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* [svn-r21125] Description:Quincey Koziol2011-07-191-31/+31
| | | | | | | | | | | | Correct char arrays that were too small for strings defined. Also, change cleanup to work correctly. Tested on: Mac OS X/32 10.6.8 (amazon) w/debug FreeBSD/32 8.2 (loyalty) w/debug FreeBSD/64 8.2 (freedom) w/debug Linux/64 2.6 (heiwa) w/debug Linux/64 2.6 (ember) w/parallel
* [svn-r21121] Description:Quincey Koziol2011-07-184-13/+13
| | | | | | | | | Switch from H5P_DATASET_ACCESS_DEFAULT to H5P_DEFAULT for calls to H5Rdereference2(). Tested on: Mac OS X/32 10.6.8 (amazon) w/debug (too minor to require h5committest)
* [svn-r21117] Issue 2763 - I added a new parameter of object access property ↵Raymond Lu2011-07-184-12/+12
| | | | | | list to the function H5Rdereference. It's called H5Rdereference2 now. H5Rdereference function has been deprecated to H5Rdereference1. I also added some test cases in trefer.c. Tested on jam, heiwa, and koala.
* [svn-r21113] Description:Jonathan Kim2011-07-182-3/+3
| | | | | | | | | | | | | | | Revert the previous makefile change as release snapshot test failed with MANIFEST check. Don't clean 'testfiles' dir via 'make distclean' for the case of build&test in source dir. In regular daily testings, we build&test in seperate dir from source dir, so no issues occurred. However for the release snapshot test, it seems that we build&test in source dir. The previous change can remove testfiles in source dir if build&test is done in source dir becasue currently the dir name 'testfiles' is same in source dir and test dir. Other task (7602) may change to use different name for the test directory, so 'make distclean' can do its job without interrupting MANIFEST.
* [svn-r21109] Renamed test files to more descriptive nameAllen Byrne2011-07-181-1/+1
| | | | Tested: local linux (after clearing old testfiles)
* [svn-r21108] Renamed test files to more descriptive nameAllen Byrne2011-07-184-8/+8
| | | | Tested: local linux
* [svn-r21105] Fixed two bugs:Peter Cao2011-07-158-94/+132
| | | | | | | - h5repack: h5repack failed to copy dataset if the layout is changed from chunked with unlimited dims to contiguous. (PC -- 2011/07/15) - h5diff: "--delta" option considers two NaN of the same type are different, which is wrong based on http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Diff. (PC -- 2011/07/15)
* [svn-r21101] HDFFV-7639Mike McGreevy2011-07-141-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Purpose: Remove H5_MPI_SPECIAL_COLLECTIVE_IO_WORKS and H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS #defines from source. Description: Two advanced parallel functionalities, special collective IO and complex derived datatypes, are not supported by older implementations of mpi, and thus our code limits the use of these features with #ifdefs and has checks in configure to set them (or not). Unfortunately, configure can't actually run a parallel check to see if these features are working (nor not) so it resorts to looking in the config files where they are explicity enabled or disabled based on versions of mpi, sytems being built on, or for no documented reason at all (i.e. just set to on or off as some 'default'). Overriding these settings is easy if need be, provided it is known that it needs to be done to get improved performance, and oftentimes it is not. Most new MPI implementations successfully handle the functionality requested when these #defines are set, and many of the "turn these features off" cases in the config files are for old (> 5 years) versions of MPI and retired systems (such as NCSA's tungsten). Therefore, the decision has been made to remove the support for these old versions of MPI and systems that cannot handle these behaviors. The #ifdefs and supporting setup in the config/ files and configure script has been removed, and the code executed when these options were not set removed from the source. In passing, this commit also cleans up some whitespace issues in both t_mpi.c and H5Dmpio.c. Furthermore, in t_mpi.c, the special collective IO test was not getting regularly run due to it being written to work only with four processes (we regularly test with six, previously with three), and thus it failed when actually run due to an out of bounds data buffer assignment. It has been modified to run at any number of processes greater than four, and the memory problem has been fixed so the test passes. Tested: jam, h5committest, ember
* [svn-r21091] Replace #ifdef WIN32 around 64 bit integers with ↵Allen Byrne2011-07-112-153/+126
| | | | | | H5_SIZEOF_LONG_LONG. This is set if 64-bit integers are supported. Tested: local linux
* [svn-r21088] Add dependicies for tests to address issues when run in parallelAllen Byrne2011-07-111-0/+10
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* [svn-r21072] Purpose:Jonathan Kim2011-07-0724-965/+1083
| | | | | | | | | | | | Work for HDFFV-7600 - GMQS: h5diff - argument options -d, -p and --use-system-epsilon should be mutually exclusive. Description: Fixed h5diff to display instructive error message and exit with 1 when mutually exclusive options (-d, -p and --use-system-epsilon) are used together. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
* [svn-r21057] [hdf5 Trunk ] TODOJonathan Kim2011-06-3010-526/+1637
| | | | | | | | | | | Purpose: Work for HDFFV-7602 - HDF5 command tools: Provide framework for reusable test files among tools Description: Provide framework to share test files among tools for tools test. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
* [svn-r21026] Add configure check for endianess and adjust test depending on ↵Allen Byrne2011-06-231-3/+3
| | | | | | status of check Tested: heiwa
* [svn-r21014] Purpose:Jonathan Kim2011-06-216-47/+128
| | | | | | | | | | | | | | HDFFV-5878 - GMQS: h5dump - incorrect output format for array type with multiple elements in an index Description: Fixed h5dump to display the first line of each element into correct position for multiple dimention array type. Before this fix, the first line of each element in array were displayed after the last line of previous element without moving to the next line (+indentation) Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
* [svn-r21011] Change how test created files are cleared by clearing the files ↵Allen Byrne2011-06-214-72/+147
| | | | | | inside the test macro. Allows individual tests to be independently executed. Tested: local linux
* [svn-r20995] Get comment section did not add null terminator.Allen Byrne2011-06-191-7/+8
| | | | Tested: Debug windows
* [svn-r20929] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-031-1/+1
| | | | | | say which filter isn't registered. The fix is simple. Most of the effort is on the test. The file with filter enabled is created in gen_filter.c. The verification of the error message is in test_error.c. The output is compared against the standard output. Tested on jam, koala, and heiwa.
* [svn-r20927] Purpose:Jonathan Kim2011-06-0255-175/+15
| | | | | | | | | | | HDFFV-7607: h5ls - improve efficiency of test scripts - removing top 3 extra lines from expected output files Description: This is a subtask from 'HDFFV-7514 - gmqs: h5dump - improve effectiveness of testing scripts for handling expected output files'. This is prerequisite for 'HDFFV-7602 tools - upgrade tools' test scripts to share test files among tools, providing framework for test file re-usability.' Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE), Cmake (jam)
* [svn-r20902] Re-ordered routines to match order of 1.8 for easier ↵Allen Byrne2011-05-251-150/+150
| | | | comparision of code changes
* [svn-r20885] Description:Quincey Koziol2011-05-202-13/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes back to trunk: r20340: Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer. r20341: Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label. Do C-style initialization AFTER all variable definitions. r20342: Fix valgrind error in H5DUMP-XML-tall.h5 r20343: Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE. r20344: Added initialization udata.path = NULL; to prevent uninitialized used after done: label r20347: Purpose: Fix memory leak in overhead.c Description: Fixed leak in test() in overhead.c where array "had" was never freed. r20348: Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h. r20392: Purpose: Fix coverity issues 1677 and 1678 Description: Added return value checking for 4 funciton calls in H5tools_get_symlink_info(). r20394: Purpose: Fix coverity issues 1674 and 1675 Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether va_start() has been called, and to call va_end() at the end if so. r20395: Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh r20396: Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh Tested on: Mac OSX/32 10.6.7 (amazon) w/debug & production (h5committested on branch)
* [svn-r20875] Refactor h5import to close files and free allocations. Also ↵Allen Byrne2011-05-203-2309/+2222
| | | | | | corrected test dependencies so that memcheck would process tests in correct order. Tested: local linux - confirmed with valgrind
* [svn-r20871] Added function to free iter structure allocations.Allen Byrne2011-05-201-0/+42
| | | | Tested: local linux - Confirmed by Valgrind
* [svn-r20869] Purpose:Jonathan Kim2011-05-19229-764/+31
| | | | | | | | | | | HDFFV-7514 - GMQS: h5dump - improve effectiveness of testing scripts for handling expected output files Description: Fist phase for h5dump test update. Next phase will be for h5ls. This is prerequisite for 'HDFFV-7602 Tools - upgrade tools' test scripts to share test files among tools, providing framework for test file re-usability.' Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE), Windows (32-LE), Cmake (jam)
* [svn-r20805] references files for jam tests are in sub-folder - testfilesAllen Byrne2011-05-131-2/+2
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* [svn-r20804] Purpose:Jonathan Kim2011-05-121-1/+1
| | | | | | | | | | | | HDFFV-7594 - GMQS: h5dump shows wrong values for H5T_STD_I8LE dataset on Blue-gene (ppc64 linux BE +@) Description: For the STD_I8 type data, updated to use 'signed char' instead of 'char' as 'char' could be defined as unsigned on a certain system, which cause h5dump to display data values incorrectly. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
* [svn-r20798] Correct name of testfile for help testsAllen Byrne2011-05-121-4/+4
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* [svn-r20796] Refactor print_data_region_blocks/ponts to remove context ↵Allen Byrne2011-05-1112-573/+895
| | | | | | | | passed in by value. The print functions needed an independent context with only the current indent level passed in by argument. Also synched the two routines logical flows and corrected a mem_space error. h5dump (and h5stat, h5jam/h5unjam) help option not tested. Added h5dump parse_command_line technique for h5stat and h5jam/unjam and created testfiles. Tested: local linux
* [svn-r20785] Revert region data print changes from yesterdayAllen Byrne2011-05-101-60/+50
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* [svn-r20783] correct type of variable for blkindxAllen Byrne2011-05-091-4/+4
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* [svn-r20781] correct typo of variable types for indx and jndxAllen Byrne2011-05-091-2/+2
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* [svn-r20779] Corrected export test to use parameters passed in from ADD_TEST()Allen Byrne2011-05-091-1/+1
| | | | Tested: local linux
* [svn-r20776] Refactor print_data_region_blocks/ponts to remove context ↵Allen Byrne2011-05-091-44/+54
| | | | | | passed in by value. The print functions needed an independent context with only the current indent level passed in by argument. Also synched the two routines logical flows and corrected a mem_space error. Tested: local linux
* [svn-r20771] Problem:Albert Cheng2011-05-075-98/+82
| | | | | | | | | | | | | | | | | | | | | | | | | | Test scripts sometimes need to filter some system-specific messages from the actual output so that it can match the correct expected output. These filtering functions, ususally called "STDOUT_FILTER()" and "STDERR_FILTER()" were being repeated in individual test scripts. This becomes a maintenance problem and is error prone. Solution: Extract the two filter functions code to bin/output_filter.sh and then each test script sources it in. This allows reuse of coding and is much easier to maintain and to add new filtering. Tested: LLNL Zeus (linux64 cluster) and Dawndev (Blue-Gene cluster), both for serial mode only. --This line, and those below, will be ignored-- M tools/misc/testh5mkgrp.sh M tools/h5dump/testh5dump.sh.in M tools/h5diff/testh5diff.sh M tools/h5copy/testh5copy.sh M tools/h5ls/testh5ls.sh.in M MANIFEST A bin/output_filter.sh
* [svn-r20767] Purpose:Jonathan Kim2011-05-066-43/+106
| | | | | | | | | | | | HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Improved performance by eliminating duplicated action for getting object information in half from the previous fixe when comparing group vs group. This is addition to the previous commit r20676. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
* [svn-r20756] Fixes h5diff test failure on BE systems.Dana Robinson2011-05-053-4/+11
| | | | | | | | | | | | | | | H5Dread() produces different output for invalid enum type values on systems of different endiannes. On BE systems, it always emits -1. On LE systems, the invalid value is emitted. This difference caused the h5diff test to fail since it tests to see if different invalid enum values are reported as different (on BE systems they are not since -1 == -1). This fix removes the "invalid vs. different invalid" test while we fix the library bug. HDFFV-7527 will be reopened in JIRA until the full test passes. Tested on: jam, heiwa, linew
* [svn-r20752] Windows does not have snprintf, need to use HDsnprintf.Allen Byrne2011-05-051-3/+3
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* [svn-r20725] Add overlooked changes from part of coverity fixAllen Byrne2011-05-042-8/+15
| | | | Tested: local linux
* [svn-r20724] Purpose: Fix a bug in h5diff when enum values are compared that doDana Robinson2011-05-045-2/+136
| | | | | | | | | | | | | | | | | not represent a valid enum value. Description: The h5diff code compares enum values by converting them to strings and then comparing them. When the enum value is out of range and can't be converted to an enum string representation, the comparison was skipped. The code now flags differences when one of the two enum values is out of range (two out of range values are compared in memory). A test has been added to the tools test script. This fixes JIRA HDFFV-7527 Tested on: jam, koala, heiwa (h5committest)
* [svn-r20721] Refactor ext lib import and install.Allen Byrne2011-05-041-5/+5
| | | | Add SOVERSION for linux
* [svn-r20717] Refactor ext lib import and install.Allen Byrne2011-05-042-8/+8
| | | | | | Change case of tools subtests to not conflict with tools tests. Tested: windows, local linux
* [svn-r20715] Remove Packed Bits if block in testsAllen Byrne2011-05-031-5/+1
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* [svn-r20713] Packed Bits Merge:Allen Byrne2011-05-0316-2267/+2288
| | | | | | | | | removed option defines and #ifdef/#endif refactored all printf to HDfprintf in h5dump.c formatted and indention improvements synched with 1.8 branch Tested: local linux
* [svn-r20677] Merge packed bits option from 1.8 branch to trunk. CMake only. ↵Allen Byrne2011-04-2960-12/+4753
| | | | | | Autotools merge to come. Tested: local Linux
* [svn-r20676] Purpose:Jonathan Kim2011-04-2913-51/+186
| | | | | | | | | | | | | | | | - HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects Description: Fixed: 1) adding h5tools_is_obj_same() function to check if two given IDs or paths point to the same object. This function can be very useful for other tools and applications. 2) using h5tools_is_obj_same() at h5diff() and diff() in h5diff.c. If two paths point to the same object, there is no need to check the details of the object since we know there is no difference. The fix will increase the performance by skipping the content comparison. It also fixed the problem of reporting difference for some cases of comparing the same file, e.g. empty files or files with incomparable objects the same file. Test update: Updat prvious test cases (171, 172, 530) affected by this fix, so they still perfrom originally intended testing without bypassing. Tested: jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
* [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
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