.addr));
HDassert(dset->shared->layout.u.contig.size > 0);
HDassert(dset->shared->space);
#ifdef H5_HAVE_PARALLEL
/* Retrieve MPI parameters */
@ -168,7 +168,7 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank")
/* Set the MPI-capable file driver flag */
using_mpi=1;
using_mpi = TRUE;
/* Fill the DXPL cache values for later use */
if (H5D_get_dxpl_cache(H5AC_ind_dxpl_id,&dxpl_cache)<0)
@ -188,61 +188,61 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
store.contig.dset_size=dset->shared->layout.u.contig.size;
/* Get size of elements */
elmt_size=H5T_get_size(dset->shared->type);
assert(elmt_size>0);
elmt_size = H5T_get_size(dset->shared->type);
HDassert(elmt_size > 0);
/* Get the number of elements in the dataset's dataspace */
snpoints = H5S_GET_EXTENT_NPOINTS(dset->shared->space);
assert(snpoints>=0);
H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t);
HDassert(snpoints >= 0);
H5_ASSIGN_OVERFLOW(npoints, snpoints, hssize_t, size_t);
/* If fill value is not library default, use it to set the element size */
if(dset->shared->fill.buf)
elmt_size=dset->shared->fill.size;
if(dset->shared->dcpl_cache.fill.buf)
elmt_size = dset->shared->dcpl_cache.fill.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/elmt_size);
bufsize = ptsperbuf*elmt_size;
ptsperbuf = MAX(1, bufsize / elmt_size);
bufsize = ptsperbuf * elmt_size;
/* Fill the buffer with the user's fill value */
if(dset->shared->fill.buf) {
if(dset->shared->dcpl_cache.fill.buf) {
/* Allocate temporary buffer */
if ((buf=H5FL_BLK_MALLOC(non_zero_fill,bufsize))==NULL)
if(NULL == (buf = H5FL_BLK_MALLOC(non_zero_fill, bufsize)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
H5V_array_fill(buf, dset->shared->fill.buf, elmt_size, ptsperbuf);
H5V_array_fill(buf, dset->shared->dcpl_cache.fill.buf, elmt_size, ptsperbuf);
/* Indicate that a non-zero fill buffer was used */
non_zero_fill_f=1;
non_zero_fill_f = 1;
} /* end if */
else { /* Fill the buffer with the default fill value */
htri_t buf_avail;
/* Check if there is an already zeroed out buffer available */
buf_avail=H5FL_BLK_AVAIL(zero_fill,bufsize);
assert(buf_avail!=FAIL);
buf_avail = H5FL_BLK_AVAIL(zero_fill, bufsize);
HDassert(buf_avail != FAIL);
/* Allocate temporary buffer (zeroing it if no buffer is available) */
if(!buf_avail)
buf=H5FL_BLK_CALLOC(zero_fill,bufsize);
buf = H5FL_BLK_CALLOC(zero_fill, bufsize);
else
buf=H5FL_BLK_MALLOC(zero_fill,bufsize);
if(buf==NULL)
buf = H5FL_BLK_MALLOC(zero_fill, bufsize);
if(buf == NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
/* Indicate that a zero fill buffer was used */
non_zero_fill_f=0;
non_zero_fill_f = 0;
} /* end else */
/* Start at the beginning of the dataset */
offset = 0;
/* Loop through writing the fill value to the dataset */
while (npoints>0) {
while(npoints > 0) {
size = MIN(ptsperbuf, npoints) * elmt_size;
#ifdef H5_HAVE_PARALLEL
@ -250,18 +250,17 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
if(using_mpi) {
/* Write the chunks out from only one process */
/* !! Use the internal "independent" DXPL!! -QAK */
if(H5_PAR_META_WRITE==mpi_rank) {
if (H5D_contig_write(dset, dxpl_cache, H5AC_ind_dxpl_id, &store, offset, size, buf)<0)
if(H5_PAR_META_WRITE == mpi_rank)
if(H5D_contig_write(dset, dxpl_cache, H5AC_ind_dxpl_id, &store, offset, size, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset")
} /* end if */
/* Indicate that blocks are being written */
blocks_written=1;
blocks_written = TRUE;
} /* end if */
else {
#endif /* H5_HAVE_PARALLEL */
H5_CHECK_OVERFLOW(size,size_t,hsize_t);
if (H5D_contig_write(dset, dxpl_cache, dxpl_id, &store, offset, size, buf)<0)
H5_CHECK_OVERFLOW(size, size_t, hsize_t);
if(H5D_contig_write(dset, dxpl_cache, dxpl_id, &store, offset, size, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset")
#ifdef H5_HAVE_PARALLEL
} /* end else */
@ -279,19 +278,19 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
* 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)))
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) {
assert(non_zero_fill_f>=0);
if(buf) {
HDassert(non_zero_fill_f >= 0);
if(non_zero_fill_f)
H5FL_BLK_FREE(non_zero_fill,buf);
H5FL_BLK_FREE(non_zero_fill, buf);
else
H5FL_BLK_FREE(zero_fill,buf);
H5FL_BLK_FREE(zero_fill, buf);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
@ -313,16 +312,16 @@ done:
herr_t
H5D_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout)
{
herr_t ret_value=SUCCEED; /* Return value */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_contig_delete, FAIL)
/* check args */
assert(f);
assert(layout);
HDassert(f);
HDassert(layout);
/* Free the file space for the chunk */
if (H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.addr, layout->u.contig.size)<0)
if(H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.addr, layout->u.contig.size) < 0)
HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free object header")
done:

181
src/H5Dio.c
View File

@ -667,9 +667,9 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, 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 && dataset->shared->efl.nused==0 &&
((dataset->shared->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))) {
if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 &&
((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))) {
H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */
/* Retrieve dataset's fill-value properties */
@ -678,15 +678,15 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
/* Should be impossible, but check anyway... */
if(fill_status == H5D_FILL_VALUE_UNDEFINED &&
(dataset->shared->dcpl_cache.fill_time == H5D_FILL_TIME_ALLOC || dataset->shared->dcpl_cache.fill_time == H5D_FILL_TIME_IFSET))
(dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET))
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read")
/* If we're never going to fill this dataset, just leave the junk in the user's buffer */
if(dataset->shared->dcpl_cache.fill_time == H5D_FILL_TIME_NEVER)
if(dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_NEVER)
HGOTO_DONE(SUCCEED)
/* Go fill the user's selection with the dataset's fill value */
if(H5D_fill(dataset->shared->dcpl_cache.fill.buf,dataset->shared->type,buf,mem_type,mem_space,dxpl_id) < 0)
if(H5D_fill(dataset->shared->dcpl_cache.fill.buf, dataset->shared->type, buf, mem_type, mem_space, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed")
else
HGOTO_DONE(SUCCEED)
@ -836,7 +836,7 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
/* <none needed currently> */
/* Allocate data space and initialize it if it hasn't been. */
if(nelmts > 0 && dataset->shared->efl.nused==0 &&
if(nelmts > 0 && dataset->shared->dcpl_cache.efl.nused==0 &&
((dataset->shared->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))) {
hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */
@ -962,11 +962,11 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts,
FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read)
/* Initialize storage info for this dataset */
if (dataset->shared->efl.nused>0)
HDmemcpy(&store.efl,&(dataset->shared->efl),sizeof(H5O_efl_t));
if (dataset->shared->dcpl_cache.efl.nused > 0)
HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
else {
store.contig.dset_addr=dataset->shared->layout.u.contig.addr;
store.contig.dset_size=dataset->shared->layout.u.contig.size;
store.contig.dset_addr = dataset->shared->layout.u.contig.addr;
store.contig.dset_size = dataset->shared->layout.u.contig.size;
} /* end if */
/* Set dataset storage for I/O info */
@ -981,9 +981,9 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts,
H5_timer_begin(&timer);
#endif
/* Sanity check dataset, then read it */
assert(((dataset->shared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->efl.nused>0 || 0 == nelmts
assert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->dcpl_cache.efl.nused > 0 || 0 == nelmts
|| dataset->shared->layout.type==H5D_COMPACT);
H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t);
@ -1095,13 +1095,11 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts,
H5_timer_begin(&timer);
#endif
/* Sanity check that space is allocated, then read data from it */
assert(((dataset->shared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->efl.nused>0 ||
dataset->shared->layout.type==H5D_COMPACT);
n = H5D_select_fgath(io_info,
file_space, &file_iter, smine_nelmts,
tconv_buf/*out*/);
HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->dcpl_cache.efl.nused > 0 ||
dataset->shared->layout.type == H5D_COMPACT);
n = H5D_select_fgath(io_info, file_space, &file_iter, smine_nelmts, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer);
@ -1225,29 +1223,29 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts,
FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write)
/* Initialize storage info for this dataset */
if (dataset->shared->efl.nused>0)
HDmemcpy(&store.efl,&(dataset->shared->efl),sizeof(H5O_efl_t));
if(dataset->shared->dcpl_cache.efl.nused > 0)
HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t));
else {
store.contig.dset_addr=dataset->shared->layout.u.contig.addr;
store.contig.dset_size=dataset->shared->layout.u.contig.size;
store.contig.dset_addr = dataset->shared->layout.u.contig.addr;
store.contig.dset_size = dataset->shared->layout.u.contig.size;
} /* end if */
/* Set dataset storage for I/O info */
io_info->store=&store;
io_info->store = &store;
/*
* If there is no type conversion then write directly from the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
if(H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t);
#ifdef H5_HAVE_PARALLEL
if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
if(H5D_contig_collective_io(io_info,file_space,mem_space,buf,TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous write failed in collective mode");
if(H5D_contig_collective_io(io_info, file_space, mem_space, buf, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous write failed in collective mode")
}
else
#endif
@ -1255,7 +1253,7 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts,
if((io_info->ops.write)(io_info, (size_t)nelmts,
H5T_get_size(dataset->shared->type), file_space, mem_space,
(haddr_t)0, buf/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous write failed ");
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous write failed ")
}
#ifdef H5S_DEBUG
@ -1469,11 +1467,11 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
hsize_t smine_start; /*strip mine start loc */
size_t n, smine_nelmts; /*elements per strip */
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */
hbool_t mem_iter_init = FALSE; /*memory selection iteration info has been initialized */
H5S_sel_iter_t bkg_iter; /*background iteration info*/
hbool_t bkg_iter_init=0; /*background iteration info has been initialized */
hbool_t bkg_iter_init = FALSE; /*background iteration info has been initialized */
H5S_sel_iter_t file_iter; /*file selection iteration info*/
hbool_t file_iter_init=0; /*file selection iteration info has been initialized */
hbool_t file_iter_init = FALSE; /*file selection iteration info has been initialized */
H5T_bkg_t need_bkg; /*type of background buf*/
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
@ -1498,34 +1496,34 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
H5_timer_begin(&timer);
#endif
/* Sanity check dataset, then read it */
assert(((dataset->shared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->efl.nused>0 || 0 == nelmts
|| dataset->shared->layout.type==H5D_COMPACT);
HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->dcpl_cache.efl.nused > 0 || 0 == nelmts
|| dataset->shared->layout.type == H5D_COMPACT);
#ifdef H5_HAVE_PARALLEL
/* Check whether the collective mode can be turned off globally*/
#ifndef H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS
if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
if(H5D_mpio_chunk_adjust_iomode(io_info,&fm))
HGOTO_ERROR(H5E_DATASET,H5E_CANTGET,FAIL,"can't adjust collective I/O")
if(H5D_mpio_chunk_adjust_iomode(io_info ,&fm))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't adjust collective I/O")
}
#endif /* H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS */
/* Temporarily shut down collective IO for chunking */
if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE) {
if(H5D_chunk_collective_io(io_info,&fm,buf,FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunked read failed in collective mode");
if(H5D_chunk_collective_io(io_info, &fm, buf, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunked read failed in collective mode")
}
else {/* sequential or independent read */
#endif
/* Get first node in chunk skip list */
chunk_node=H5SL_first(fm.fsel);
chunk_node = H5SL_first(fm.fsel);
while(chunk_node) {
H5D_chunk_info_t *chunk_info; /* chunk information */
/* Get the actual chunk information from the skip list node */
chunk_info=H5SL_item(chunk_node);
chunk_info = H5SL_item(chunk_node);
/* Pass in chunk's coordinates in a union. */
store.chunk.offset = chunk_info->coords;
@ -1539,7 +1537,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
/* Advance to next chunk in list */
chunk_node = H5SL_next(chunk_node);
}
} /* end while */
#ifdef H5_HAVE_PARALLEL
}
#endif
@ -1628,13 +1626,13 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
/* initialize selection iterator */
if (H5S_select_iter_init(&file_iter, chunk_info->fspace, src_type_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
file_iter_init=1; /*file selection iteration info has been initialized */
file_iter_init = TRUE; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&mem_iter, chunk_info->mspace, dst_type_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init=1; /*file selection iteration info has been initialized */
mem_iter_init = TRUE; /*file selection iteration info has been initialized */
if (H5S_select_iter_init(&bkg_iter, chunk_info->mspace, dst_type_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information")
bkg_iter_init=1; /*file selection iteration info has been initialized */
bkg_iter_init = TRUE; /*file selection iteration info has been initialized */
/* Pass in chunk's coordinates in a union*/
store.chunk.offset = chunk_info->coords;
@ -1654,33 +1652,30 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
H5_timer_begin(&timer);
#endif
/* Sanity check that space is allocated, then read data from it */
assert(((dataset->shared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->efl.nused>0 || dataset->shared->layout.type==H5D_COMPACT);
n = H5D_select_fgath(io_info,
chunk_info->fspace, &file_iter, smine_nelmts,
tconv_buf/*out*/);
HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr))
|| (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
|| dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT);
n = H5D_select_fgath(io_info, chunk_info->fspace, &file_iter, smine_nelmts, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer);
io_info->stats->stats[1].gath_nbytes += n * src_type_size;
io_info->stats->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts)
if(n != smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed")
if (H5T_BKG_YES==need_bkg) {
if(H5T_BKG_YES == need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = H5D_select_mgath(buf, chunk_info->mspace, &bkg_iter,
smine_nelmts, dxpl_cache, bkg_buf/*out*/);
n = H5D_select_mgath(buf, chunk_info->mspace, &bkg_iter, smine_nelmts, dxpl_cache, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(io_info->stats->stats[1].bkg_timer), &timer);
io_info->stats->stats[1].bkg_nbytes += n * dst_type_size;
io_info->stats->stats[1].bkg_ncalls++;
#endif
if (n!=smine_nelmts)
if(n != smine_nelmts)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "mem gather failed")
} /* end if */
@ -1692,8 +1687,8 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
/* Do the data transform after the conversion (since we're using type mem_type) */
if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, mem_type) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
if(H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, mem_type) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
/*
* Scatter the data into memory.
@ -1701,14 +1696,13 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = H5D_select_mscat(tconv_buf, chunk_info->mspace,
&mem_iter, smine_nelmts, dxpl_cache, buf/*out*/);
status = H5D_select_mscat(tconv_buf, chunk_info->mspace, &mem_iter, smine_nelmts, dxpl_cache, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(io_info->stats->stats[1].scat_timer), &timer);
io_info->stats->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
io_info->stats->stats[1].scat_ncalls++;
#endif
if (status<0)
if(status < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed")
} /* end for */
@ -1716,17 +1710,17 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts,
if(file_iter_init) {
if(H5S_SELECT_ITER_RELEASE(&file_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
file_iter_init=0;
file_iter_init = FALSE;
} /* end if */
if(mem_iter_init) {
if(H5S_SELECT_ITER_RELEASE(&mem_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
mem_iter_init=0;
mem_iter_init = FALSE;
} /* end if */
if(bkg_iter_init) {
if(H5S_SELECT_ITER_RELEASE(&bkg_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
bkg_iter_init=0;
bkg_iter_init = FALSE;
} /* end if */
/* Get the next chunk node in the skip list */
@ -1748,10 +1742,10 @@ done:
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
} /* end if */
if (tconv_buf && NULL==dxpl_cache->tconv_buf)
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==dxpl_cache->bkgr_buf)
H5FL_BLK_FREE(type_conv,bkg_buf);
if(tconv_buf && NULL == dxpl_cache->tconv_buf)
H5FL_BLK_FREE(type_conv, tconv_buf);
if(bkg_buf && NULL == dxpl_cache->bkgr_buf)
H5FL_BLK_FREE(type_conv, bkg_buf);
/* Release chunk mapping information */
if(H5D_destroy_chunk_map(&fm) < 0)
@ -2102,13 +2096,13 @@ static herr_t
H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space,
const H5S_t *mem_space, fm_map *fm)
{
H5S_t *tmp_mspace=NULL; /* Temporary memory dataspace */
H5S_t *equiv_mspace=NULL; /* Equivalent memory dataspace */
hbool_t equiv_mspace_init=0;/* Equivalent memory dataspace was created */
H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */
H5S_t *equiv_mspace = NULL; /* Equivalent memory dataspace */
hbool_t equiv_mspace_init = FALSE;/* Equivalent memory dataspace was created */
hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */
hbool_t file_space_normalized = FALSE; /* File dataspace was normalized */
hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */
hbool_t iter_init=0; /* Selection iteration info has been initialized */
hid_t f_tid = (-1); /* Temporary copy of file datatype for iteration */
hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */
unsigned f_ndims; /* The number of dimensions of the file's dataspace */
int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */
H5SL_node_t *curr_node; /* Current node in skip list */
@ -2137,20 +2131,20 @@ H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *f
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create equivalent dataspace for scalar space")
/* Indicate that this space needs to be released */
equiv_mspace_init=1;
equiv_mspace_init = TRUE;
/* Set the number of dimensions for the memory dataspace */
fm->m_ndims=dataset->shared->layout.u.chunk.ndims-1;
fm->m_ndims = dataset->shared->layout.u.chunk.ndims - 1;
} /* end else */
else {
equiv_mspace=(H5S_t *)mem_space; /* Casting away 'const' OK... */
equiv_mspace = (H5S_t *)mem_space; /* Casting away 'const' OK... */
/* Set the number of dimensions for the memory dataspace */
H5_ASSIGN_OVERFLOW(fm->m_ndims,sm_ndims,int,unsigned);
H5_ASSIGN_OVERFLOW(fm->m_ndims, sm_ndims, int, unsigned);
} /* end else */
/* Get dim number and dimensionality for each dataspace */
fm->f_ndims=f_ndims=dataset->shared->layout.u.chunk.ndims-1;
fm->f_ndims = f_ndims = dataset->shared->layout.u.chunk.ndims - 1;
if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
@ -2201,21 +2195,22 @@ H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *f
fm->last_chunk_info=NULL;
/* Point at the dataspaces */
fm->file_space=file_space;
fm->mem_space=equiv_mspace;
fm->mem_space_copy=equiv_mspace_init; /* Make certain to copy memory dataspace if necessary */
fm->file_space = file_space;
fm->mem_space = equiv_mspace;
fm->mem_space_copy = equiv_mspace_init; /* Make certain to copy memory dataspace if necessary */
/* Get type of selection on disk & in memory */
if((fsel_type=H5S_GET_SELECT_TYPE(file_space))<H5S_SEL_NONE)
if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
if((fm->msel_type=H5S_GET_SELECT_TYPE(equiv_mspace))<H5S_SEL_NONE)
if((fm->msel_type = H5S_GET_SELECT_TYPE(equiv_mspace)) < H5S_SEL_NONE)
HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space")
/* If the selection is NONE or POINTS, set the flag to FALSE */
if(fsel_type == H5S_SEL_POINTS || fsel_type == H5S_SEL_NONE)
sel_hyper_flag = FALSE;
sel_hyper_flag = FALSE;
else
sel_hyper_flag = TRUE;
sel_hyper_flag = TRUE;
/* Check if file selection is a point selection */
if(!sel_hyper_flag) {
/* Create temporary datatypes for selection iteration */
@ -2289,14 +2284,14 @@ H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *f
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
if (H5S_select_iter_init(&(fm->mem_iter), equiv_mspace, elmt_size) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init=1; /* Selection iteration info has been initialized */
iter_init = TRUE; /* Selection iteration info has been initialized */
/* Spaces aren't the same shape, iterate over the memory selection directly */
if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
/* Clean up hyperslab stuff, if necessary */
if(fm->msel_type!=H5S_SEL_POINTS) {
if(fm->msel_type != H5S_SEL_POINTS) {
/* Clean memory chunks' hyperslab span "scratch" information */
curr_node=H5SL_first(fm->fsel);
while(curr_node) {
@ -2329,17 +2324,17 @@ done:
} /* end if */
/* Reset the global dataspace info */
fm->file_space=NULL;
fm->mem_space=NULL;
fm->file_space = NULL;
fm->mem_space = NULL;
if(equiv_mspace_init && equiv_mspace) {
if(H5S_close(equiv_mspace) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template")
} /* end if */
if(iter_init) {
if (H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0)
if(H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
}
} /* end if */
if(f_tid!=(-1)) {
if(H5I_dec_ref(f_tid) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID")

442
src/H5Distore.c
View File

@ -917,11 +917,11 @@ H5D_istore_iter_chunkmap (H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_lt
hsize_t chunk_index;
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_iter_chunkmap);
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_iter_chunkmap)
rank = udata->common.mesg->u.chunk.ndims - 1;
if(H5V_chunk_index(rank,lt_key->offset,udata->common.mesg->u.chunk.dim,udata->down_chunks,&chunk_index)<0)
if(H5V_chunk_index(rank, lt_key->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
udata->chunk_addr[chunk_index] = addr;
@ -1366,37 +1366,37 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
H5D_istore_flush (H5D_t *dset, hid_t dxpl_id, unsigned flags)
H5D_istore_flush(H5D_t *dset, hid_t dxpl_id, unsigned flags)
{
H5D_io_info_t io_info; /* Temporary I/O info object */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);
int nerrors=0;
H5D_rdcc_ent_t *ent=NULL, *next=NULL;
herr_t ret_value=SUCCEED; /* Return value */
unsigned nerrors = 0;
H5D_rdcc_ent_t *ent, *next;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_flush, FAIL)
/* Fill the DXPL cache values for later use */
if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Construct dataset I/O info */
H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,NULL);
H5D_BUILD_IO_INFO(&io_info, dset, dxpl_cache, dxpl_id, NULL);
for (ent=rdcc->head; ent; ent=next) {
/* Loop over all entries in the chunk cache */
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
if ((flags&H5F_FLUSH_INVALIDATE)) {
if (H5D_istore_preempt(&io_info, ent, TRUE )<0)
if((flags & H5F_FLUSH_INVALIDATE)) {
if(H5D_istore_preempt(&io_info, ent, TRUE) < 0)
nerrors++;
} else {
if (H5D_istore_flush_entry(&io_info, ent, FALSE)<0)
if(H5D_istore_flush_entry(&io_info, ent, FALSE) < 0)
nerrors++;
}
} /* end for */
if (nerrors)
if(nerrors)
HGOTO_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
done:
@ -1696,43 +1696,42 @@ done:
*-------------------------------------------------------------------------
*/
static void *
H5D_istore_lock(const H5D_io_info_t *io_info,
H5D_istore_ud1_t *udata, hbool_t relax, unsigned *idx_hint/*in,out*/)
H5D_istore_lock(const H5D_io_info_t *io_info, H5D_istore_ud1_t *udata,
hbool_t relax, unsigned *idx_hint/*in,out*/)
{
H5D_t *dset=io_info->dset; /* Local pointer to the dataset info */
const H5O_pline_t *pline=&(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_layout_t *layout=&(dset->shared->layout); /* Dataset layout */
const H5O_fill_t *fill=&(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_time_t fill_time=dset->shared->dcpl_cache.fill_time; /* Fill time */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/
H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */
const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache*/
H5D_rdcc_ent_t *ent = NULL; /*cache entry */
unsigned idx=0; /*hash index number */
unsigned idx = 0; /*hash index number */
hbool_t found = FALSE; /*already in cache? */
size_t chunk_size; /*size of a chunk */
void *chunk = NULL; /*the file chunk */
unsigned u; /*counters */
size_t chunk_size=0; /*size of a chunk */
void *chunk=NULL; /*the file chunk */
void *ret_value; /*return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_istore_lock)
assert(io_info);
assert(dset);
assert(io_info->dxpl_cache);
assert(io_info->store);
assert(TRUE==H5P_isa_class(io_info->dxpl_id,H5P_DATASET_XFER));
HDassert(io_info);
HDassert(dset);
HDassert(io_info->dxpl_cache);
HDassert(io_info->store);
HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER));
/* Get the chunk's size */
assert(layout->u.chunk.size>0);
H5_ASSIGN_OVERFLOW(chunk_size,layout->u.chunk.size,hsize_t,size_t);
HDassert(layout->u.chunk.size > 0);
H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, hsize_t, size_t);
/* Search for the chunk in the cache */
if (rdcc->nslots>0) {
idx=H5D_HASH(dset->shared,io_info->store->chunk.index);
if(rdcc->nslots > 0) {
idx = H5D_HASH(dset->shared,io_info->store->chunk.index);
ent = rdcc->slot[idx];
if (ent) {
for (u=0, found=TRUE; u<layout->u.chunk.ndims; u++) {
if (io_info->store->chunk.offset[u]!=ent->offset[u]) {
if(ent) {
for(u = 0, found = TRUE; u < layout->u.chunk.ndims; u++) {
if(io_info->store->chunk.offset[u] != ent->offset[u]) {
found = FALSE;
break;
} /* end if */
@ -1740,15 +1739,15 @@ H5D_istore_lock(const H5D_io_info_t *io_info,
} /* end if */
} /* end if */
if (found) {
if(found) {
/*
* Already in the cache. Count a hit.
*/
#ifdef H5D_ISTORE_DEBUG
rdcc->nhits++;
#endif /* H5D_ISTORE_DEBUG */
} else if (relax) {
} /* end if */
else if(relax) {
/*
* Not in the cache, but we're about to overwrite the whole thing
* anyway, so just allocate a buffer for it but don't initialize that
@ -1760,10 +1759,11 @@ H5D_istore_lock(const H5D_io_info_t *io_info,
HDfflush(stderr);
rdcc->nhits++;
#endif
if (NULL==(chunk=H5D_istore_chunk_alloc (chunk_size,pline)))
if(NULL == (chunk = H5D_istore_chunk_alloc(chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
} else {
} /* end if */
else {
H5D_istore_ud1_t tmp_udata; /*B-tree pass-through */
haddr_t chunk_addr; /* Address of chunk on disk */
@ -1812,41 +1812,42 @@ H5D_istore_lock(const H5D_io_info_t *io_info,
/* Chunk size on disk isn't [likely] the same size as the final chunk
* size in memory, so allocate memory big enough. */
if (NULL==(chunk = H5D_istore_chunk_alloc (chunk_size,pline)))
if(NULL == (chunk = H5D_istore_chunk_alloc (chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk")
if (H5P_is_fill_value_defined(fill, &fill_status) < 0)
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined")
if(fill_time==H5D_FILL_TIME_ALLOC ||
(fill_time==H5D_FILL_TIME_IFSET && fill_status==H5D_FILL_VALUE_USER_DEFINED)) {
if (fill && fill->buf) {
if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
if(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);
} else {
HDassert(0 == (chunk_size % (size_t)fill->size));
H5V_array_fill(chunk, fill->buf, (size_t)fill->size, chunk_size / fill->size);
} /* end if */
else {
/*
* The chunk doesn't exist in the file and no fill value was
* specified. Assume all zeros.
*/
HDmemset (chunk, 0, chunk_size);
HDmemset(chunk, 0, chunk_size);
} /* end else */
} /* end if */
#ifdef H5_USING_PURIFY
else
HDmemset(chunk,0,chunk_size);
HDmemset(chunk, 0, chunk_size);
#endif /* H5_USING_PURIFY */
#ifdef H5D_ISTORE_DEBUG
rdcc->ninits++;
#endif /* H5D_ISTORE_DEBUG */
} /* end else */
}
assert (found || chunk_size>0);
} /* end else */
HDassert(found || chunk_size > 0);
if (!found && rdcc->nslots>0 && chunk_size<=rdcc->nbytes &&
if(!found && rdcc->nslots > 0 && chunk_size <= rdcc->nbytes &&
(!ent || !ent->locked)) {
/*
* Add the chunk to the cache only if the slot is not already locked.
@ -2128,21 +2129,18 @@ HDfprintf(stderr,"%s: buf=%p\n",FUNC,buf);
* the entire I/O operation on the chunk will be skipped. -QAK
*/
if(!H5F_addr_defined(chunk_addr)) {
const H5O_fill_t *fill=&(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_time_t fill_time=dset->shared->dcpl_cache.fill_time; /* Fill time */
H5D_fill_value_t fill_status;
H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk);/*raw data chunk cache*/
hbool_t found = FALSE; /*already in cache? */
/* Check if the chunk is in the cache (but hasn't been written to disk yet) */
if (rdcc->nslots>0) {
unsigned idx=H5D_HASH(dset->shared, io_info->store->chunk.index); /* Cache entry index */
if(rdcc->nslots>0) {
unsigned idx = H5D_HASH(dset->shared, io_info->store->chunk.index); /* Cache entry index */
H5D_rdcc_ent_t *ent = rdcc->slot[idx]; /* Cache entry */
/* Potential match... */
if (ent) {
for (u=0, found=TRUE; u<dset->shared->layout.u.chunk.ndims; u++) {
if (io_info->store->chunk.offset[u]!=ent->offset[u]) {
if(ent) {
for(u = 0, found = TRUE; u < dset->shared->layout.u.chunk.ndims; u++) {
if(io_info->store->chunk.offset[u] != ent->offset[u]) {
found = FALSE;
break;
} /* end if */
@ -2152,47 +2150,50 @@ HDfprintf(stderr,"%s: buf=%p\n",FUNC,buf);
/* If the chunk is in the cache, then it must have valid data */
if(!found) {
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status;
/* Check if the fill value is defined */
if (H5P_is_fill_value_defined(fill, &fill_status) < 0)
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If we are never to return fill values, or if we would return them
* but they aren't set, process the entire set of I/O vectors and
* get out now.
*/
if(fill_time==H5D_FILL_TIME_NEVER ||
(fill_time==H5D_FILL_TIME_IFSET && fill_status!=H5D_FILL_VALUE_USER_DEFINED)) {
if(fill->fill_time == H5D_FILL_TIME_NEVER ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status!=H5D_FILL_VALUE_USER_DEFINED)) {
size_t size; /* Size of sequence in bytes */
size_t v; /* Local index variable */
ssize_t bytes_processed=0; /* Eventual return value */
ssize_t bytes_processed = 0; /* Eventual return value */
/* Work through all the sequences */
for(u=*mem_curr_seq, v=*chunk_curr_seq; u<mem_max_nseq && v<chunk_max_nseq; ) {
for(u = *mem_curr_seq, v = *chunk_curr_seq; u < mem_max_nseq && v < chunk_max_nseq; ) {
/* Choose smallest buffer to write */
if(chunk_len_arr[v]<mem_len_arr[u])
size=chunk_len_arr[v];
if(chunk_len_arr[v] < mem_len_arr[u])
size = chunk_len_arr[v];
else
size=mem_len_arr[u];
size = mem_len_arr[u];
/* Update source information */
chunk_len_arr[v]-=size;
chunk_offset_arr[v]+=size;
if(chunk_len_arr[v]==0)
chunk_len_arr[v] -= size;
chunk_offset_arr[v] += size;
if(chunk_len_arr[v] == 0)
v++;
/* Update destination information */
mem_len_arr[u]-=size;
mem_offset_arr[u]+=size;
if(mem_len_arr[u]==0)
mem_len_arr[u] -= size;
mem_offset_arr[u] += size;
if(mem_len_arr[u] == 0)
u++;
/* Increment number of bytes copied */
bytes_processed+=(ssize_t)size;
bytes_processed += (ssize_t)size;
} /* end for */
/* Update current sequence vectors */
*mem_curr_seq=u;
*chunk_curr_seq=v;
*mem_curr_seq = u;
*chunk_curr_seq = v;
HGOTO_DONE(bytes_processed)
} /* end if */
@ -2203,19 +2204,19 @@ HDfprintf(stderr,"%s: buf=%p\n",FUNC,buf);
* Lock the chunk, copy from application to chunk, then unlock the
* chunk.
*/
if (NULL==(chunk=H5D_istore_lock(io_info, &udata, FALSE, &idx_hint)))
if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
/* Use the vectorized memory copy routine to do actual work */
if((naccessed=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_len_arr,mem_offset_arr,chunk,chunk_max_nseq,chunk_curr_seq,chunk_len_arr,chunk_offset_arr))<0)
if((naccessed = H5V_memcpyvv(buf, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, chunk, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr)) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "vectorized memcpy failed")
H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
if (H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, (size_t)naccessed)<0)
H5_CHECK_OVERFLOW(naccessed, ssize_t, size_t);
if(H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, (size_t)naccessed) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk")
/* Set return value */
ret_value=naccessed;
ret_value = naccessed;
} /* end else */
done:
@ -2675,14 +2676,11 @@ H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline)
* Return: Non-negative on success/Negative on failure
*
* Note: Current implementation relies on cache_size being 0,
* thus no chunk is cashed and written to disk immediately
* thus no chunk is cached and written to disk immediately
* when a chunk is unlocked (via H5F_istore_unlock)
* This should be changed to do a direct flush independent
* of the cache value.
*
* This routine might be called before the dcpl_cache is set up
* correctly, so don't use those values.
*
* Programmer: Albert Cheng
* June 26, 1998
*
@ -2695,60 +2693,43 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
H5D_storage_t store; /* Dataset storage information */
hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /* Offset of current chunk */
hsize_t chunk_size; /* Size of chunk in bytes */
unsigned filter_mask=0; /* Filter mask for chunks that have them */
H5O_pline_t pline; /* I/O pipeline information */
hbool_t pline_initialized=FALSE; /* Flag to indicate that pline has valid info */
H5O_fill_t fill; /* Fill value information */
H5D_fill_time_t fill_time; /* When to write fill values */
H5D_fill_value_t fill_status; /* The fill value status */
unsigned should_fill=0; /* Whether fill values should be written */
void *chunk=NULL; /* Chunk buffer for writing fill values */
unsigned filter_mask = 0; /* Filter mask for chunks that have them */
const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info */
const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */
H5D_fill_value_t fill_status; /* The fill value status */
hbool_t should_fill = FALSE; /* Whether fill values should be written */
void *chunk = NULL; /* Chunk buffer for writing fill values */
H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */
H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
#ifdef H5_HAVE_PARALLEL
MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank=(-1); /* This process's rank */
MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank = (-1); /* This process's rank */
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 */
hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */
hbool_t using_mpi = FALSE; /* 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 */
H5P_genplist_t *dc_plist; /* Property list */
hbool_t carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
int space_ndims; /* Dataset's space rank */
hsize_t space_dim[H5O_LAYOUT_NDIMS]; /* Dataset's dataspace dimensions */
herr_t ret_value=SUCCEED; /* Return value */
int i; /* Local index variable */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_allocate, FAIL)
/* Check args */
assert(dset && H5D_CHUNKED==dset->shared->layout.type);
assert(dset->shared->layout.u.chunk.ndims>0 && dset->shared->layout.u.chunk.ndims<=H5O_LAYOUT_NDIMS);
assert(H5F_addr_defined(dset->shared->layout.u.chunk.addr));
assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER));
/* Get dataset's creation property list */
if (NULL == (dc_plist = H5I_object(dset->shared->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
HDassert(dset && H5D_CHUNKED == dset->shared->layout.type);
HDassert(dset->shared->layout.u.chunk.ndims > 0 && dset->shared->layout.u.chunk.ndims <= H5O_LAYOUT_NDIMS);
HDassert(H5F_addr_defined(dset->shared->layout.u.chunk.addr));
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
/* We only handle simple data spaces so far */
if ((space_ndims=H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL))<0)
if((space_ndims = H5S_get_simple_extent_dims(dset->shared->space, space_dim, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info")
space_dim[space_ndims] = dset->shared->layout.u.chunk.dim[space_ndims];
/* 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_DATA_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get data pipeline")
pline_initialized=TRUE;
if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time")
/* Fill the DXPL cache values for later use */
if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
#ifdef H5_HAVE_PARALLEL
@ -2759,24 +2740,24 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator")
/* Get the MPI rank */
if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file))<0)
if((mpi_rank = H5F_mpi_get_rank(dset->oloc.file)) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank")
/* Set the MPI-capable file driver flag */
using_mpi=1;
using_mpi = TRUE;
} /* end if */
#endif /* H5_HAVE_PARALLEL */
/*
* Setup indice to go through all chunks. (Future improvement
* should allocate only chunks that have no file space assigned yet.
* Setup indice to go through all chunks. (Future improvement:
* should allocate only chunks that have no file space assigned yet).
*/
for (u=0; u<dset->shared->layout.u.chunk.ndims; u++)
for(u = 0; u < dset->shared->layout.u.chunk.ndims; u++)
chunk_offset[u] = 0;
chunk_size = dset->shared->layout.u.chunk.size;
/* Check the dataset's fill-value status */
if (H5P_is_fill_value_defined(&fill, &fill_status) < 0)
if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
/* If we are filling the dataset on allocation or "if set" and
@ -2784,69 +2765,67 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
* or if there are any pipeline filters defined,
* set the "should fill" flag
*/
if((!full_overwrite && (fill_time == H5D_FILL_TIME_ALLOC ||
(fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)))
|| pline.nused > 0)
should_fill = 1;
if((!full_overwrite && (fill->fill_time == H5D_FILL_TIME_ALLOC ||
(fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)))
|| pline->nused > 0)
should_fill = TRUE;
/* Check if fill values should be written to blocks */
if(should_fill) {
/* Allocate chunk buffer for processes to use when writing fill values */
H5_CHECK_OVERFLOW(chunk_size, hsize_t, size_t);
if(NULL == (chunk = H5D_istore_chunk_alloc((size_t)chunk_size, &pline)))
if(NULL == (chunk = H5D_istore_chunk_alloc((size_t)chunk_size, pline)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for chunk")
/* Fill the chunk with the proper values */
if(fill.buf) {
/*
* Replicate the fill value throughout the chunk.
*/
assert(0==chunk_size % fill.size);
H5V_array_fill(chunk, fill.buf, fill.size, (size_t)chunk_size/fill.size);
} else {
/*
* No fill value was specified, assume all zeros.
*/
HDmemset (chunk, 0, (size_t)chunk_size);
} /* end else */
if(fill->buf) {
/* Replicate the fill value throughout the chunk */
HDassert(0 == (chunk_size % (size_t)fill->size));
H5V_array_fill(chunk, fill->buf, (size_t)fill->size, (size_t)(chunk_size / fill->size));
} /* end if */
else
/* No fill value was specified, assume all zeros. */
HDmemset(chunk, 0, (size_t)chunk_size);
/* Check if there are filters which need to be applied to the chunk */
if (pline.nused>0) {
size_t buf_size=(size_t)chunk_size;
size_t nbytes=(size_t)chunk_size;
if(pline->nused > 0) {
size_t buf_size = (size_t)chunk_size;
size_t nbytes = (size_t)chunk_size;
/* Push the chunk through the filters */
if (H5Z_pipeline(&pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &chunk)<0)
if(H5Z_pipeline(pline, 0, &filter_mask, dxpl_cache->err_detect, dxpl_cache->filter_cb, &nbytes, &buf_size, &chunk) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed")
/* Keep the number of bytes the chunk turned in to */
chunk_size=nbytes;
chunk_size = nbytes;
} /* end if */
} /* end if */
/* Set up dataset I/O info */
store.chunk.offset=chunk_offset;
H5D_BUILD_IO_INFO(&io_info,dset,dxpl_cache,dxpl_id,&store);
store.chunk.offset = chunk_offset;
H5D_BUILD_IO_INFO(&io_info, dset, dxpl_cache, dxpl_id, &store);
/* Loop over all chunks */
carry=0;
while (carry==0) {
carry = FALSE;
while(!carry) {
hbool_t chunk_exists; /* Flag to indicate whether a chunk exists already */
/* Check if the chunk exists yet on disk */
chunk_exists=1;
if(H5D_istore_get_addr(&io_info,NULL)==HADDR_UNDEF) {
chunk_exists = TRUE;
if(H5D_istore_get_addr(&io_info, NULL) == HADDR_UNDEF) {
const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /*raw data chunk cache */
H5D_rdcc_ent_t *ent = NULL; /*cache entry */
H5D_rdcc_ent_t *ent; /*cache entry */
/* Didn't find the chunk on disk */
chunk_exists = 0;
chunk_exists = FALSE;
/* Look for chunk in cache */
for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
/* Assume a match */
chunk_exists = 1;
chunk_exists = TRUE;
for(u = 0; u < dset->shared->layout.u.chunk.ndims && chunk_exists; u++) {
if(ent->offset[u] != chunk_offset[u])
chunk_exists = 0; /* Reset if no match */
chunk_exists = FALSE; /* Reset if no match */
} /* end for */
} /* end for */
} /* end if */
@ -2874,13 +2853,12 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
if(using_mpi) {
/* Write the chunks out from only one process */
/* !! Use the internal "independent" DXPL!! -QAK */
if(H5_PAR_META_WRITE==mpi_rank) {
if(H5_PAR_META_WRITE == mpi_rank)
if(H5F_block_write(dset->oloc.file, H5FD_MEM_DRAW, udata.addr, udata.common.key.nbytes, H5AC_ind_dxpl_id, chunk) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file")
} /* end if */
/* Indicate that blocks are being written */
blocks_written=1;
blocks_written = TRUE;
} /* end if */
else {
#endif /* H5_HAVE_PARALLEL */
@ -2893,12 +2871,12 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
} /* end if */
/* Increment indices */
for (i=(int)dset->shared->layout.u.chunk.ndims-1, carry=1; i>=0 && carry; --i) {
for(i = (int)dset->shared->layout.u.chunk.ndims - 1, carry = TRUE; i >= 0 && carry; --i) {
chunk_offset[i] += dset->shared->layout.u.chunk.dim[i];
if (chunk_offset[i] >= space_dim[i])
chunk_offset[i] = 0;
else
carry = 0;
carry = FALSE;
} /* end for */
} /* end while */
@ -2911,31 +2889,30 @@ H5D_istore_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite)
* them in, getting bogus data.
*/
if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code)
} /* end if */
#endif /* H5_HAVE_PARALLEL */
done:
/* Free the chunk for fill values */
if(chunk!=NULL && pline_initialized)
chunk=H5D_istore_chunk_xfree(chunk,&pline);
if(chunk)
chunk = H5D_istore_chunk_xfree(chunk, pline);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_istore_allocate() */
/*-------------------------------------------------------------------------
* Function: H5D_istore_prune_by_extent
* Function: H5D_istore_prune_by_extent
*
* Purpose: This function searches for chunks that are no longer necessary both in the
* raw data cache and in the B-tree.
* Purpose: This function searches for chunks that are no longer necessary both in the
* raw data cache and in the B-tree.
*
* Return: Success: 0, Failure: -1
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* Algorithm: Robb Matzke
*
* Date: March 27, 2002
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* Algorithm: Robb Matzke
* March 27, 2002
*
* The algorithm is:
*
@ -3098,17 +3075,14 @@ done:
/*-------------------------------------------------------------------------
* Function: H5D_istore_prune_extent
* Function: H5D_istore_prune_extent
*
* Purpose: Search for chunks that are no longer necessary in the B-tree.
* Purpose: Search for chunks that are no longer necessary in the B-tree.
*
* Return: Success: 0, Failure: -1
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: March 26, 2002
*
* Comments: Called by H5D_prune_by_extent
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* March 26, 2002
*
*-------------------------------------------------------------------------
*/
@ -3149,18 +3123,15 @@ done:
/*-------------------------------------------------------------------------
* Function: H5D_istore_remove
* Function: H5D_istore_remove
*
* Purpose: Removes chunks that are no longer necessary in the B-tree.
* Purpose: Removes chunks that are no longer necessary in the B-tree.
*
* Return: Success: 0, Failure: -1
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: March 28, 2002
*
* Comments: Part of H5B_ISTORE
* March 28, 2002
*
*-------------------------------------------------------------------------
*/
@ -3191,16 +3162,15 @@ done:
/*-------------------------------------------------------------------------
* Function: H5D_istore_initialize_by_extent
* Function: H5D_istore_initialize_by_extent
*
* Purpose: This function searches for chunks that have to be initialized with the fill
* value both in the raw data cache and in the B-tree.
* Purpose: This function searches for chunks that have to be initialized with the fill
* value both in the raw data cache and in the B-tree.
*
* Return: Success: 0, Failure: -1
* Return: Non-negative on success/Negative on failure
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: April 4, 2002
* April 4, 2002
*
* Comments:
*
@ -3215,7 +3185,7 @@ done:
herr_t
H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
{
const H5O_layout_t *layout=&(io_info->dset->shared->layout); /* Dataset layout */
const H5O_layout_t *layout = &(io_info->dset->shared->layout); /* Dataset layout */
uint8_t *chunk = NULL; /*the file chunk */
unsigned idx_hint = 0; /*input value for H5F_istore_lock */
hsize_t chunk_offset[H5O_LAYOUT_NDIMS]; /*logical location of the chunks */
@ -3224,7 +3194,7 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hsize_t naccessed; /*bytes accessed in chunk */
hsize_t end_chunk; /*chunk position counter */
hsize_t start[H5O_LAYOUT_NDIMS]; /*starting location of hyperslab */
hsize_t start[H5O_LAYOUT_NDIMS]; /*starting location of hyperslab */
hsize_t count[H5O_LAYOUT_NDIMS]; /*element count of hyperslab */
hsize_t size[H5O_LAYOUT_NDIMS]; /*current size of dimensions */
H5S_t *space_chunk = NULL; /*dataspace for a chunk */
@ -3235,34 +3205,18 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
int srank; /*current # of dimensions (signed) */
unsigned rank; /*current # of dimensions */
int i, carry; /*counters */
unsigned u;
int found = 0; /*initialize this entry */
H5P_genplist_t *dc_plist; /* Property list */
H5O_pline_t pline; /* I/O pipeline information */
H5O_fill_t fill; /* Fill value information */
H5D_fill_time_t fill_time; /* Fill time information */
H5D_storage_t store; /* Dataset storage information */
herr_t ret_value=SUCCEED; /* Return value */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_istore_initialize_by_extent, FAIL)
/* Check args */
assert(io_info);
assert(io_info->dset && H5D_CHUNKED == layout->type);
assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
assert(H5F_addr_defined(layout->u.chunk.addr));
/* Get dataset's creation property list */
if (NULL == (dc_plist = H5I_object(io_info->dset->shared->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list")
/* Get necessary properties from property list */
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value")
if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill time")
if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data pipeline")
HDassert(io_info);
HDassert(io_info->dset && H5D_CHUNKED == layout->type);
HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
HDassert(H5F_addr_defined(layout->u.chunk.addr));
/* Reset start & count arrays */
HDmemset(start, 0, sizeof(start));
@ -3270,8 +3224,8 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
/* Go get the rank & dimensions */
if((srank = H5S_get_simple_extent_dims(io_info->dset->shared->space, curr_dims, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned);
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
H5_ASSIGN_OVERFLOW(rank, srank, int, unsigned);
/* Copy current dimensions */
for(u = 0; u < rank; u++) {
@ -3303,17 +3257,17 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
} /* end for */
/* Point to local dataset storage info */
assert(io_info->store==NULL); /* Make certain we aren't blowing anything away */
io_info->store=&store;
HDassert(io_info->store == NULL); /* Make certain we aren't blowing anything away */
io_info->store = &store;
/* Loop over all chunks */
carry=0;
while(carry==0) {
carry = 0;
while(carry == 0) {
for(u = 0, naccessed = 1; u < layout->u.chunk.ndims; u++) {
/* The location and size of the chunk being accessed */
chunk_offset[u] = idx_cur[u] * layout->u.chunk.dim[u];
sub_size[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u],
size[u]) - chunk_offset[u];
sub_size[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u], size[u])
- chunk_offset[u];
naccessed *= sub_size[u];
} /* end for */
@ -3327,19 +3281,20 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
found = 1;
break;
}
} /* end for */
} /* end for */
if(found) {
const H5O_fill_t *fill = &io_info->dset->shared->dcpl_cache.fill; /* Fill value information */
/* Calculate the index of this chunk */
if(H5V_chunk_index(rank,chunk_offset,layout->u.chunk.dim,down_chunks,&store.chunk.index)<0)
if(H5V_chunk_index(rank, chunk_offset, layout->u.chunk.dim, down_chunks, &store.chunk.index) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
store.chunk.offset=chunk_offset;
store.chunk.offset = chunk_offset;
if(NULL == (chunk = H5D_istore_lock(io_info, NULL, FALSE, &idx_hint)))
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk")
if(H5S_select_all(space_chunk,1) < 0)
if(H5S_select_all(space_chunk, 1) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select space")
for(u = 0; u < rank; u++)
@ -3356,8 +3311,7 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
HDfputs("]\n", stdout);
#endif
if(H5S_select_hyperslab(space_chunk, H5S_SELECT_NOTB, start, NULL,
count, NULL) < 0)
if(H5S_select_hyperslab(space_chunk, H5S_SELECT_NOTB, start, NULL, count, NULL) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select hyperslab")
/* Fill the selection in the memory buffer */
@ -3365,7 +3319,7 @@ H5D_istore_initialize_by_extent(H5D_io_info_t *io_info)
/* relying on the fill.size, which might be set to 0 if there is */
/* no fill-value defined for the dataset -QAK */
H5_CHECK_OVERFLOW(size[rank],hsize_t,size_t);
if(H5S_select_fill(fill.buf, (size_t)size[rank], space_chunk, chunk) < 0)
if(H5S_select_fill(fill->buf, (size_t)size[rank], space_chunk, chunk) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed")
if(H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, (size_t)naccessed) < 0)
@ -3487,11 +3441,11 @@ H5D_istore_update_cache(H5D_t *dset, hid_t dxpl_id)
chunks[u] = ((curr_dims[u]+dset->shared->layout.u.chunk.dim[u])-1) / dset->shared->layout.u.chunk.dim[u];
/* Get the "down" sizes for each dimension */
if(H5V_array_down(rank,chunks,down_chunks)<0)
if(H5V_array_down(rank,chunks,down_chunks) < 0)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
/* Fill the DXPL cache values for later use */
if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
/* Construct dataset I/O info */

6
src/H5Dpkg.h
View File

@ -159,12 +159,6 @@ typedef struct H5D_shared_t {
H5O_layout_t layout; /* data layout */
hbool_t checked_filters;/* TRUE if dataset passes can_apply check */
/* Cache some frequently accessed values from the DCPL */
H5O_efl_t efl; /* External file list information */
H5D_alloc_time_t alloc_time; /* Dataset allocation time */
H5D_fill_time_t fill_time; /* Dataset fill value writing time */
H5O_fill_t fill; /* Dataset fill value information */
/* Buffered/cached information for types of raw data storage*/
struct {
H5D_rdcdc_t contig; /* Information about contiguous data */

6
src/H5Dprivate.h
View File

@ -45,9 +45,7 @@
#define H5D_CRT_CHUNK_DIM_NAME "chunk_ndims" /* Chunk dimensionality */
#define H5D_CRT_CHUNK_SIZE_NAME "chunk_size" /* Chunk size */
#define H5D_CRT_FILL_VALUE_NAME "fill_value" /* Fill value */
#define H5D_CRT_ALLOC_TIME_NAME "alloc_time" /* Space allocation time */
#define H5D_CRT_ALLOC_TIME_STATE_NAME "alloc_time_state" /* Space allocation time state */
#define H5D_CRT_FILL_TIME_NAME "fill_time" /* Time of fill value writing */
#define H5D_CRT_EXT_FILE_LIST_NAME "efl" /* External file list */
#define H5D_CRT_DATA_PIPELINE_NAME "pline" /* Data filter pipeline */
@ -144,9 +142,9 @@ typedef struct H5D_dxpl_cache_t {
/* Typedef for cached dataset creation property list information */
typedef struct H5D_dcpl_cache_t {
H5O_pline_t pline; /* I/O pipeline info (H5D_CRT_DATA_PIPELINE_NAME) */
H5O_fill_t fill; /* Fill value info (H5D_CRT_FILL_VALUE_NAME) */
H5D_fill_time_t fill_time; /* Fill time (H5D_CRT_FILL_TIME_NAME) */
H5O_pline_t pline; /* I/O pipeline info (H5D_CRT_DATA_PIPELINE_NAME) */
H5O_efl_t efl; /* External file list info (H5D_CRT_EXT_FILE_LIST_NAME) */
} H5D_dcpl_cache_t;
/*****************************/

26
src/H5Dpublic.h
View File

@ -44,27 +44,27 @@ typedef enum H5D_layout_t {
/* Values for the space allocation time property */
typedef enum H5D_alloc_time_t {
H5D_ALLOC_TIME_ERROR =-1,
H5D_ALLOC_TIME_DEFAULT =0,
H5D_ALLOC_TIME_EARLY =1,
H5D_ALLOC_TIME_LATE =2,
H5D_ALLOC_TIME_INCR =3
H5D_ALLOC_TIME_ERROR = -1,
H5D_ALLOC_TIME_DEFAULT = 0,
H5D_ALLOC_TIME_EARLY = 1,
H5D_ALLOC_TIME_LATE = 2,
H5D_ALLOC_TIME_INCR = 3
} H5D_alloc_time_t;
/* Values for the status of space allocation */
typedef enum H5D_space_status_t {
H5D_SPACE_STATUS_ERROR =-1,
H5D_SPACE_STATUS_NOT_ALLOCATED =0,
H5D_SPACE_STATUS_PART_ALLOCATED =1,
H5D_SPACE_STATUS_ALLOCATED =2
H5D_SPACE_STATUS_ERROR = -1,
H5D_SPACE_STATUS_NOT_ALLOCATED = 0,
H5D_SPACE_STATUS_PART_ALLOCATED = 1,
H5D_SPACE_STATUS_ALLOCATED = 2
} H5D_space_status_t;
/* Values for time of writing fill value property */
typedef enum H5D_fill_time_t {
H5D_FILL_TIME_ERROR =-1,
H5D_FILL_TIME_ALLOC =0,
H5D_FILL_TIME_NEVER =1,
H5D_FILL_TIME_IFSET =2
H5D_FILL_TIME_ERROR = -1,
H5D_FILL_TIME_ALLOC = 0,
H5D_FILL_TIME_NEVER = 1,
H5D_FILL_TIME_IFSET = 2
} H5D_fill_time_t;
/* Values for fill value status */

6
src/H5MM.c
View File

@ -239,8 +239,6 @@ done:
* matzke@llnl.gov
* Jul 10 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void *
@ -249,8 +247,8 @@ H5MM_xfree(void *mem)
/* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5MM_xfree);
if (mem)
if(mem)
HDfree(mem);
FUNC_LEAVE_NOAPI(NULL);
}
} /* end H5MM_xfree() */

32
src/H5Oefl.c
View File

@ -269,36 +269,34 @@ H5O_efl_copy(const void *_mesg, void *_dest)
size_t u; /* Local index variable */
void *ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5O_efl_copy);
FUNC_ENTER_NOAPI_NOINIT(H5O_efl_copy)
/* check args */
assert(mesg);
if (!dest) {
if (NULL==(dest = H5MM_calloc(sizeof(H5O_efl_t))) ||
NULL==(dest->slot=H5MM_malloc(mesg->nalloc* sizeof(H5O_efl_entry_t))))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed");
} else if (dest->nalloc<mesg->nalloc) {
HDassert(mesg);
if(!dest) {
if(NULL == (dest = H5MM_calloc(sizeof(H5O_efl_t))) ||
NULL == (dest->slot = H5MM_malloc(mesg->nalloc * sizeof(H5O_efl_entry_t))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
} else if(dest->nalloc < mesg->nalloc) {
H5MM_xfree(dest->slot);
if (NULL==(dest->slot = H5MM_malloc(mesg->nalloc*
sizeof(H5O_efl_entry_t))))
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed");
if(NULL == (dest->slot = H5MM_malloc(mesg->nalloc * sizeof(H5O_efl_entry_t))))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
}
dest->heap_addr = mesg->heap_addr;
dest->nalloc = mesg->nalloc;
dest->nused = mesg->nused;
for (u = 0; u < mesg->nused; u++) {
for(u = 0; u < mesg->nused; u++) {
dest->slot[u] = mesg->slot[u];
dest->slot[u].name = H5MM_xstrdup (mesg->slot[u].name);
}
dest->slot[u].name = H5MM_xstrdup(mesg->slot[u].name);
} /* end for */
/* Set return value */
ret_value=dest;
ret_value = dest;
done:
FUNC_LEAVE_NOAPI(ret_value);
}
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_efl_copy() */
/*-------------------------------------------------------------------------

315
src/H5Ofill.c
View File

@ -30,38 +30,34 @@
#include "H5Pprivate.h" /* Property lists */
static void *H5O_fill_decode(H5F_t *f, hid_t dxpl_id, const uint8_t *p);
static herr_t H5O_fill_encode(H5F_t *f, uint8_t *p, const void *_mesg);
static size_t H5O_fill_size(const H5F_t *f, const void *_mesg);
static herr_t H5O_fill_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE *stream,
int indent, int fwidth);
static void *H5O_fill_new_decode(H5F_t *f, hid_t dxpl_id, const uint8_t *p);
static herr_t H5O_fill_new_encode(H5F_t *f, uint8_t *p, const void *_mesg);
static void *H5O_fill_new_copy(const void *_mesg, void *_dest);
static size_t H5O_fill_new_size(const H5F_t *f, const void *_mesg);
static herr_t H5O_fill_new_reset(void *_mesg);
static herr_t H5O_fill_new_free(void *_mesg);
static herr_t H5O_fill_new_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE *stream,
int indent, int fwidth);
static void *H5O_fill_decode(H5F_t *f, hid_t dxpl_id, const uint8_t *p);
static herr_t H5O_fill_encode(H5F_t *f, uint8_t *p, const void *_mesg);
static void *H5O_fill_copy(const void *_mesg, void *_dest);
static size_t H5O_fill_size(const H5F_t *f, const void *_mesg);
static herr_t H5O_fill_reset(void *_mesg);
static herr_t H5O_fill_free(void *_mesg);
static void *H5O_fill_new_get_share(const void *_mesg, H5O_shared_t *sh);
static herr_t H5O_fill_new_set_share(void *_mesg, const H5O_shared_t *sh);
static htri_t H5O_fill_new_is_shared(const void *_mesg);
static herr_t H5O_fill_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE *stream,
static herr_t H5O_fill_new_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE *stream,
int indent, int fwidth);
/* This message derives from H5O message class, for old fill value before version 1.5 */
const H5O_msg_class_t H5O_MSG_FILL[1] = {{
H5O_FILL_ID, /*message id number */
"fill", /*message name for debugging */
sizeof(H5O_fill_t), /*native message size */
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_new_copy, /*copy the native value */
H5O_fill_size, /*raw message size */
H5O_fill_reset, /*free internal memory */
H5O_fill_free, /* free method */
H5O_fill_new_reset, /*free internal memory */
H5O_fill_new_free, /* free method */
NULL, /* file delete method */
NULL, /* link method */
H5O_fill_new_get_share, /* get share method */
@ -80,7 +76,7 @@ const H5O_msg_class_t H5O_MSG_FILL[1] = {{
const H5O_msg_class_t H5O_MSG_FILL_NEW[1] = {{
H5O_FILL_NEW_ID, /*message id number */
"fill_new", /*message name for debugging */
sizeof(H5O_fill_new_t), /*native message size */
sizeof(H5O_fill_t), /*native message size */
H5O_fill_new_decode, /*decode message */
H5O_fill_new_encode, /*encode message */
H5O_fill_new_copy, /*copy the native value */
@ -106,9 +102,6 @@ const H5O_msg_class_t H5O_MSG_FILL_NEW[1] = {{
/* Revised version of the "new" fill value information */
#define H5O_FILL_VERSION_2 2
/* Declare a free list to manage the H5O_fill_new_t struct */
H5FL_DEFINE(H5O_fill_new_t);
/* Declare a free list to manage the H5O_fill_t struct */
H5FL_DEFINE(H5O_fill_t);
@ -134,16 +127,16 @@ H5FL_DEFINE(H5O_fill_t);
static void *
H5O_fill_new_decode(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const uint8_t *p)
{
H5O_fill_new_t *mesg = NULL;
int version;
void *ret_value;
H5O_fill_t *mesg = NULL;
int version;
void *ret_value;
FUNC_ENTER_NOAPI_NOINIT(H5O_fill_new_decode)
HDassert(f);
HDassert(p);
if(NULL == (mesg = H5FL_CALLOC(H5O_fill_new_t)))
if(NULL == (mesg = H5FL_CALLOC(H5O_fill_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value message")
/* Version */
@ -180,7 +173,7 @@ done:
if(!ret_value && mesg) {
if(mesg->buf)
H5MM_xfree(mesg->buf);
H5FL_FREE(H5O_fill_new_t,mesg);
H5FL_FREE(H5O_fill_t, mesg);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
@ -199,15 +192,13 @@ done:
* Programmer: Robb Matzke
* Wednesday, September 30, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5O_fill_decode(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const uint8_t *p)
{
H5O_fill_t *mesg = NULL;
void *ret_value;
H5O_fill_t *mesg = NULL; /* Decoded fill value message */
void *ret_value; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5O_fill_decode)
@ -217,14 +208,18 @@ H5O_fill_decode(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const uint8_t *p)
if(NULL == (mesg = H5FL_CALLOC(H5O_fill_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value message")
/* Set non-zero default fields */
mesg->alloc_time = H5D_ALLOC_TIME_LATE;
mesg->fill_time = H5D_FILL_TIME_IFSET;
/* Fill value size */
UINT32DECODE(p, mesg->size);
/* Only encode the fill value itself if there is one */
/* Only decode the fill value itself if there is one */
if(mesg->size > 0) {
if(NULL == (mesg->buf = H5MM_malloc(mesg->size)))
if(NULL == (mesg->buf = H5MM_malloc((size_t)mesg->size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value")
HDmemcpy(mesg->buf, p, mesg->size);
HDmemcpy(mesg->buf, p, (size_t)mesg->size);
} /* end if */
/* Set return value */
@ -260,7 +255,7 @@ done:
static herr_t
H5O_fill_new_encode(H5F_t UNUSED *f, uint8_t *p, const void *_mesg)
{
const H5O_fill_new_t *mesg = (const H5O_fill_new_t *)_mesg;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_encode)
@ -311,7 +306,7 @@ H5O_fill_new_encode(H5F_t UNUSED *f, uint8_t *p, const void *_mesg)
static herr_t
H5O_fill_encode(H5F_t UNUSED *f, uint8_t *p, const void *_mesg)
{
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_encode)
@ -321,7 +316,7 @@ H5O_fill_encode(H5F_t UNUSED *f, uint8_t *p, const void *_mesg)
UINT32ENCODE(p, mesg->size);
if(mesg->buf)
HDmemcpy(p, mesg->buf, mesg->size);
HDmemcpy(p, mesg->buf, (size_t)mesg->size);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5O_fill_encode() */
@ -342,24 +337,25 @@ H5O_fill_encode(H5F_t UNUSED *f, uint8_t *p, const void *_mesg)
* Programmer: Raymond Lu
* Feb 26, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5O_fill_new_copy(const void *_mesg, void *_dest)
{
const H5O_fill_new_t *mesg = (const H5O_fill_new_t *)_mesg;
H5O_fill_new_t *dest = (H5O_fill_new_t *)_dest;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
H5O_fill_t *dest = (H5O_fill_t *)_dest;
void *ret_value;
FUNC_ENTER_NOAPI_NOINIT(H5O_fill_new_copy)
HDassert(mesg);
if(!dest && NULL == (dest = H5FL_MALLOC(H5O_fill_new_t)))
if(!dest && NULL == (dest = H5FL_MALLOC(H5O_fill_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill message")
/* Copy fill value attributes */
*dest = *mesg;
/* Copy shared message information */
if(NULL == H5O_msg_copy(H5O_SHARED_ID, &(mesg->sh_loc), &(dest->sh_loc)))
HGOTO_ERROR(H5E_OHDR, H5E_BADMESG, NULL, "unable to copy fill value shared info");
@ -381,12 +377,6 @@ H5O_fill_new_copy(const void *_mesg, void *_dest)
} /* end if */
else
dest->buf = NULL;
dest->size = mesg->size;
/* Copy three fill value attributes */
dest->alloc_time = mesg->alloc_time;
dest->fill_time = mesg->fill_time;
dest->fill_defined = mesg->fill_defined;
/* Set return value */
ret_value = dest;
@ -398,76 +388,12 @@ done:
if(dest->type)
H5T_close(dest->type);
if(!_dest)
H5FL_FREE(H5O_fill_new_t, dest);
H5FL_FREE(H5O_fill_t, dest);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_fill_new_copy() */
/*-------------------------------------------------------------------------
* 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;
FUNC_ENTER_NOAPI_NOINIT(H5O_fill_copy)
HDassert(mesg);
if(!dest && NULL == (dest = H5FL_CALLOC(H5O_fill_t)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill message")
if(mesg->type) {
if(NULL == (dest->type = H5T_copy(mesg->type, H5T_COPY_TRANSIENT)))
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "unable to copy fill value data type")
} /* end if */
else
dest->type = NULL;
if(mesg->buf) {
if(NULL == (dest->buf = H5MM_malloc(mesg->size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value")
HDmemcpy(dest->buf, mesg->buf, mesg->size);
} /* end if */
else
dest->buf = NULL;
dest->size = mesg->size;
/* Set return value */
ret_value = dest;
done:
if (!ret_value && dest) {
if(dest->buf)
H5MM_xfree(dest->buf);
if (dest->type)
H5T_close(dest->type);
if (!_dest)
H5FL_FREE(H5O_fill_t,dest);
}
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5O_fill_copy() */
/*-------------------------------------------------------------------------
* Function: H5O_fill_new_size
@ -485,14 +411,12 @@ done:
* Programmer: Robb Matzke
* Thursday, October 1, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
H5O_fill_new_size(const H5F_t UNUSED *f, const void *_mesg)
{
const H5O_fill_new_t *mesg = (const H5O_fill_new_t *)_mesg;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
size_t ret_value;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_size)
@ -526,23 +450,51 @@ H5O_fill_new_size(const H5F_t UNUSED *f, const void *_mesg)
* Programmer: Robb Matzke
* Thursday, October 1, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
H5O_fill_size(const H5F_t UNUSED *f, const void *_mesg)
{
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_size)
HDassert(f);
HDassert(mesg);
FUNC_LEAVE_NOAPI(4 + mesg->size)
} /* end H5O_fill_size() */
/*-------------------------------------------------------------------------
* Function: H5O_fill_reset_dyn
*
* Purpose: Resets dynamic fill value fields
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Monday, January 22, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5O_fill_reset_dyn(H5O_fill_t *fill)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_reset_dyn)
HDassert(fill);
if(fill->buf)
fill->buf = H5MM_xfree(fill->buf);
fill->size = -1;
if(fill->type) {
H5T_close(fill->type);
fill->type = NULL;
} /* end if */
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5O_fill_reset_dyn() */
/*-------------------------------------------------------------------------
* Function: H5O_fill_new_reset
@ -556,68 +508,28 @@ H5O_fill_size(const H5F_t UNUSED *f, const void *_mesg)
* Programmer: Robb Matzke
* Thursday, October 1, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_fill_new_reset(void *_mesg)
{
H5O_fill_new_t *mesg = (H5O_fill_new_t *)_mesg;
H5O_fill_t *mesg = (H5O_fill_t *)_mesg;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_reset)
HDassert(mesg);
if(mesg->buf)
mesg->buf = H5MM_xfree(mesg->buf);
mesg->size = -1;
if(mesg->type) {
H5T_close(mesg->type);
mesg->type = NULL;
} /* end if */
mesg->alloc_time = (H5D_alloc_time_t)0;
mesg->fill_time = (H5D_fill_time_t)0;
/* Reset dynamic fields */
H5O_fill_reset_dyn(mesg);
/* Reset value fields */
mesg->alloc_time = H5D_ALLOC_TIME_LATE;
mesg->fill_time = H5D_FILL_TIME_IFSET;
mesg->fill_defined = FALSE;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5O_fill_new_reset() */
/*-------------------------------------------------------------------------
* Function: H5O_fill_reset
*
* Purpose: Resets a message to an initial state
*
* Return: Non-negative on success/Negative on failure
*
* 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_NOAPI_NOINIT_NOFUNC(H5O_fill_reset)
HDassert(mesg);
if(mesg->buf)
mesg->buf = H5MM_xfree(mesg->buf);
mesg->size = 0;
if(mesg->type) {
H5T_close(mesg->type);
mesg->type = NULL;
} /* end if */
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5O_fill_reset() */
/*-------------------------------------------------------------------------
* Function: H5O_fill_new_free
@ -629,44 +541,15 @@ H5O_fill_reset(void *_mesg)
* Programmer: Quincey Koziol
* Thursday, December 5, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_fill_new_free (void *mesg)
H5O_fill_new_free(void *mesg)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_free)
HDassert(mesg);
H5FL_FREE(H5O_fill_new_t, mesg);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5O_fill_new_free() */
/*-------------------------------------------------------------------------
* Function: H5O_fill_free
*
* Purpose: Frees the message
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, December 5, 2002
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_fill_free (void *mesg)
{
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_free)
HDassert(mesg);
H5FL_FREE(H5O_fill_t, mesg);
FUNC_LEAVE_NOAPI(SUCCEED)
@ -688,12 +571,12 @@ H5O_fill_free (void *mesg)
static void *
H5O_fill_new_get_share(const void *_mesg, H5O_shared_t *sh /*out*/)
{
const H5O_fill_new_t *mesg = (const H5O_fill_new_t *)_mesg;
void *ret_value = NULL;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
void *ret_value;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_get_share)
HDassert (mesg);
HDassert(mesg);
ret_value = H5O_msg_copy(H5O_SHARED_ID, &(mesg->sh_loc), sh);
@ -716,13 +599,13 @@ H5O_fill_new_get_share(const void *_mesg, H5O_shared_t *sh /*out*/)
static herr_t
H5O_fill_new_set_share(void *_mesg/*in,out*/, const H5O_shared_t *sh)
{
H5O_fill_new_t *mesg = (H5O_fill_new_t *)_mesg;
H5O_fill_t *mesg = (H5O_fill_t *)_mesg;
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_set_share)
HDassert (mesg);
HDassert (sh);
HDassert(mesg);
HDassert(sh);
if(NULL == H5O_msg_copy(H5O_SHARED_ID, sh, &(mesg->sh_loc)))
ret_value = FAIL;
@ -749,7 +632,7 @@ H5O_fill_new_set_share(void *_mesg/*in,out*/, const H5O_shared_t *sh)
static htri_t
H5O_fill_new_is_shared(const void *_mesg)
{
const H5O_fill_new_t *mesg = (const H5O_fill_new_t *)_mesg;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_is_shared)
@ -781,7 +664,7 @@ static herr_t
H5O_fill_new_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FILE *stream,
int indent, int fwidth)
{
const H5O_fill_new_t *mesg = (const H5O_fill_new_t *)_mesg;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
H5D_fill_value_t fill_status; /* Whether the fill value is defined */
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_new_debug)
@ -852,7 +735,7 @@ H5O_fill_new_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FIL
break;
} /* end switch */
HDfprintf(stream, "%*s%-*s %Zu\n", indent, "", fwidth,
HDfprintf(stream, "%*s%-*s %Zd\n", indent, "", fwidth,
"Size:", mesg->size);
fprintf(stream, "%*s%-*s ", indent, "", fwidth, "Data type:");
if(mesg->type) {
@ -882,19 +765,19 @@ H5O_fill_new_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FIL
*/
static herr_t
H5O_fill_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FILE *stream,
int indent, int fwidth)
int indent, int fwidth)
{
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
const H5O_fill_t *mesg = (const H5O_fill_t *)_mesg;
FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5O_fill_debug)
HDassert(f);
HDassert(mesg);
HDassert(stream);
HDassert(indent>=0);
HDassert(fwidth>=0);
HDassert(indent >= 0);
HDassert(fwidth >= 0);
HDfprintf(stream, "%*s%-*s %Zu\n", indent, "", fwidth,
HDfprintf(stream, "%*s%-*s %Zd\n", indent, "", fwidth,
"Bytes:", mesg->size);
fprintf(stream, "%*s%-*s ", indent, "", fwidth, "Data type:");
if(mesg->type) {
@ -926,9 +809,8 @@ H5O_fill_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FILE *s
*-------------------------------------------------------------------------
*/
herr_t
H5O_fill_convert(void *_fill, H5T_t *dset_type, hid_t dxpl_id)
H5O_fill_convert(H5O_fill_t *fill, H5T_t *dset_type, hbool_t *fill_changed, hid_t dxpl_id)
{
H5O_fill_new_t *fill = _fill;
H5T_path_t *tpath; /* Type conversion info */
void *buf = NULL, *bkg = NULL; /* Conversion buffers */
hid_t src_id = -1, dst_id = -1; /* Datatype identifiers */
@ -938,12 +820,18 @@ H5O_fill_convert(void *_fill, H5T_t *dset_type, hid_t dxpl_id)
HDassert(fill);
HDassert(dset_type);
HDassert(fill_changed);
/* No-op cases */
if(!fill->buf || !fill->type || 0 == H5T_cmp(fill->type, dset_type, FALSE)) {
/* Don't need datatype for fill value */
if(fill->type)
H5T_close(fill->type);
fill->type = NULL;
/* Note that the fill value info has changed */
*fill_changed = TRUE;
HGOTO_DONE(SUCCEED);
} /* end if */
@ -955,10 +843,8 @@ H5O_fill_convert(void *_fill, H5T_t *dset_type, hid_t dxpl_id)
/* Don't bother doing anything if there will be no actual conversion */
if(!H5T_path_noop(tpath)) {
if ((src_id = H5I_register(H5I_DATATYPE,
H5T_copy(fill->type, H5T_COPY_ALL))) < 0 ||
(dst_id = H5I_register(H5I_DATATYPE,
H5T_copy(dset_type, H5T_COPY_ALL))) < 0)
if((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill->type, H5T_COPY_ALL))) < 0 ||
(dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dset_type, H5T_COPY_ALL))) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy/register data type")
/*
@ -987,6 +873,9 @@ H5O_fill_convert(void *_fill, H5T_t *dset_type, hid_t dxpl_id)
H5T_close(fill->type);
fill->type = NULL;
H5_ASSIGN_OVERFLOW(fill->size, H5T_get_size(dset_type), size_t, ssize_t);
/* Note that the fill value info has changed */
*fill_changed = TRUE;
} /* end if */
done:

26
src/H5Oprivate.h
View File

@ -182,31 +182,24 @@ typedef struct H5O_linfo_t {
} H5O_linfo_t;
/*
* Fill Value Message. (Old)
* (Data structure in memory)
*/
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;
/*
* New Fill Value Message. The new fill value message is fill value plus
* New Fill Value Message.
* (Data structure in memory for both "old" and "new" fill value messages)
*
* The new fill value message is fill value plus
* space allocation time, fill value writing time, whether fill
* value is defined, and the location of the message if it's shared
*/
typedef struct H5O_fill_new_t {
typedef struct H5O_fill_t {
H5O_shared_t sh_loc; /* Shared message info (must be first) */
H5T_t *type; /*type. Null implies same as dataset */
ssize_t size; /*number of bytes in the fill value */
void *buf; /*the fill value */
H5D_alloc_time_t alloc_time; /* time to allocate space */
H5D_fill_time_t fill_time; /* time to write fill value */
hbool_t fill_defined; /* whether fill value is defined */
H5O_shared_t sh_loc; /* Shared message info (must be first) */
} H5O_fill_new_t;
} H5O_fill_t;
/*
* Link message.
@ -467,7 +460,8 @@ H5_DLL size_t H5O_layout_meta_size(const H5F_t *f, const void *_mesg);
H5_DLL hsize_t H5O_efl_total_size(H5O_efl_t *efl);
/* Fill value operators */
H5_DLL herr_t H5O_fill_convert(void *_fill, H5T_t *type, hid_t dxpl_id);
H5_DLL herr_t H5O_fill_reset_dyn(H5O_fill_t *fill);
H5_DLL herr_t H5O_fill_convert(H5O_fill_t *fill, H5T_t *type, hbool_t *fill_changed, hid_t dxpl_id);
/* Link operators */
H5_DLL herr_t H5O_link_delete(H5F_t *f, hid_t dxpl_id, const void *_mesg, hbool_t adj_link);

601
src/H5Pdcpl.c
View File

File diff suppressed because it is too large Load Diff

2
src/H5Spublic.h
View File

@ -83,7 +83,7 @@ typedef enum {
H5S_SEL_POINTS = 1, /* Sequence of points selected */
H5S_SEL_HYPERSLABS = 2, /* "New-style" hyperslab selection defined */
H5S_SEL_ALL = 3, /* Entire extent selected */
H5S_SEL_N = 4 /*THIS MUST BE LAST */
H5S_SEL_N /*THIS MUST BE LAST */
}H5S_sel_type;
#ifdef __cplusplus

24
src/H5private.h
View File

@ -474,29 +474,29 @@
* A macro for detecting over/under-flow when casting between types
*/
#ifndef NDEBUG
#define H5_CHECK_OVERFLOW(var,vartype,casttype) \
{ \
casttype _tmp_overflow=(casttype)(var); \
assert((var)==(vartype)_tmp_overflow); \
#define H5_CHECK_OVERFLOW(var, vartype, casttype) \
{ \
casttype _tmp_overflow = (casttype)(var); \
assert((var) == (vartype)_tmp_overflow); \
}
#else /* NDEBUG */
#define H5_CHECK_OVERFLOW(var,vartype,casttype)
#define H5_CHECK_OVERFLOW(var, vartype, casttype)
#endif /* NDEBUG */
/*
* A macro for detecting over/under-flow when assigning between types
*/
#ifndef NDEBUG
#define H5_ASSIGN_OVERFLOW(var,expr,exprtype,vartype) \
#define H5_ASSIGN_OVERFLOW(dst, src, srctype, dsttype) \
{ \
exprtype _tmp_overflow=(exprtype)(expr); \
vartype _tmp_overflow2=(vartype)(_tmp_overflow); \
assert((vartype)_tmp_overflow==_tmp_overflow2); \
(var)=_tmp_overflow2; \
srctype _tmp_overflow = (srctype)(src); \
dsttype _tmp_overflow2 = (dsttype)(_tmp_overflow); \
assert((dsttype)_tmp_overflow == _tmp_overflow2); \
(dst) = _tmp_overflow2; \
}
#else /* NDEBUG */
#define H5_ASSIGN_OVERFLOW(var,expr,exprtype,vartype) \
(var)=(vartype)(expr);
#define H5_ASSIGN_OVERFLOW(dst, src, srctype, dsttype) \
(dst) = (dsttype)(src);
#endif /* NDEBUG */
/*

2
test/tvltypes.c
View File

@ -1189,7 +1189,7 @@ test_vltypes_compound_vlstr(void)
hsize_t maxdims[] = {H5S_UNLIMITED};
hsize_t size[] = {SPACE1_DIM1};
hsize_t offset[] = {0};
unsigned i,j,k; /* counting variables */
unsigned i,j; /* counting variables */
s2 *t1, *t2; /* Temporary pointer to VL information */
int val;
herr_t ret; /* Generic return value */