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[svn-r4965] Purpose:

Browse Source 
Bug Fix
Description:
    If a non-zero fill-value is used for a chunked dataset, any non-existent
    chunked read with an "all" selection (or a contiguous hyperslab selection)
    will return zero for those instead of the user's fill-value.
Solution:
    Fixed I/O code to pass down fill-value to "optimized" I/O routines, so it
    will be available to fill the user's buffer with.
Platforms tested:
    FreeBSD 4.5 (sleipnir)
This commit is contained in:
Quincey Koziol 2002-02-14 10:57:48 -05:00
parent a1c37b6eb8
commit 5883b9d67d
7 changed files with 134 additions and 35 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
release_docs/RELEASE.txt
View File

@ -106,6 +106,9 @@ Library
* Fixed bug where a preempted chunk in the chunk data could still be
used by an internal pointer and cause an assertion failure or core
dump. QAK - 2/13/02
* Fixed bug where non-zero fill-value was not being read correctly from
certain chunked datasets when using an "all" or contiguous hyperslab
selection. QAK - 2/14/02
Configuration
-------------

13
src/H5D.c
View File

@ -2238,11 +2238,13 @@ printf("%s: check 1.1, \n",FUNC);
#endif
if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get pipeline");
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value");
if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list");
status = (sconv->read)(dataset->ent.file, &(dataset->layout), &pline,
&efl, H5T_get_size(dataset->type), file_space,
mem_space, dxpl_id, buf/*out*/, &must_convert);
&fill, &efl, H5T_get_size(dataset->type), file_space,
mem_space, dxpl_id, buf/*out*/, &must_convert);
/* Supports only no conversion, type or space, for now. */
if (status<0)
@ -2725,11 +2727,14 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
#endif
if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get pipeline");
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value");
if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list");
status = (sconv->write)(dataset->ent.file, &(dataset->layout), &pline,
&efl, H5T_get_size(dataset->type), file_space,
mem_space, dxpl_id, buf/*out*/, &must_convert);
&fill, &efl, H5T_get_size(dataset->type), file_space,
mem_space, dxpl_id, buf/*out*/, &must_convert);
/* Supports only no conversion, type or space, for now. */
if (status<0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed");

15
src/H5Sall.c
View File

@ -393,6 +393,7 @@ H5S_all_mscat (const void *tconv_buf, size_t elmt_size,
*/
herr_t
H5S_all_read(H5F_t *f, const H5O_layout_t *layout, const H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id, void *_buf/*out*/,
hbool_t *must_convert/*out*/)
@ -623,7 +624,7 @@ for (u=0; u<=mem_space->extent.u.simple.rank; u++)
printf("file_offset[%u]=%lu\n",u,(unsigned long)file_offset[u]);
#endif /* QAK */
/* Read data from the file */
if (H5F_arr_read(f, dxpl_id, layout, pline, NULL, efl, size,
if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, size,
size, mem_offset, file_offset, buf/*out*/)<0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read data from the file");
@ -661,10 +662,12 @@ done:
*/
herr_t
H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
const H5O_pline_t *pline, const H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id, const void *_buf,
hbool_t *must_convert/*out*/)
const H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id, const void *_buf,
hbool_t *must_convert/*out*/)
{
H5S_hyper_span_t *file_span=NULL,*mem_span=NULL; /* Hyperslab span node */
const char *buf=(const char*)_buf; /* Get pointer to buffer */
@ -880,7 +883,7 @@ H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
} /* end if */
/* Write data to the file */
if (H5F_arr_write(f, dxpl_id, layout, pline, NULL, efl, size,
if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, size,
size, mem_offset, file_offset, buf)<0) {
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"unable to write data to the file");

17
src/H5Smpio.c
View File

@ -551,6 +551,7 @@ H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size,
herr_t
H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t UNUSED *pline,
const struct H5O_fill_t UNUSED *fill,
const struct H5O_efl_t UNUSED *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, void *buf /*out*/,
@ -720,6 +721,7 @@ done:
herr_t
H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, void *buf/*out*/,
@ -729,7 +731,7 @@ H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout,
FUNC_ENTER (H5S_mpio_spaces_read, FAIL);
ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
ret_value = H5S_mpio_spaces_xfer(f, layout, pline, fill, efl, elmt_size,
file_space, mem_space, dxpl_id,
buf, must_convert/*out*/, 0/*read*/);
@ -755,17 +757,18 @@ H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout,
*/
herr_t
H5S_mpio_spaces_write(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/)
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/)
{
herr_t ret_value = FAIL;
FUNC_ENTER (H5S_mpio_spaces_write, FAIL);
ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
ret_value = H5S_mpio_spaces_xfer(f, layout, pline, fill, efl, elmt_size,
file_space, mem_space, dxpl_id,
(void*)buf, must_convert/*out*/,
1/*write*/);

12
src/H5Spkg.h
View File

@ -146,16 +146,18 @@ __DLL__ herr_t H5S_all_select_deserialize(H5S_t *space, const uint8_t *buf);
__DLL__ herr_t H5S_all_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
__DLL__ herr_t H5S_all_read(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, void *buf/*out*/,
hbool_t *must_convert/*out*/);
__DLL__ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/);
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/);
__DLL__ herr_t H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space,
H5D_operator_t op, void *operator_data);

28
src/H5Sprivate.h
View File

@ -142,6 +142,7 @@ typedef struct H5S_conv_t {
/* Read from file to application w/o intermediate scratch buffer */
herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, void *buf/*out*/,
@ -150,11 +151,12 @@ typedef struct H5S_conv_t {
/* Write directly from app buffer to file */
herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/);
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
hid_t dxpl_id, const void *buf,
hbool_t *must_convert/*out*/);
#ifdef H5S_DEBUG
struct {
@ -227,6 +229,7 @@ __DLL__ herr_t H5S_sel_iter_release(const H5S_t *space,
__DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
@ -235,13 +238,14 @@ __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
/* MPI-IO function to write directly from app buffer to file rky980813 */
__DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
const void *buf,
hbool_t *must_convert /*out*/ );
const struct H5O_layout_t *layout,
const struct H5O_pline_t *pline,
const struct H5O_fill_t *fill,
const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, hid_t dxpl_id,
const void *buf,
hbool_t *must_convert /*out*/ );
#ifndef _H5S_IN_H5S_C
/* Global var whose value comes from environment variable */
__DLLVAR__ hbool_t H5_mpi_opt_types_g;

81
test/tmisc.c
View File

@ -41,6 +41,16 @@ typedef struct {
char *string;
} misc2_struct;
/* Definitions for misc. test #3 */
#define MISC3_FILE "tmisc3.h5"
#define MISC3_RANK 2
#define MISC3_DIM1 6
#define MISC3_DIM2 6
#define MISC3_CHUNK_DIM1 2
#define MISC3_CHUNK_DIM2 2
#define MISC3_FILL_VALUE 2
#define MISC3_DSET_NAME "/chunked"
/****************************************************************
**
** test_misc1(): test unlinking a dataset from a group and immediately
@ -252,7 +262,7 @@ static void test_misc2_read_attribute(const char *filename, const char *att_name
free(data_check.string);
ret = H5Aclose(att);
CHECK(ret, FAIL, "HAclose");
CHECK(ret, FAIL, "H5Aclose");
ret = H5Tclose(type);
CHECK(ret, FAIL, "H5Tclose");
@ -283,6 +293,73 @@ test_misc2(void)
test_misc2_read_attribute(MISC2_FILE_2, MISC2_ATT_NAME_2);
} /* end test_misc2() */
/****************************************************************
**
** test_misc3(): Test reading from chunked dataset with non-zero
** fill value
**
****************************************************************/
static void
test_misc3(void)
{
hid_t file, dataspace, dataset, dcpl;
int rank=MISC3_RANK;
hsize_t dims[MISC3_RANK]={MISC3_DIM1,MISC3_DIM2};
hsize_t chunk_dims[MISC3_RANK]={MISC3_CHUNK_DIM1,MISC3_CHUNK_DIM2};
int fill=MISC3_FILL_VALUE;
int read_buf[MISC3_DIM1][MISC3_DIM2];
int i,j;
herr_t ret;
/* Output message about test being performed */
MESSAGE(5, ("Testing reading from chunked dataset with non-zero fill-value\n"));
file = H5Fcreate(MISC3_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(file, FAIL, "H5Fcreate");
/* Create a simple dataspace */
dataspace = H5Screate_simple(rank,dims,NULL);
CHECK(dataspace, FAIL, "H5Screate_simple");
/* Create a dataset creation property list */
dcpl = H5Pcreate(H5P_DATASET_CREATE);
CHECK(dcpl, FAIL, "H5Pcreate");
/* Set the chunk information */
ret = H5Pset_chunk(dcpl,rank,chunk_dims);
CHECK(dcpl, FAIL, "H5Pset_chunk");
/* Set the fill-value information */
ret = H5Pset_fill_value(dcpl,H5T_NATIVE_INT,&fill);
CHECK(dcpl, FAIL, "H5Pset_fill_value");
/* Create the dataset */
dataset = H5Dcreate(file, MISC3_DSET_NAME, H5T_NATIVE_INT, dataspace, dcpl);
CHECK(dataset, FAIL, "H5Dcreate");
/* Read from the dataset (should be fill-values) */
ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &read_buf);
CHECK(ret, FAIL, "H5Dread");
for(i=0; i<MISC3_DIM1; i++)
for(j=0; j<MISC3_DIM2; j++)
VERIFY(read_buf[i][j],fill,"H5Dread");
/* Release resources */
ret = H5Pclose(dcpl);
CHECK(ret, FAIL, "H5Pclose");
ret = H5Sclose(dataspace);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Dclose(dataset);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Fclose(file);
CHECK(ret, FAIL, "H5Fclose");
} /* end test_misc3() */
/****************************************************************
**
** test_misc(): Main misc. test routine.
@ -296,6 +373,7 @@ test_misc(void)
test_misc1(); /* Test unlinking a dataset & immediately re-using name */
test_misc2(); /* Test storing a VL-derived datatype in two different files */
test_misc3(); /* Test reading from chunked dataset with non-zero fill value */
} /* test_misc() */
@ -320,4 +398,5 @@ cleanup_misc(void)
remove(MISC1_FILE);
remove(MISC2_FILE_1);
remove(MISC2_FILE_2);
remove(MISC3_FILE);
}