Commit Graph

443 Commits

Author SHA1 Message Date
Allen Byrne
827cbbba31 [svn-r21982] Correct HD prefix in tools for exit
Checked for HD support.
2012-02-24 10:45:54 -05:00
Allen Byrne
5b1c9ffe2d [svn-r21980] Correct HD prefix in tools for *alloc
Checked for HD support.
2012-02-24 09:39:17 -05:00
Allen Byrne
944f2cdf8d [svn-r21979] Correct HD prefix in tools for strlen and memcpy
Checked for HD support.
2012-02-24 09:27:57 -05:00
Allen Byrne
0b4463911f [svn-r21974] Update HSIZE_T print statements to use correct macro.
Fix some more HD prefix issues in tools.

Tested: local linux
2012-02-23 14:08:09 -05:00
Jonathan Kim
75e9bf9e2c [svn-r21902] Description:
update a comment from buzilla# (1797) to jira# (2605). Also prevent conflict from merging source.
2012-01-30 13:35:54 -05:00
Jonathan Kim
e18315c9c1 [svn-r21897] Purpose:
HDFFV-7602 - GMQS: HDF5 command tools: Provide framework for reusable test files among tools
  Stage2 working for h5repack cmake test.

Description:
  Update cmake script to clean up correctly.
  Revisit h5repack cmake test script updated from r21869.
  
Tested:
 cmake test for Windows (32-LE) and jam (linux32-LE)
2012-01-26 15:48:00 -05:00
Jonathan Kim
429a51a6c3 [svn-r21872] Update a comment to make clear from the previous commit (r21869) for HDFFV-7840. 2012-01-11 09:39:49 -05:00
Jonathan Kim
00b9f24d9b [svn-r21869] Purpose:
Fix for HDFFV-7840 h5repack: memory leak over one of the h5diff test file

Description:
  Turned out that there were two causes of memory leaks.
  1. for handling variable length string in attribute. 
  2. for handling compound type with non-reference members.  
  The first issue is fixed in copy_attr() which is updated to use h5tools_detect_vlen to take care of vlen string as well as vlen data. 
  The second is fixed in copy_refs_attr() of compound handling code.
  
Tested:
 jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE),  Windows (32-LE), Cmake (jam)
2012-01-09 16:24:50 -05:00
Allen Byrne
cc3eb8da73 [svn-r21804] Update CMake Required version in all folders to match current standard 2.8.6 2011-12-05 11:19:09 -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
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
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
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
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
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
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
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
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
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
b72157681c [svn-r20249] Add test properties to H5LS for expected fail
Add SKIPPED to test name if test skipped, also do not run skipped tests if doing memcheck
2011-03-15 12:28:18 -05:00
Allen Byrne
484b1f5cfa [svn-r20171] Add HDF5_USING_MEMCHECKER guards around script mode ADD_TEST. This will replace the list of ignore tests in CTestCustom.cmake file.
Tested: local linux
2011-03-01 14:20:20 -05:00
Allen Byrne
600bcf0dc3 [svn-r20161] Correct test properties for test order
Tested: local linux
2011-02-25 12:51:15 -05:00
Allen Byrne
05dfc85de8 [svn-r20153] Move ext lib handling for ext project building to a common macro. Update HDF5 project to use HDFMacros.cmake file. Add test properties for test ordering.
Tested: local linux, windows
2011-02-24 14:43:07 -05:00
Allen Byrne
5d320f5c89 [svn-r20141] Bring 1.8 r20139 cmake and windows changes to trunk 2011-02-22 09:55:04 -05:00
Jonathan Kim
23a80ac554 [svn-r20103] Purpose:
Change to use HDxxx macros.

Description:
    Originally this started for fixing incorrect pointer usage. But that got
    fixed through coverity merge. So this is mainly changing to use HDxxx 
    macros and clean up some related code.
     
Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
2011-02-14 17:20:32 -05:00
Quincey Koziol
a6d5fa2c7d [svn-r20061] Description:
Bring changes from Coverity branch to trunk:

r19930:
Fix memory leaks involving VL attributes in h5repack and h5diff.  The buffers in
copy_attr and diff_attr were not checked for the presence of a vlen before being
freed, and vlen storage was never reclaimed.  Added checks and calls to
H5D_vlen_reclaim().

r19933:
Purpose: Fix memory leak in H5L_move_cb()

Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed
it manually using H5MM_xfree().  Since H5O_link_copy allocates the link using
H5FL_MALLOC, this causes the link to be allocated from the free list but is
never put back on the free list when it is freed.  This prevents the link free
list from shutting down properly.  Modified H5L_move_cb() and H5L_move_dest_cb()
to free the link properly using H5O_msg_free().

r19973:
Fix resource leaks by freeing string created by HD5f2string

r19974:
Issue #345: Inialize buf variable to null

Tested on:
    Mac OS X/32 10.6.6 (amazon) w/debug & production
    (h5committested on Coverity branch)
2011-02-07 19:53:45 -05:00
Quincey Koziol
ff845ed8b1 [svn-r20052] Description:
Clean up Coverity warnings, and fix some style issues:

r19735:
Fix for memory leak in test/mf found by valgrind.

r19736:
Fix memory leak in h5repack.  The buffer in copy_objects, when copying the
entire dataset at once, was not checked for the presence of a vlen, and vlen
storage was never reclaimed.  Added check and call to H5D_vlen_reclaim().

r19772:
Change H5assert() to
   if (H5T_VLEN != src->shared->type || H5T_VLEN != dst->shared->type)
          HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a H5T_VLEN datatype")

r19774:
removed unused priv.

r19775:
removed unused variables

r19778:
Fix memory leak comparing for variable length data types.

r19834:
Fixed memory leaks found by valgrind.  Memory errors remain for another day.

Tested on:
    Mac OS X/32 10.6.6 (amazon) w/debug & production
    (h5committested on branch)
2011-02-05 22:24:42 -05:00
Peter Cao
c439bb5d29 [svn-r20012] Use "if...else" to exclude the use when travt is null. 2011-01-27 09:22:03 -05:00
Peter Cao
72938585be [svn-r20011] make sure that travt is nor null 2011-01-27 08:50:04 -05:00
Jonathan Kim
2f60f82453 [svn-r20005] Purpose:
Clean up tool code. 
    Remove "h5test.h" from tool code. Currently only in h5repack.

Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), linew (solaris-BE)
2011-01-26 16:05:57 -05:00
Allen Byrne
9449cfa361 [svn-r19907] Windows: Correct how fortran links in CRT library. Also correct macro use for checking libtype.
bring r19906 from 1.8 branch
2011-01-04 13:40:26 -05:00
Allen Byrne
86313eb281 [svn-r19895] Remove use of /MT compile flag for building static libs and programs. Added BUILT_AS_STATIC_LIBRARY define to set the windows import/export defines correctly for static libraries. 2010-12-29 13:52:34 -05:00
Larry Knox
72634b34e4 [svn-r19839] Updated to libtool v 2.4, autoconf 2.68 and m4-1.4.15.
Tested with h5committest on amani, heiwa, and jam.
2010-11-23 17:56:59 -05:00
Jonathan Kim
5f1db21f84 [svn-r19818] Purpose:
Change to skip copying when a dataset is not allocated.

Tested:
 jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
2010-11-18 09:35:57 -05:00
Allen Byrne
2b0d8d59ae [svn-r19706] Added VFD test options.
Bring r19705 from branch
2010-11-01 17:10:50 -05:00
Allen Byrne
1f2c4afe77 [svn-r19527] Add clear generated objects commands to test blocks.
Add configurefile command to copy CTestCustom to build folder.

Tested: local linux
2010-10-06 15:49:54 -05:00
Larry Knox
155b00d8ff [svn-r19506] Bring changes from revisions 19408, 19421, and 19442 from branches/hdf5_1_8 to trunk. These revisions reorganize the compile scripts using h5cc.in, h5fc.in, and h5c++.in, add checks for installed examples to the scripts that run them after installation, and add DESTDIR for install as needed for RPMs.
Tested on amani, heiwa and jam by h5committest and with CYGWIN.
2010-10-04 12:15:30 -05:00
Allen Byrne
b4be8ae3d5 [svn-r19434] Correct use of lib, include, bin in INSTALL commands to use proper variables.
Tested: local linux
2010-09-20 15:38:35 -05:00
Allen Byrne
4bae291b1f [svn-r19403] Update to H5REPACK tests for layout info required a grep script like runTest.cmake.
Update CMakeLists.txt for new h5repack  layout tests.

Tested: local linux
2010-09-16 15:31:06 -05:00
Jonathan Kim
4c436595ab [svn-r19392] Purpose:
Additional fix for Bug 1821 - h5repack outputs compression information where it is not supposed to

Description:
 Remove unnecessary lopping code, which only lowers performance.

Tested:
 jam, amani, heiwa
2010-09-15 14:23:25 -05:00
Jonathan Kim
a6b6b75a79 [svn-r19389] Purpose:
Fix for Bug1896 h5repack - changing layout to COMPACT does not work

Description:
Make h5repack be able to convert a layout to COMPACT for small size dataset as default.  Also add verifying layout changes in our test script.

Tested:
 jam, amani, heiwa
2010-09-15 13:32:07 -05:00