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[svn-r5882]

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Purpose:
    Bug fix.
Description:
    In H5D_init_storage, contiguous dataset is not initialized properly when
    fill value is library default.
Platforms tested:
    eirene
This commit is contained in:
Raymond Lu 2002-08-20 16:28:31 -05:00
parent b35b6c0411
commit 250bbd4aba
1 changed files with 71 additions and 73 deletions
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144
src/H5D.c
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@ -3274,83 +3274,81 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space)
if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time");
switch (dset->layout.type) {
case H5D_COMPACT:
/*
* zero set data buf. If fill value is defined, fall through
* the H5D_CONTIGUOUS case and initialize with fill value.
*/
if(!fill.buf)
HDmemset(dset->layout.buf, 0, dset->layout.size);
case H5D_CONTIGUOUS:
/*
* If the fill value is set then write it to the entire extent
* of the dataset. Note: library default(fill.buf is NULL) is
* not handled here. How to do it?
*/
snpoints = H5S_get_simple_extent_npoints(space);
assert(snpoints>=0);
H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t);
if (fill.buf) {
/*
* Fill the entire current extent with the fill value. We can do
* this quite efficiently by making sure we copy the fill value
* in relatively large pieces.
*/
ptsperbuf = MAX(1, bufsize/fill.size);
bufsize = ptsperbuf*fill.size;
/* Allocate temporary buffer */
if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer");
/* Fill the buffer with the fill value */
H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf);
/* Start at the beginning of the dataset */
addr = 0;
/* Loop through writing the fill value to the dataset */
while (npoints>0) {
size = MIN(ptsperbuf, npoints) * fill.size;
if (H5F_seq_write(dset->ent.file, H5P_DATASET_XFER_DEFAULT,
&(dset->layout), plist, space, fill.size, size, addr, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset");
npoints -= MIN(ptsperbuf, npoints);
addr += size;
} /* end while */
} /* end if */
break;
case H5D_CHUNKED:
/*
* If the dataset is accessed via parallel I/O, allocate file space
* for all chunks now and initialize each chunk with the fill value.
*/
if (space_time==H5D_SPACE_ALLOC_EARLY
if(dset->layout.type==H5D_CHUNKED) {
/*
* If the dataset is accessed via parallel I/O, allocate file space
* for all chunks now and initialize each chunk with the fill value.
*/
if (space_time==H5D_SPACE_ALLOC_EARLY
#ifdef H5_HAVE_PARALLEL
|| (IS_H5FD_MPIO(dset->ent.file) || IS_H5FD_MPIPOSIX(dset->ent.file))
|| (IS_H5FD_MPIO(dset->ent.file) || IS_H5FD_MPIPOSIX(dset->ent.file))
#endif /*H5_HAVE_PARALLEL*/
) {
/* We only handle simple data spaces so far */
int ndims;
hsize_t dim[H5O_LAYOUT_NDIMS];
if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info");
dim[ndims] = dset->layout.dim[ndims];
ndims++;
) {
/* We only handle simple data spaces so far */
int ndims;
hsize_t dim[H5O_LAYOUT_NDIMS];
if (H5F_istore_allocate(dset->ent.file, H5P_DATASET_XFER_DEFAULT,
&(dset->layout), dim, plist)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset");
} /* end if */
break;
} /* end switch */
if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info");
dim[ndims] = dset->layout.dim[ndims];
ndims++;
if (H5F_istore_allocate(dset->ent.file, H5P_DATASET_XFER_DEFAULT,
&(dset->layout), dim, plist)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset");
} /* end if */
} else { /* case for compact and contiguous dataset. */
/*
* If the fill value is default and dataset is compact, zero set data buf.
*/
if(!fill.buf && dset->layout.type==H5D_COMPACT) {
HDmemset(dset->layout.buf, 0, dset->layout.size);
goto done;
}
snpoints = H5S_get_simple_extent_npoints(space);
assert(snpoints>=0);
H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t);
/* If fill value is library default, simply define it as one-byte 0-value
* buffer */
if(!fill.buf) {
fill.size=1;
fill.buf=H5MM_calloc(fill.size);
}
/* write fill value to the entire extent of the dataset.*/
if (fill.buf) {
/*
* Fill the entire current extent with the fill value. We can do
* this quite efficiently by making sure we copy the fill value
* in relatively large pieces.
*/
ptsperbuf = MAX(1, bufsize/fill.size);
bufsize = ptsperbuf*fill.size;
/* Allocate temporary buffer */
if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer");
/* Fill the buffer with the fill value */
H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf);
/* Start at the beginning of the dataset */
addr = 0;
/* Loop through writing the fill value to the dataset */
while (npoints>0) {
size = MIN(ptsperbuf, npoints) * fill.size;
if (H5F_seq_write(dset->ent.file, H5P_DATASET_XFER_DEFAULT,
&(dset->layout), plist, space, fill.size, size, addr, buf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset");
npoints -= MIN(ptsperbuf, npoints);
addr += size;
} /* end while */
} /* end if */
}
done:
if (buf)
H5FL_BLK_FREE(type_conv,buf);