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* [svn-r20626] Albert's test on bp reveals that the dumper had assertion ↵Raymond Lu2011-04-252-38/+46
| | | | | | | | failure when it tried to display empty attribute data. I added a check for empty attribute in h5dump.c. I also added a check for empty dataset in tools/lib/h5tools.c. Tested on jam. But I tested the same changes in 1.8 on jam, linew, and amani.
* [svn-r20600] Purpose:Jonathan Kim2011-04-221-1/+1
| | | | | | | | | | | | | | HDFFV-5948 - CHICAGO: Tools - implement missing external link test cases Description: Correct mistake in cmake script from previous commit r20595. Add three test cases for h5dump and h5ls. - h5ls: external link to soft link with follow symlink. - h5dump: external link to soft link with follow symlink. - h5ls: external link to soft link without follow symlink. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20595] Purpose:Jonathan Kim2011-04-2113-0/+62
| | | | | | | | | | | | | HDFFV-5948 - CHICAGO: Tools - implement missing external link test cases Description: Add three test cases for h5dump and h5ls. - h5ls: external link to soft link with follow symlink. - h5dump: external link to soft link with follow symlink. - h5ls: external link to soft link without follow symlink. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20581] Bug 1386 - allowing dimension size to be zero. I forgot to ↵Raymond Lu2011-04-202-0/+0
| | | | | | check in these 2 data files for the test. Now test is needed.
* [svn-r20577] Bug 1386 - allowing dimension size to be zero. I added test ↵Raymond Lu2011-04-209-2/+161
| | | | | | | | cases in the tests for h5dump and h5diff. I also added the test cases in the CMAKE script. Tested on jam, linew, and amani. Tested CMAKE on jam.
* [svn-r20539] Description:Quincey Koziol2011-04-182-152/+202
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes back to trunk: r20276: Add recursive is vlen string function. Cleanup resource leaks for issues: 200,202,329,688,811,812 r20277: Check types and close by adding error section: issue 687 r20278: Replaced implicit pointer conversion with (ocrt_info.new_obj != NULL). r20280: Addressed coverity issues 927-929 & 583. The real issue is failure to check file name length -- at least at the H5FD interface level. This needs more work, but at least I have dealt with the issue in H5FDfamily.c r20337: H5O_type_t obj_type = H5O_TYPE_UNKNOWN; r20338: Added udata.name = NULL; to prevent potential uninitialized use after done: label. r20339: coverity issues: 686,828,1670-1673,1707-1711 Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode FreeBSD/32 8.2 (loyalty) w/gcc4.6, in debug mode FreeBSD/64 8.2 (freedom) w/gcc4.6, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
* [svn-r20536] Description:Quincey Koziol2011-04-172-13/+28
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Clean up various warnings & code formatting issues. Bring changes from Coverity branch to trunk: r20085: Purpose: Fix coverity issue 793 Description: Modified H5S_hyper_project_simple_higher() to free the entire span list in new_space on failure. r20091: This is a fix for coverity bug #1683. Changed the two printfs to use %lu (unsigned long) for printing "dset_size". r20162: Purpose: Fix coverity issue 785 Description: Modified H5T_enum_nameof() to free "name" on failure if it was allocated. Also clarified some code in H5S_hyper_rebuild_helper(). r20189: Addressed coverity defect 783. H5SL_new_node() in H5SL.c was failing to free space allocated in its first alloc if the second alloc failed. Added a call to H5FL_FREE to address this issue. This is purely to keep coverity happy -- if this code is ever triggered, we have much larger problems. Note that this fix will trigger an unused return value complaint from coverity next week. r20190: Fixed Coverity issues 1561 1565 and 1678 (UNUSED_VALUES) by moving checks of return values to after the function call. r20191: Fixed coverity issues 643 644 and 1678 (CHECKED_RETURN). r20232: Addressed coverity issues 923-925. Replaced calls to sprintf with calls to HDsnprintf. r20233: Fix coverity issue 662. Don't try to sort 0 attributes in H5Aint.c. r20234: Fix coverity issue 664. Check for NULL before dereferencing in H5Gdeprec.c. r20271: Purpose: Fix coverity issue 784 Description: Modified H5_debug_mask() to keep a list of files opened for use as a debugging output stream, and modified H5_term_library to close these files on exit. r20272: addressed coverity issues 838 & 955. Issue was use of strcpy() -- existing code was safe, but modified to use strncpy() to keep coverity happy. r20273: Addresed coverity issues 1388 and 1389. Initialized sel_iter->type to NULL in H5S_select_iter_init. r20275: Purpose: Fix valgrind issue in mf.c Description: Fixed bug (incomplete if statement) in test_mf_fs_alloc_free() so the retrieved node gets freed. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
* [svn-r20519] Description:Quincey Koziol2011-04-151-49/+48
| | | | | | | Correct macro names to be more consistent. Tested on: Eyeballed (very simple)
* [svn-r20515] Description:Quincey Koziol2011-04-151-6/+13
| | | | | | | | | | | | Remove old, uneeded configuration customizations for FreeBSD systems. (config/freebsd) Also, convert a large stack variable into a dynamic memory allocation and clean up a few compiler warnings (tools/h5dump/h5dumpgentest.c) Tested on: FreeBSD/32 8.2 (loyalty) w/debug & production FreeBSD/64 8.2 (freedom) w/debug & production
* [svn-r20504] Purpose:Mike McGreevy2011-04-1411-11/+44
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | General shared library improvements for CYGWIN / AIX Description: Shared libraries are disabled on both CYGWIN and AIX due to inability to build them correctly. Part of the problem in both of these situations is the lack of the libtool flag -no-undefined, which tells libtool that all needed symbols are defined at link time (a requirement on these systems) and that it's okay to build shared libraries. Another problem are lack of dependencies between wrapper libraries and core C HDF5 library. This patch addresses both of these by fixing configure to add in -no-undefined flag for libtool during linking and adds automake dependencies in the Makefile.am files. After testing, both CYGWIN and AIX now generate shared libraries, but there are still some test failures in each. (cache_api, dt_arith, and testerror.sh on CYGWIN, and fortran tests on AIX). Even though the shared libraries are not quite perfect, this is a general improvement to what we had before, so I'm applying the patch anyways. Note that default behavior of shared libraries on these systems being disabled has NOT been changed and requires the use of the --enable-unsupported to attempt to build them. We will need to address the test failures in each architecture prior to formally supporting shared libraries on each. Tested: h5committested & CYGWIN tested (on bangan) (AIX tested by Albert on bp-login2)
* [svn-r20502] Purpose:Mike McGreevy2011-04-1411-184/+391
| | | | | | | | | | | | | | | | | | | | | | | | Add "silent make" mode configure option. Description: Automake 1.11 has a new option available that allows for a silent make mode. This functionality needs to be explicitly enabled in configure.in via the use of the automake macro AM_SILENT_RULES, which is what this commit is adding. This introduces a new configure option: --{en|dis}able-silent-rules This option is on by default, and simplies compile and link line outputs when building the library. Disabling this option will print full "verbose" output (i.e., full compile and linking lines for each target). Tested: This was tested on jam & h5committested
* [svn-r20490] Purpose:Jonathan Kim2011-04-131-1/+19
| | | | | | | | | | | | | | Fixed HDFFV-4342 : GMQS: h5dump test fails when source directory is read-only Description: Updated CMake script to prevent stripping top 3 lines from expected output file for cmake testing. Also added missing test cases for "# Exceed the dimensions for subsetting" from different Bug fix in the past. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20488] Purpose:Jonathan Kim2011-04-122-5/+1
| | | | | | | | | | | Fix HDFFV-4342 : GMQS: h5dump test fails when source directory is read-only Description: Updated h5dump test case script to prevent entire test failure upon source code directory is read-only. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20480] Description:Quincey Koziol2011-04-121-4/+10
| | | | | | | | | | | Remove global variable for the path name in the group traversal code. Also clean up a bunch of compiler warnings. Tested on: Mac OS X/32 10.6.7 (amazon) w/debug & production FreeBSD/32 6.3 (duty) w/debug FreeBSD/64 6.3 (liberty) w/debug Solaris/32 2.7 (linew) w/debug
* [svn-r20477] remove duplicated -f option from a test case script. Jonathan Kim2011-04-111-1/+1
| | | | jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20476] Removed all references to memory.hDana Robinson2011-04-111-1/+0
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* [svn-r20475] Purpose:Mike McGreevy2011-04-1111-0/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Revise shared Fortran library disabling scenarios in configure - Improve configure output summary Description: Shared Fortran libraries are not supported on Mac, but were being disabled by configure in a way that also forced the C libraries to be static-only. This has been fixed, so now only shared Fortran is disabled while shared C can remain. This prompted two additional changes: 1. While working on the check that addresses whether or not shared Fortran libraries are allowed, removed old and no longer needed check(s) that disable shared Fortran libraries with HP, Intel 8, PGI, and Absoft compilers. (Essentially, Mac is the only situation in which Fortran shared are disabled by configure.) 2. Having two different states of libraries (i.e. shared C library with static-only Fortran library) was not apparent in the configure summary, which labeled all libraries as either shared and/or static. I've added lines to both the C++ and Fortran output sections to list shared/static-ness of these libraries specifically. Additionally, I've made sure that the new --enable-unsupported configure option correctly overrides configure if it tries to disable a shared library. Tested: jam, fred, & h5committest
* [svn-r20467] Change test option to use --enable-error-stack instead of -EAllen Byrne2011-04-111-1/+1
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* [svn-r20458] Change handling of reference files so that the output of import ↵Allen Byrne2011-04-081-11/+3
| | | | | | is restored HDFFV-5930
* [svn-r20452] Pass value of last test variable into sub-macro of add-test for ↵Allen Byrne2011-04-081-6/+4
| | | | diff tests.
* [svn-r20429] CMake: correct h5copy test macros, add userblock script test to ↵Allen Byrne2011-04-072-102/+147
| | | | | | h5jam tests, and correct h5jam tests Tested: local linux
* [svn-r20427] Purpose:Jonathan Kim2011-04-0611-33/+33
| | | | | | | | | | | | Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for --use-system-epsilon option Description: Additional check in from the previous checkin r20424. Updated help page again. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20424] Purpose:Jonathan Kim2011-04-0611-11/+22
| | | | | | | | | | | | Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for --use-system-epsilon option Description: Additional check in from the previous checkin r20384. Updated help page. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20384] Purpose:Jonathan Kim2011-03-3124-125/+145
| | | | | | | | | | | | | | | | | | Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for --use-system-epsilon option Description: Merged from HDF5 1.8 branch r20369. Fixed h5diff for --use-system-epsilon option: the calculation changed from ( |a - b| / b ) to ( |a - b| ). This was decided for better performance and was corrected only in HDF5 trunk, so 1.8 got updated. Also comments for equal_XXX() function were updated correctly. Also help page and RM got updated correctly. Also add test cases for testing the differences w/wo the option. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
* [svn-r20379] Missed test file from previous checkin r20378.Jonathan Kim2011-03-301-1/+1
| | | | Bug 2182 - h5ls and h5dump: update to use --enable-error-stack among tools, also update related descriptions
* [svn-r20378] Purpose:Jonathan Kim2011-03-309-10/+34
| | | | | | | | | | | | | | | | | | | Bug 2182 - h5ls and h5dump: update to use --enable-error-stack among tools, also update related descriptions Description: Decided to use --enable-error-stack long option name only to display error stack messages from HDF5 lib among tools. Updated to unify option name to '--enable-error-stack' for printing HDF5 error stack messages for HDF5 tools. h5ls and h5dump for now. For h5ls, this replaces "-e/--errors" option, which is deprecated. For h5dump, remove -E from help page and RM , which was added by mistake before release1.8.7. Help page and RM got updated. Updated test case. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
* [svn-r20372] Separate no option test within ADD_TEST so depends behaves ↵Allen Byrne2011-03-291-29/+53
| | | | correctly
* [svn-r20363] Updated commands to properly clear generated filesAllen Byrne2011-03-292-5/+2
| | | | Tested: local linux
* [svn-r20362] Added missing character in CMake commandAllen Byrne2011-03-291-1/+1
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* [svn-r20349] BZ1725: H5DUMP displays type of reference for H5T_REFERENCEAllen Byrne2011-03-254-18/+14
| | | | Tested: local linux
* [svn-r20334] Purpose:Jonathan Kim2011-03-2511-11/+110
| | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: This is related to previous checkin r20294. Add help page update for verbose option level feature, which displays useful information about attribute difference with -v1, --verbose=1 -v2 or --verbose=2 option. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20332] Correct clear-misc filenameAllen Byrne2011-03-251-3/+3
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* [svn-r20330] Adjust H5JAM tests for valgind executionAllen Byrne2011-03-251-11/+19
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* [svn-r20320] Correct clear objects for H5MKGRP testsAllen Byrne2011-03-241-0/+9
| | | | Tested:local linux
* [svn-r20318] Correct depends of test for ADD_H5COPY_TESTAllen Byrne2011-03-241-4/+5
| | | | Tested:local linux
* [svn-r20310] Change incorrect use of "struct stat" to use "h5_stat_t". On ↵Allen Byrne2011-03-242-20/+4
| | | | | | windows, this used the wrong structure and caused crashes. Also removed includes from top of file - they are included with proper config checks in h5private.h. Tested: local linux, windows
* [svn-r20305] Add tests to h5import and 80% of h5jamAllen Byrne2011-03-232-3/+537
| | | | Tested: local linux
* [svn-r20294] Purpose:Jonathan Kim2011-03-2222-1219/+10497
| | | | | | | | | | | | | | | | Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the different set of attributes (different number and names) Description: Previously h5diff compared attributes correctly only when two objects have the same number of attributes and attribute names are identical. This fix covers all other cases. Also didn't display useful information about attribute difference. This fixes both issues. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
* [svn-r20285] Purpose:Jonathan Kim2011-03-216-58/+75
| | | | | | | | | | | | | | | | | Improve the previous fix for Bug 2216 - GMQS: h5diff - memory leak when compares vlen string in dataset or attributes Description: Related to the previous checkin r20270 and r20266. Improve h5tools_detect_vlen() code for better performance. H5Tdetect_class already recusive on given type so don't need to be part of recusive call again. Also improve error handlings in h5tools_detect_vlen and h5tools_detect_vlen_str functions. Also updated h5ls and h5dump code accordingly. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
* [svn-r20282] Corrected expected fail tests for use during valgrindAllen Byrne2011-03-191-0/+3
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* [svn-r20274] Purpose:Jonathan Kim2011-03-181-7/+6
| | | | | | | | | | | | | | Fixed Bug 2214 - GMQS: h5diff - memory leak in diff() Description: Memory leaks occurred when accessing symbolic links with --follow-symlink option. Test cases are in testing script. (400 - 456, 501 - 518) An example test : valgrind --leak-check=full h5diff --follow-symlinks -v h5diff_softlinks.h5 h5diff_softlinks.h5 Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
* [svn-r20270] Purpose:Jonathan Kim2011-03-186-21/+58
| | | | | | | | | | | | | | | | Improve the previous fix for Bug 2216 - GMQS: h5diff - memory leak when compares vlen string in dataset or attributes Description: Improve the fix along with the previous checkin r20266. Add a new function to tool lib, h5tools_detect_vlen_data() which return TRUE if include any kind of vlen data all at once, either VLEN-data or VLEN-string and so on. Also updated h5ls and h5dump code accordingly. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
* [svn-r20267] Corrected expected fail tests for use during valgrindAllen Byrne2011-03-181-25/+6
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* [svn-r20266] Purpose:Jonathan Kim2011-03-172-46/+67
| | | | | | | | | | | | | | Fixed Bug 2216 - GMQS: h5diff - memory leak when compares vlen string in dataset or attributes Description: Test for dataset : valgrind --leak-check=full ./h5diff -v h5diff_dset1.h5 h5diff_dset2.h5 /g1/VLstring Test for attr : valgrind --leak-check=full ./h5diff h5diff_attr1.h5 h5diff_attr2.h5 Both test cases are in testing script. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
* [svn-r20260] Windows compilers insist that variable declarations are before ↵Allen Byrne2011-03-161-5/+5
| | | | assignement statements
* [svn-r20257] Corect name of test in test propertyAllen Byrne2011-03-161-1/+1
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* [svn-r20254] Description:Jonathan Kim2011-03-152-4/+4
| | | | | | | | | h5ls is used to verify for the result, so change the two tests not to run h5diff like others. This is related to the previous checkin SVN r18398 for Bug#1733. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), cmake (jam)
* [svn-r20252] Add comment that indicates a "2" in the resultcode param means ↵Allen Byrne2011-03-151-0/+1
| | | | "skip h5diff" component of test
* [svn-r20251] Correct expected fail tests to check a result code of NOT 0Allen Byrne2011-03-151-2/+2
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* [svn-r20249] Add test properties to H5LS for expected failAllen Byrne2011-03-153-27/+45
| | | | Add SKIPPED to test name if test skipped, also do not run skipped tests if doing memcheck
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