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[svn-r21658] Purpose:
HDFFV-7770 - h5diff segmentation fault on JPSS files
Description:
Fixed segfault over non-comparable attribute with different dimention or
rank, along with '-c' option to display details.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows, Cmake
This commit is contained in:
Jonathan Kim
parent
1dcc75407e
commit
e54d15a26c
@ -624,24 +624,27 @@ Bug Fixes since HDF5-1.8.0 release
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Tools
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-----
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- Fixed h5diff to display all the comparable object and attribute
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regardless of non-comparables. HDFFV-7693 (JKM 09/16/2011)
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- Fixed h5repack to update values of references(object and region) of
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attributes in h5repack for 1) references, 2) ARRAY of references,
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3) VLEN of references, and 4) COMPOUND of references.
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(JIRA HDF5 5932) PC -2011/09/14
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- h5diff: fixed segfault over non-comparable attribute with different
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dimention or rank, along with '-c' option to display details.
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HDFFV-7770 (JKM 2011/10/24)
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- Fixed h5diff to display all the comparable object and attribute
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regardless of non-comparables. HDFFV-7693 (JKM 2011/09/16)
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- Fixed h5repack to update values of references(object and region) of
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attributes in h5repack for 1) references, 2) ARRAY of references,
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3) VLEN of references, and 4) COMPOUND of references.
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(JIRA HDF5 5932) PC -2011/09/14
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- h5diff: fixed segfault over dataset with container types
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(array,lven) with multiple nested compound types.
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(ex: compound->array->compound, compound->vlen->compound)
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HDFFV-7712 JKM (09/01/2011)
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HDFFV-7712 JKM (2011/09/01)
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- h5repack: added macro to handle failure in H5Dread/write when memory
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allocation failed inside the library. (PC -- 2011/08/19)
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- Fixed h5jam not to allow specifying an HDF5 formatted file as input
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file for -u (user block file) option, because the original HDF5 file
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will not be accessible if allows. HDFFV-5941 (JKM 08/15/2011)
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will not be accessible if allows. HDFFV-5941 (JKM 2011/08/15)
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- Revised command help pages of h5jam and h5unjam. The descriptions
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were not up to date and some were missing.
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HDFFV-7515 (JKM 08/15/2011)
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HDFFV-7515 (JKM 2011/08/15)
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- h5repack: h5repack failed to copy dataset if the layout is changed
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from chunked with unlimited dims to contiguous. HDFFV-7649
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(PC -- 2011/07/15)
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@ -650,29 +653,29 @@ Bug Fixes since HDF5-1.8.0 release
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Manual. HDFFV-7656 (PC -- 2011/07/15)
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- Fixed h5diff to display instructive error message and exit with 1
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when mutually exclusive options (-d, -p and --use-system-epsilon)
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are used together. HDFFV-7600 (JKM 07/07/2011)
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are used together. HDFFV-7600 (JKM 2011/07/07)
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- Fixed h5dump to display the first line of each element into correct
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position for multiple dimention array type.
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Before this fix, the first line of each element in array were
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displayed after the last line of previous element without
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moving to the next line (+indentation).
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Bug #HDFFV-5878 (JKM 06/15/2011)
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Bug #HDFFV-5878 (JKM 2011/06/15)
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- Fixed h5dump to display correct value for H5T_STD_I8LE dataset
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on a system (ppc64, linux, Big-Endian, clustering).
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Bug #HDFFV-7594 (ABERT & JKM 05/12/2011)
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Bug #HDFFV-7594 (ABERT & JKM 2011/05/12)
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- Fixed h5diff to compare file itself correctly. Previously h5diff
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reported either different or not compatible in certain cases even
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comparing file itself. This fix also improve performance when
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comparing same target objects through verifying the obj&file
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addresses before comparing the details in the objects (ex: datasets
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or attributes) Bug #HDFFV-5928 (XCAO & JKM 05/06/2011)
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or attributes) Bug #HDFFV-5928 (XCAO & JKM 2011/05/06)
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- Updated h5dump test case script to prevent entire test failure upon
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source directory is read-only. Bug# HDFFV-4342 (JKM 2011/4/12)
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- Fixed h5dump displaying incorrect values for H5T_STD_I8BE type data in
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attribute on Big-Endian machine. H5T_STD_I8BE is unsigned 8bit type,
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so h5dump is supposed to display -2 instead of 254. It worked
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correctly on Little-Endian system , but not on Big-Endian system.
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Bug #HDFFV-4358 (JKM 04/08/2011)
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Bug #HDFFV-4358 (JKM 2011/04/08)
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- Updated to unify option name to '--enable-error-stack' for printing
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HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now.
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For h5ls, this replaces "-e/--errors" option, which is deprecated.
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@ -1131,6 +1131,7 @@ ADD_H5_TEST (h5diff_208 0 -c ${FILE19} ${FILE20})
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ADD_H5_TEST (h5diff_220 1 -c non_comparables1.h5 non_comparables2.h5 /g1)
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# comparable dataset with non-comparable attribute and other comparable attributes.
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# Also test non-compatible attributes with different type, dimention, rank.
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# All the rest comparables should display differences.
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ADD_H5_TEST (h5diff_221 1 -c non_comparables1.h5 non_comparables2.h5 /g2)
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@ -4701,9 +4701,14 @@ static void test_non_comparables (const char * fname, int make_diffs)
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hid_t sid1=0;
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hid_t tid_dset1=0;
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hid_t tid_attr1=0;
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hsize_t dims1[1] = {DIM_ARRY};
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hsize_t dims1_1[1] = {DIM_ARRY};
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hsize_t dims1_2[1] = {DIM_ARRY+1};
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hsize_t dims2[2] = {DIM_ARRY, 1};
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int data1[DIM_ARRY] = {0,0,0};
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int data2[DIM_ARRY] = {1,1,1};
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int data3[DIM_ARRY+1] = {1,1,1,1};
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int data1_dim2[DIM_ARRY][1] = {0,0,0};
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int rank_attr;
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char data1_str[DIM_ARRY][STR_SIZE]= {"ab","cd","ef"};
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herr_t status = SUCCEED;
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int i;
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@ -4713,6 +4718,9 @@ static void test_non_comparables (const char * fname, int make_diffs)
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void *attr_data_ptr1=NULL;
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void *attr_data_ptr2=NULL;
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void *attr_data_ptr3=NULL;
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void *attr_data_ptr4=NULL;
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void *attr2_dim_ptr=NULL;
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void *attr3_dim_ptr=NULL;
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/* init */
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tid_dset1=H5Tcopy(H5T_NATIVE_INT);
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@ -4722,6 +4730,10 @@ static void test_non_comparables (const char * fname, int make_diffs)
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tid_attr1=H5Tcopy(H5T_NATIVE_INT);
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attr_data_ptr1=(int*)&data1;
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attr_data_ptr3=(int*)&data1;
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attr_data_ptr4=(int*)&data1;
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attr2_dim_ptr=(hsize_t*)&dims1_1;
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attr3_dim_ptr=(hsize_t*)&dims1_1;
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rank_attr=1;
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if (make_diffs)
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{
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@ -4737,12 +4749,22 @@ static void test_non_comparables (const char * fname, int make_diffs)
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* group2
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*/
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dset_data_ptr3=(int*)&data2;
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/* attr1 */
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/* dset1/attr1 */
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tid_attr1=H5Tcopy(H5T_C_S1);
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H5Tset_size(tid_attr1, (size_t)STR_SIZE);
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attr_data_ptr2=(char*)&data1_str;
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/* attr2 */
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attr_data_ptr3=(int*)&data2;
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/* dset1/attr2 */
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attr2_dim_ptr=(hsize_t*)&dims1_2;
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/* dset1/attr3 */
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attr_data_ptr3=(int*)&data1_dim2;
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attr3_dim_ptr=(hsize_t*)&dims2;
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rank_attr=2;
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/* dset1/attr4 */
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attr_data_ptr4=(int*)&data2;
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}
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@ -4779,7 +4801,7 @@ static void test_non_comparables (const char * fname, int make_diffs)
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/*-----------------------------------------------------------------------
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* Datasets in /g1
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*------------------------------------------------------------------------*/
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if((sid1 = H5Screate_simple(1, dims1, NULL)) < 0)
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if((sid1 = H5Screate_simple(1, dims1_1, NULL)) < 0)
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goto out;
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/* dset1 */
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@ -4796,10 +4818,10 @@ static void test_non_comparables (const char * fname, int make_diffs)
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status = FAIL;
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goto out;
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}
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write_attr(did1,1,dims1,"attr", H5T_NATIVE_INT, attr_data_ptr1);
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write_attr(did1,1,dims1_1,"attr", H5T_NATIVE_INT, attr_data_ptr1);
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/* dset2 */
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status = write_dset(gid1, 1, dims1,"dset2", H5T_NATIVE_INT, dset_data_ptr2);
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status = write_dset(gid1, 1, dims1_1,"dset2", H5T_NATIVE_INT, dset_data_ptr2);
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if (status == FAIL)
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{
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fprintf(stderr, "Error: %s> write_dset failed\n", fname);
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@ -4809,7 +4831,8 @@ static void test_non_comparables (const char * fname, int make_diffs)
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/*-----------------------------------------------------------------------
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* Datasets in /g2
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*------------------------------------------------------------------------*/
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/* dset1 */
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/* ---------
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* dset1 */
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if((did2 = H5Dcreate2(gid2, "dset1", H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
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{
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fprintf(stderr, "Error: %s> H5Dcreate2 failed.\n", "dset1");
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@ -4823,14 +4846,22 @@ static void test_non_comparables (const char * fname, int make_diffs)
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status = FAIL;
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goto out;
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}
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/* attr1 */
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write_attr(did2,1,dims1,"attr1", tid_attr1, attr_data_ptr2);
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/* attr1 - non-compatible : different type */
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write_attr(did2,1,dims1_1,"attr1", tid_attr1, attr_data_ptr2);
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/* attr2 */
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write_attr(did2,1,dims1,"attr2", H5T_NATIVE_INT, attr_data_ptr3);
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/* dset2 */
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status = write_dset(gid2, 1, dims1,"dset2", H5T_NATIVE_INT, dset_data_ptr3);
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/* attr2 - non-compatible : same rank, different dimention */
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write_attr(did2,1, attr2_dim_ptr,"attr2", H5T_NATIVE_INT, data3);
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/* attr3 - non-compatible : different rank */
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write_attr(did2, rank_attr,attr3_dim_ptr,"attr3", H5T_NATIVE_INT, attr_data_ptr3);
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/* attr4 - compatible : different data values */
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write_attr(did2,1,dims1_1,"attr4", H5T_NATIVE_INT, attr_data_ptr4);
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/*----------
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* dset2 */
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status = write_dset(gid2, 1, dims1_1,"dset2", H5T_NATIVE_INT, dset_data_ptr3);
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if (status == FAIL)
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{
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fprintf(stderr, "Error: %s> write_dset failed\n", fname);
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@ -1,5 +1,9 @@
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Not comparable: <attr1> is of class H5T_INTEGER and <attr1> is of class H5T_STRING
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attribute: <attr2 of </g2/dset1>> and <attr2 of </g2/dset1>>
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Not comparable: <attr2> has rank 1, dimensions [3], max dimensions [3]
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and <attr2> has rank 1, dimensions [4], max dimensions [4]
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Not comparable: <attr3> has rank 1, dimensions [3], max dimensions [3]
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and <attr3> has rank 2, dimensions [3x1], max dimensions [3x1]
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attribute: <attr4 of </g2/dset1>> and <attr4 of </g2/dset1>>
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3 differences found
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dataset: </g2/dset1> and </g2/dset1>
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6 differences found
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@ -6,7 +6,11 @@ dataset: </g1/dset1> and </g1/dset1>
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dataset: </g1/dset2> and </g1/dset2>
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3 differences found
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Not comparable: <attr1> is of class H5T_INTEGER and <attr1> is of class H5T_STRING
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attribute: <attr2 of </g2/dset1>> and <attr2 of </g2/dset1>>
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Not comparable: <attr2> has rank 1, dimensions [3], max dimensions [3]
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and <attr2> has rank 1, dimensions [4], max dimensions [4]
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Not comparable: <attr3> has rank 1, dimensions [3], max dimensions [3]
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and <attr3> has rank 2, dimensions [3x1], max dimensions [3x1]
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attribute: <attr4 of </g2/dset1>> and <attr4 of </g2/dset1>>
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3 differences found
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dataset: </g2/dset1> and </g2/dset1>
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6 differences found
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Binary file not shown.
Binary file not shown.
@ -799,7 +799,8 @@ TOOLTEST h5diff_207.txt -c h5diff_basic2.h5 h5diff_basic2.h5 g2/dset8 g2/dset9
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# not comparable in dataspace of zero dimension size
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TOOLTEST h5diff_208.txt -c h5diff_dset_zero_dim_size1.h5 h5diff_dset_zero_dim_size2.h5
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# non-comparable dataset with comparable attribute, and other comparable datasets.
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# non-comparable dataset with comparable attribute, and other comparable datasets.
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# Also test non-compatible attributes with different type, dimention, rank.
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# All the comparables should display differences.
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TOOLTEST h5diff_220.txt -c non_comparables1.h5 non_comparables2.h5 /g1
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@ -380,8 +380,10 @@ hsize_t diff_attr(hid_t loc1_id,
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*----------------------------------------------------------------------
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*/
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/* pass dims1 and dims2 for maxdims as well since attribute's maxdims
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* are always same */
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if( diff_can_type(ftype1_id, ftype2_id, rank1, rank2, dims1, dims2,
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NULL, NULL, name1, name2, options, 0) != 1 )
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dims1, dims2, name1, name2, options, 0) != 1 )
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{
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if(H5Tclose(ftype1_id) < 0)
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goto error;
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@ -35,24 +35,27 @@ print_dimensions (int rank, hsize_t *dims)
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{
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int i;
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if ( rank > 0 )
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{
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parallel_print("[" );
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for ( i = 0; i < rank-1; i++)
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{
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parallel_print(HSIZE_T_FORMAT, dims[i]);
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parallel_print("x");
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}
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parallel_print(HSIZE_T_FORMAT, dims[rank-1]);
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parallel_print("]" );
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}
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else
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if ( rank <= 0 )
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{
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parallel_print("H5S_SCALAR" );
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}
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else
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{
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if (!dims)
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parallel_print("dimension is NULL");
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else
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{
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parallel_print("[");
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for ( i = 0; i < rank-1; i++)
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{
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parallel_print(HSIZE_T_FORMAT, dims[i]);
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parallel_print("x");
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}
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parallel_print(HSIZE_T_FORMAT, dims[rank-1]);
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parallel_print("]" );
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}
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}
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}
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