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(fix) Segmentation fault when using a compound type. (#143)

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* (fix) Segmentation fault when using a compound type.

In the case when a compounded attribute is written to dataset
followed by writing the data with a data transform function
to the dataset will result in a segmentation fault. It turns out
the data is classified as compounded while it is not. Now, the
state is always reset first to not compounded followed by the
existing check if the variable is compounded.

* (fix) Removed undesired comment lines.

* (fix) Segmentation fault when using a compound type: added test.

* (fix) Added the missing cmpd_transform.c file to MANIFEST.

* (fix) cmpd_dtransform test: autotools and source header.

Added the cmp_dtransform test to the autotools configuration and
updated the HDF Group copyright header.

Co-authored-by: Jan-Willem Blokland <Jan-Willem.Blokland@Shell.com>
This commit is contained in:
Jan-Willem Blokland 2020-12-02 18:52:09 +01:00 committed by GitHub
parent c7c1046d49
commit bf0cbcbea5
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 153 additions and 12 deletions
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1
MANIFEST
View File

@ -1096,6 +1096,7 @@
./test/cache_tagging.c
./test/chunk_info.c
./test/cmpd_dset.c
./test/cmpd_dtransform.c
./test/cork.c
./test/corrupt_stab_msg.h5
./test/cross_read.c

25
src/H5T.c
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@ -3405,8 +3405,8 @@ done:
* Note: Common code for both H5T_copy and H5T_copy_reopen, as part of
* the const-correct datatype copying routines.
*
* Programmer: David Young
* January 18, 2020
* Programmer: David Young
* January 18, 2020
*
*-------------------------------------------------------------------------
*/
@ -3453,8 +3453,8 @@ done:
* Return: Success: Pointer to a new copy of the OLD_DT argument.
* Failure: NULL
*
* Programmer: David Young
* January 18, 2020
* Programmer: David Young
* January 18, 2020
*
*-------------------------------------------------------------------------
*/
@ -3481,8 +3481,8 @@ done:
* Return: Success: Pointer to a new copy of the OLD_DT argument.
* Failure: NULL
*
* Programmer: David Young
* January 18, 2020
* Programmer: David Young
* January 18, 2020
*
*-------------------------------------------------------------------------
*/
@ -3512,8 +3512,8 @@ done:
*
* Note: Common code for both H5T_copy and H5T_copy_reopen.
*
* Programmer: David Young
* January 18, 2020
* Programmer: David Young
* January 18, 2020
*
*-------------------------------------------------------------------------
*/
@ -3783,8 +3783,8 @@ done:
* Return: Success: Pointer to a new copy of the OLD_DT argument.
* Failure: NULL
*
* Programmer: David Young
* January 18, 2020
* Programmer: David Young
* January 18, 2020
*
*-------------------------------------------------------------------------
*/
@ -5217,7 +5217,10 @@ H5T__path_find_real(const H5T_t *src, const H5T_t *dst, const char *name, H5T_co
} /* end else-if */
/* Set the flag to indicate both source and destination types are compound types
* for the optimization of data reading (in H5Dio.c). */
* for the optimization of data reading (in H5Dio.c).
* Make sure that path->are_compounds is only TRUE for compound types.
*/
path->are_compounds = FALSE;
if (H5T_COMPOUND == H5T_get_class(src, TRUE) && H5T_COMPOUND == H5T_get_class(dst, TRUE))
path->are_compounds = TRUE;

1
test/CMakeLists.txt
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@ -332,6 +332,7 @@ set (H5_TESTS
thread_id # special link
vol
timer
cmpd_dtransform
)
macro (ADD_H5_EXE file)

2
test/Makefile.am
View File

@ -60,7 +60,7 @@ TEST_PROG= testhdf5 \
cache cache_api cache_image cache_tagging lheap ohdr \
stab gheap evict_on_close farray earray btree2 fheap \
pool accum hyperslab istore bittests dt_arith page_buffer \
dtypes dsets chunk_info cmpd_dset filter_fail extend direct_chunk \
dtypes dsets chunk_info cmpd_dset cmpd_dtransform filter_fail extend direct_chunk \
external efc objcopy objcopy_ref links unlink twriteorder big mtime \
fillval mount \
flush1 flush2 app_ref enum set_extent ttsafe enc_dec_plist \

136
test/cmpd_dtransform.c Normal file
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@ -0,0 +1,136 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Jan-Willem Blokland
* December 1, 2020
*
* Purpose: Test writing compounded attribute followed by
* writing data with a data transform function.
*/
#include "h5test.h"
#define FILENAME "cmpd_dtransform.h5"
#define LENGTH 11
typedef struct {
char name[64];
char unit[64];
} att_t;
int
main(void)
{
hsize_t dima[] = { 1 };
hsize_t dims[] = { LENGTH };
hid_t str_dtyp_id, att_dtyp_id, file_id, fspace_id, dset_id, att_dspc_id, att_attr_id, dxpl_id;
/* Compound datatype */
att_t *atts = HDmalloc(sizeof(att_t));
HDstrcpy(atts[0].name, "Name");
HDstrcpy(atts[0].unit, "Unit");
/* String type */
if ((str_dtyp_id = H5Tcopy(H5T_C_S1)) < 0)
TEST_ERROR;
H5Tset_size(str_dtyp_id, 64);
/* Attribute type */
if ((att_dtyp_id = H5Tcreate(H5T_COMPOUND, sizeof(att_t))) < 0)
TEST_ERROR;
H5Tinsert(att_dtyp_id, "NAME", HOFFSET(att_t, name), str_dtyp_id);
H5Tinsert(att_dtyp_id, "UNIT", HOFFSET(att_t, unit), str_dtyp_id);
/* Create file. */
if ((file_id = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Create file dataspace. */
if ((fspace_id = H5Screate_simple(1, dims, NULL)) < 0)
TEST_ERROR;
/* Create dataset. */
if ((dset_id = H5Dcreate2(file_id, "test_dset", H5T_NATIVE_INT, fspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Write the attribute (compound) to the dataset */
if ((att_dspc_id = H5Screate_simple(1, dima, NULL)) < 0)
TEST_ERROR;
if ((att_attr_id = H5Acreate2(dset_id, "ATTRIBUTES", att_dtyp_id, att_dspc_id,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
if (H5Awrite(att_attr_id, att_dtyp_id, atts) < 0)
TEST_ERROR;
/* Create dataset transfer property list */
const char *expr = "2*x";
if ((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
TEST_ERROR;
if (H5Pset_data_transform(dxpl_id, expr) < 0) {
HDprintf("**** ERROR: H5Pset_data_transform (expression: %s) ****\n", expr);
TEST_ERROR;
}
int *data = HDmalloc(LENGTH * sizeof(int));
int *data_res = HDmalloc(LENGTH * sizeof(int));
for (unsigned i = 0; i < LENGTH; i++) {
data[i] = 10;
data_res[i] = 2 * data[i];
}
/* Write the data */
if (H5Dwrite(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl_id, data) < 0)
TEST_ERROR;
/* Read attribute */
att_t *atts_res =HDmalloc(sizeof(att_t));
if (H5Aread(att_attr_id, att_dtyp_id, atts_res) < 0)
TEST_ERROR;
/* Verify attribute */
if (HDstrcmp(atts_res[0].name, atts[0].name) != 0)
TEST_ERROR;
if (HDstrcmp(atts_res[0].unit, atts[0].unit) != 0)
TEST_ERROR;
/* Read the data */
if (H5Dread(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data) < 0)
TEST_ERROR;
/* Verify data */
for (unsigned idx = 0; idx < LENGTH; idx++) {
if (data[idx] != data_res[idx])
TEST_ERROR;
}
HDfree(atts);
HDfree(atts_res);
HDfree(data);
HDfree(data_res);
/* Close all identifiers. */
H5Pclose(dxpl_id);
H5Aclose(att_attr_id);
H5Sclose(att_dspc_id);
H5Dclose(dset_id);
H5Sclose(fspace_id);
H5Fclose(file_id);
H5Tclose(att_dtyp_id);
H5Tclose(str_dtyp_id);
return 0;
error:
return 1;
}