Commit Graph

2166 Commits

Author SHA1 Message Date
Allen Byrne
4c5c484b99 [svn-r21715] Correct SET_TARGET_PROPERTIES commands 2011-11-04 12:31:32 -05:00
Allen Byrne
c5e075851a [svn-r21667] Update FOLDER solution option for target properties. Added OPTION command for solution folder and no packaging.
Tested: local linux
2011-10-25 11:52:58 -05:00
Dana Robinson
fa4ab23b9e [svn-r21664] Added solution folders for most of the projects. This still needs some polish - the solution folder assignment should go closer to the target declaration and not all projects are grouped (parallel, c++, fortran, hl, and a few others).
Tested on Windows.
2011-10-25 01:59:10 -05:00
Jonathan Kim
e54d15a26c [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
2011-10-24 16:50:13 -05:00
Neil Fortner
72702153d2 [svn-r21629] Purpose: Update fix committed in r21556
Description:
An old patch was mistakenly committed in r21556.  Replaced this fix with the
latest.

Tested: jam, koala, heiwa (h5committest)
2011-10-20 17:01:21 -05:00
Neil Fortner
395c1c7db5 [svn-r21603] Purpose: Add generic skip list implementation
Description:
Added new H5SL_TYPE_GENERIC skip list type, which uses void *'s as keys and a
client-supplied callback for key comparison.  This was added to support the
upcoming "merge named datatype" feature for H5Ocopy, but may be used in other
places as well.  Also added testing.

Also fixed a potential bug with the H5SL_TYPE_OBJ implementation, and added
testing for that.

Tested: jam, koala, heiwa (h5committest), durandal
2011-10-18 16:27:58 -05:00
Jonathan Kim
664c013fc7 [svn-r21586] Description:
Added a funtion to reset dataset & hyperslab buffer size for h5repack from an 
    environment variable.
    This is performance debugging purpose for now.

Tested:
 jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), Windows (32-LE), cmake
2011-10-14 17:44:11 -05:00
Albert Cheng
c470efd00d [svn-r21489] Bug:
h5dump was used in test script but was not invoked by RUNSERIAL.
THis does not work in batch machines like Blue Gene in LLNL.

Solution:
Added $RUNSERIAL to invoke $H5DUMP_BIN.

Tested:
LLNL BlueGene (udawn)
2011-10-07 15:16:20 -05:00
Albert Cheng
082a3ce442 [svn-r21457] Problem:
Function TOOLTEST_OUTPUT does not filter the extra system messages sent to
stdout or stderr, thus causing output mismatched with expected output.

Solution:
Added STDOUT_FILTER and STDERR_FILTER to filter them out.

Tested:
Tested LLNL uDawn (Blue-Gene cluster), for serial mode only.
2011-10-04 03:16:00 -05:00
Jonathan Kim
7d53789366 [svn-r21413] Description:
Skip parallel diff test "-c non_comparables1.h5 non_comparables2.h5" due
    to hanging issue occurring on koala (linux64-LE) intermittently.
    Plan to put back when resolved.
    The test was related to J7693.

Tested:
 jam (linux32-LE), koala (linux64-LE)
2011-09-23 16:36:19 -05:00
Jonathan Kim
86faf0b302 [svn-r21396] Purpose:
HDFFV-7693 - h5diff produces different behavior between versions: 1.8.3 and 1.8.6

Description:
    There were two issues on this. 
    One was not displaying all the comparable objects if non-comparable 
    object/attribute exist and compared before comparables ones. This issue
    occurred after 1.8.4 release. This is the issue from user.
    The other issue was not displaying all the comparable attributes, 
    if non-comparable object/attribute exist and compared ahead. This issue 
    were exist even before 1.8.4 release. So it's possible some attribute 
    comparison may have not displayed correctly in the past, if non-comparable 
    data were exist in common object.
    Fixed h5diff to display all the comparable object and attribute regardless 
    of non-comparables. 

Tested:
 jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Windows)
2011-09-16 14:29:03 -05:00
Jonathan Kim
4d4bbf0e81 [svn-r21389] Test case added for HDFFV-5932 - h5repack breaks files with dimension scales.
Tested:
 jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
2011-09-14 16:04:41 -05:00
Peter Cao
0d106f126d [svn-r21386] Fixed a void pointer (need to cast it to char*) because it causes problem on Windows. 2011-09-14 14:27:08 -05:00
Peter Cao
91f38293fa [svn-r21382] Update values of references(object and region) of attributes in h5repack for 1) references, 2) ARRAY of references, 3) VLEN of references, and 4) COMPOUND of references. 2011-09-14 10:48:50 -05:00
Raymond Lu
64b1807783 [svn-r21378] The tools used "%hhd" to print signed char. But VMS doesn't know it. So I used H5_VMS to have a different way ("%hd") to print it.
Tested on jam.  Not tested on VMS yet.  Simple change.
2011-09-13 10:45:34 -05:00
Allen Byrne
2457d8ecaf [svn-r21366] JIRA HDFFV-2748 replace use of _WIN32 in source. Created new defines H5_HAVE_WIN32_API and H5_HAVE_VISUAL_STUDIO defines to use. These can be properly set during configurration.
Tested: windows and local linux - reviewed internally
2011-09-06 11:50:32 -05:00
Jonathan Kim
cf81925931 [svn-r21358] Purpose:
HDFFV-7712 - h5diff: segfault over combinations of complex container types (compound, array, vlen)


Description:
    - Fixed segfault over dataset with container types (array,lven) with multiple nested compound types. (ex: compound->array->compound, compound->vlen->compound)

Tested:
    jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
2011-09-02 11:29:45 -05:00
Raymond Lu
d08f89f07d [svn-r21354] Issue 7674 - CLANG compiler complained about the line (about 800):
tempint = (tempint >> packed_data_offset) & packed_data_mask;
The right shift may cause undefined behavior if PACKED_DATA_OFFSET is 
32-bit or more. For every kind of native integers, I changed the code 
to make it zero if PACKED_DATA_OFFSET is greater than or equal to the
size of integer.

Tested on Mac OS Lion with CLANG compiler and jam, koala, and linew.
2011-09-01 15:51:43 -05:00
Allen Byrne
57fbbeb2b9 [svn-r21297] Move all tests into DEPENDS structure so that clear-all-objects is first.
Also preface all tests with H5REPACK.
2011-08-23 08:50:31 -05:00
Peter Cao
80a409e14d [svn-r21283] H5Eget_major() is depreciated. use the H5Eget_msg() instead. 2011-08-22 11:05:42 -05:00
Allen Byrne
39a79934ca [svn-r21280] Correct IF/ENDIF arguments 2011-08-22 10:41:29 -05:00
Peter Cao
23c7adeca8 [svn-r21265] h5repack: added macro to handle failure in H5Dread/write when memory allocation failed inside the library 2011-08-19 12:00:14 -05:00
Scot Breitenfeld
9eb1d607d8 [svn-r21249] Description: Part II of F2003 branch merge into the trunk.
Ran bin/reconfigure to update the Makefile.in in directories not part of the fortran directory check=in. Updates Makefile.in due to changes made in configure.in for the Fortran 2003 additions.

Tested on all platforms run under daily tests.
2011-08-18 09:38:53 -05:00
Allen Byrne
a968e2d409 [svn-r21243] Add resultcode check to MemTest test sections 2011-08-17 13:42:22 -05:00
Jonathan Kim
7a6f281a8b [svn-r21237] Description:
Add test cases for HDFFV-7656 - "--delta=something" considers two NaN of the same type are different.
  The fix was added (r21105) before but test cases were incorrectly added and missing for cmake script.

Tested:
  jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
2011-08-16 17:40:36 -05:00
Jonathan Kim
e703a6a2a4 [svn-r21236] Purpose:
Work for:
   HDFFV-7515 - GMQS: h5unjam - incorrect help page and should display when 
   no file is given.
   and
   HDFFV-5941 - h5jam: specifying a user block file with a proper HDF5 magic
   number will result in a corrupted HDF5 file.


Description:
   - Revised command help pages of h5jam and h5unjam. The descriptions
     were not up to date and some were missing. (HDFFV-7515)
   - Fixed h5jam not to allow specifying an HDF5 formatted file as input 
     file for -u (user block file) option, because the original HDF5 file 
     will not be accessible if allows. (HDFFV-5941)

Tested:
    jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Wondows)
2011-08-16 15:41:47 -05:00
Allen Byrne
14f8f4d437 [svn-r21210] Correct location of xml schema files. JIRA HDFFV-7688
Tested: local linux
2011-08-10 15:48:05 -05:00
Allen Byrne
4d83d62eb3 [svn-r21208] Add fortran COMPILE_FLAGS
remove benchpar and mpi-perf tests
add new prunTest.cmake that will be modified for parallel tests
2011-08-10 14:49:00 -05:00
Allen Byrne
5173111832 [svn-r21201] Prepend test folder name to perform and testpar cmake tests
Replace runTest command param spaces with ;
Change CTEST_NAME to HDF5 - the project name

Tested: local linux, windows
2011-08-09 14:13:26 -05:00
Allen Byrne
dd7693bde0 [svn-r21195] Correct windows exports for h5diff. 2011-08-08 16:59:09 -05:00
Allen Byrne
4eb2b76737 [svn-r21166] Remove subfolder in library install
Tested: local linux
2011-08-01 14:37:34 -05:00
Quincey Koziol
27775305d6 [svn-r21125] Description:
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
2011-07-19 17:45:55 -05:00
Quincey Koziol
a777619a6b [svn-r21121] Description:
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)
2011-07-18 18:12:28 -05:00
Raymond Lu
304f19d730 [svn-r21117] Issue 2763 - I added a new parameter of object access property 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.
2011-07-18 16:23:02 -05:00
Jonathan Kim
cc0486926f [svn-r21113] Description:
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.
2011-07-18 11:13:34 -05:00
Allen Byrne
46049ef382 [svn-r21109] Renamed test files to more descriptive name
Tested: local linux (after clearing old testfiles)
2011-07-18 09:28:11 -05:00
Allen Byrne
05d13386f2 [svn-r21108] Renamed test files to more descriptive name
Tested: local linux
2011-07-18 09:25:42 -05:00
Peter Cao
877b7aed1b [svn-r21105] Fixed two bugs:
- 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)
2011-07-15 18:02:50 -05:00
Mike McGreevy
dc9288a447 [svn-r21101] HDFFV-7639
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
2011-07-14 15:33:21 -05:00
Allen Byrne
3397a114ce [svn-r21091] Replace #ifdef WIN32 around 64 bit integers with H5_SIZEOF_LONG_LONG. This is set if 64-bit integers are supported.
Tested: local linux
2011-07-11 10:39:02 -05:00
Allen Byrne
eddfc8bbc3 [svn-r21088] Add dependicies for tests to address issues when run in parallel 2011-07-11 10:17:25 -05:00
Jonathan Kim
5e69ec06ff [svn-r21072] Purpose:
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)
2011-07-07 18:12:51 -05:00
Jonathan Kim
11349c2361 [svn-r21057] [hdf5 Trunk ] TODO
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)
2011-06-30 16:36:34 -05:00
Allen Byrne
0e907c2d10 [svn-r21026] Add configure check for endianess and adjust test depending on status of check
Tested: heiwa
2011-06-23 15:56:24 -05:00
Jonathan Kim
83b77cb4eb [svn-r21014] Purpose:
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)
2011-06-21 13:24:35 -05:00
Allen Byrne
82a2e4ebca [svn-r21011] Change how test created files are cleared by clearing the files inside the test macro. Allows individual tests to be independently executed.
Tested: local linux
2011-06-21 12:43:16 -05:00
Allen Byrne
1056623523 [svn-r20995] Get comment section did not add null terminator.
Tested: Debug windows
2011-06-19 09:38:52 -05:00
Raymond Lu
4bffd76b3c [svn-r20929] Issue 4278 - When reading data fails, the error message should 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.
2011-06-03 10:58:49 -05:00
Jonathan Kim
b71a597e86 [svn-r20927] Purpose:
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)
2011-06-02 16:35:03 -05:00
Allen Byrne
843879de95 [svn-r20902] Re-ordered routines to match order of 1.8 for easier comparision of code changes 2011-05-25 10:16:01 -05:00
Quincey Koziol
1d9307bd91 [svn-r20885] Description:
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)
2011-05-20 17:04:03 -05:00
Allen Byrne
3f11adaec2 [svn-r20875] Refactor h5import to close files and free allocations. Also corrected test dependencies so that memcheck would process tests in correct order.
Tested: local linux - confirmed with valgrind
2011-05-20 12:09:57 -05:00
Allen Byrne
0982e11bb4 [svn-r20871] Added function to free iter structure allocations.
Tested: local linux - Confirmed by Valgrind
2011-05-20 09:44:55 -05:00
Jonathan Kim
a558128a18 [svn-r20869] Purpose:
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)
2011-05-19 17:51:36 -05:00
Allen Byrne
7f9ac481b7 [svn-r20805] references files for jam tests are in sub-folder - testfiles 2011-05-13 08:47:17 -05:00
Jonathan Kim
b9e1b158a5 [svn-r20804] Purpose:
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)
2011-05-12 18:12:29 -05:00
Allen Byrne
00716a21ab [svn-r20798] Correct name of testfile for help tests 2011-05-12 08:18:58 -05:00
Allen Byrne
f49dc38127 [svn-r20796] Refactor print_data_region_blocks/ponts to remove context 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
2011-05-11 15:45:54 -05:00
Allen Byrne
2e7d42a43c [svn-r20785] Revert region data print changes from yesterday 2011-05-10 08:52:13 -05:00
Allen Byrne
3b06122b50 [svn-r20783] correct type of variable for blkindx 2011-05-09 16:50:35 -05:00
Allen Byrne
8e30e8da7b [svn-r20781] correct typo of variable types for indx and jndx 2011-05-09 16:36:34 -05:00
Allen Byrne
67d4653d0f [svn-r20779] Corrected export test to use parameters passed in from ADD_TEST()
Tested: local linux
2011-05-09 16:09:29 -05:00
Allen Byrne
a4c349dece [svn-r20776] Refactor print_data_region_blocks/ponts to remove context 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
2011-05-09 14:56:32 -05:00
Albert Cheng
e21992e08f [svn-r20771] Problem:
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
2011-05-07 12:05:56 -05:00
Jonathan Kim
054ca47350 [svn-r20767] Purpose:
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
2011-05-06 17:02:24 -05:00
Dana Robinson
42301788bc [svn-r20756] Fixes h5diff test failure on BE systems.
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
2011-05-05 14:37:19 -05:00
Allen Byrne
84effee753 [svn-r20752] Windows does not have snprintf, need to use HDsnprintf. 2011-05-05 10:56:36 -05:00
Allen Byrne
c5e00232ff [svn-r20725] Add overlooked changes from part of coverity fix
Tested: local linux
2011-05-04 15:28:09 -05:00
Dana Robinson
fbba9db955 [svn-r20724] Purpose: Fix a bug in h5diff when enum values are compared that do
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)
2011-05-04 15:07:38 -05:00
Allen Byrne
2ee1841187 [svn-r20721] Refactor ext lib import and install.
Add SOVERSION for linux
2011-05-04 14:42:03 -05:00
Allen Byrne
ece690cdb6 [svn-r20717] Refactor ext lib import and install.
Change case of tools subtests to not conflict with tools tests.

Tested: windows, local linux
2011-05-04 11:18:22 -05:00
Allen Byrne
82e9f22912 [svn-r20715] Remove Packed Bits if block in tests 2011-05-03 14:01:30 -05:00
Allen Byrne
907a5a1df0 [svn-r20713] Packed Bits Merge:
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
2011-05-03 12:56:23 -05:00
Allen Byrne
87994982f9 [svn-r20677] Merge packed bits option from 1.8 branch to trunk. CMake only. Autotools merge to come.
Tested: local Linux
2011-04-29 13:38:41 -05:00
Jonathan Kim
170e7e53a5 [svn-r20676] Purpose:
- 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
2011-04-29 12:02:31 -05:00
Raymond Lu
65794c39bf [svn-r20626] Albert's test on bp reveals that the dumper had assertion 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.
2011-04-25 11:59:51 -05:00
Jonathan Kim
cefb43df91 [svn-r20600] Purpose:
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)
2011-04-22 11:59:31 -05:00
Jonathan Kim
375dda3d58 [svn-r20595] Purpose:
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)
2011-04-21 18:54:22 -05:00
Raymond Lu
19b21f1b18 [svn-r20581] Bug 1386 - allowing dimension size to be zero. I forgot to check in these 2 data files for the test.
Now test is needed.
2011-04-20 16:42:14 -05:00
Raymond Lu
614e46f270 [svn-r20577] Bug 1386 - allowing dimension size to be zero. I added test 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.
2011-04-20 15:51:22 -05:00
Quincey Koziol
53eb528071 [svn-r20539] Description:
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
2011-04-18 05:18:47 -05:00
Quincey Koziol
9431c7a97e [svn-r20536] Description:
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
2011-04-17 13:57:07 -05:00
Quincey Koziol
e23baa9009 [svn-r20519] Description:
Correct macro names to be more consistent.

Tested on:
	Eyeballed (very simple)
2011-04-15 14:48:30 -05:00
Quincey Koziol
7ff9a8b54a [svn-r20515] Description:
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
2011-04-15 14:20:33 -05:00
Mike McGreevy
98362b664c [svn-r20504] Purpose:
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)
2011-04-14 16:21:59 -05:00
Mike McGreevy
a45c7424b2 [svn-r20502] Purpose:
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
2011-04-14 14:45:57 -05:00
Jonathan Kim
3ca91ad9dc [svn-r20490] Purpose:
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)
2011-04-13 15:23:36 -05:00
Jonathan Kim
eb4a8c7e7d [svn-r20488] Purpose:
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)
2011-04-12 18:02:33 -05:00
Quincey Koziol
e4c6ef2f06 [svn-r20480] Description:
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
2011-04-12 11:59:33 -05:00
Jonathan Kim
9af7a65b4f [svn-r20477] remove duplicated -f option from a test case script.
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
2011-04-11 17:45:04 -05:00
Dana Robinson
3fbbb862a9 [svn-r20476] Removed all references to memory.h 2011-04-11 16:43:15 -05:00
Mike McGreevy
e006157deb [svn-r20475] Purpose:
- 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
2011-04-11 16:00:38 -05:00
Allen Byrne
338beff4e4 [svn-r20467] Change test option to use --enable-error-stack instead of -E 2011-04-11 10:20:20 -05:00
Allen Byrne
0c032eef21 [svn-r20458] Change handling of reference files so that the output of import is restored
HDFFV-5930
2011-04-08 16:20:47 -05:00
Allen Byrne
e4c9340564 [svn-r20452] Pass value of last test variable into sub-macro of add-test for diff tests. 2011-04-08 15:01:10 -05:00
Allen Byrne
7728391265 [svn-r20429] CMake: correct h5copy test macros, add userblock script test to h5jam tests, and correct h5jam tests
Tested: local linux
2011-04-07 09:03:08 -05:00
Jonathan Kim
00b2dc9137 [svn-r20427] Purpose:
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)
2011-04-06 15:59:37 -05:00
Jonathan Kim
b64aad457c [svn-r20424] Purpose:
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)
2011-04-06 14:02:42 -05:00
Jonathan Kim
553e452ce4 [svn-r20384] Purpose:
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)
2011-03-31 16:43:46 -05:00
Jonathan Kim
d03182a94e [svn-r20379] Missed test file from previous checkin r20378.
Bug 2182 - h5ls and h5dump: update to use --enable-error-stack among tools, also update related descriptions
2011-03-30 13:22:10 -05:00