| Commit message (Collapse) | Author | Age | Files | Lines |
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Fix for HDFFV-7838 h5ls: segfault for handling region reference in attribute with -v option
Description:
Segfault occurred when h5ls access region reference data in an attribute.
This didn't occurred when -v option was used.
The cause was "h5tool_format_t info;" struct variable members were accessed
without proper values were assigned (was NULL), so printf failed later in the code.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake-Windows (32-LE)
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Add test case to unix test-script for "HDFFV-2567 - added test for be generated files with at least 9 attributes at root". It's committed previously as r21812 along with Cmake test.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)
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attributes at root
Tested: local linux
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standard 2.8.6
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OPTION command for solution folder and no packaging.
Tested: local linux
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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.
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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
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Description:
An old patch was mistakenly committed in r21556. Replaced this fix with the
latest.
Tested: jam, koala, heiwa (h5committest)
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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
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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
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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)
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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.
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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)
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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)
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dimension scales.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE)
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causes problem on Windows.
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h5repack for 1) references, 2) ARRAY of references, 3) VLEN of references, and 4) COMPOUND of references.
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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.
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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
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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)
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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.
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is first.
Also preface all tests with H5REPACK.
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memory allocation failed inside the library
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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.
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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
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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)
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Tested: local linux
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remove benchpar and mpi-perf tests
add new prunTest.cmake that will be modified for parallel tests
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Replace runTest command param spaces with ;
Change CTEST_NAME to HDF5 - the project name
Tested: local linux, windows
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Tested: local linux
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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
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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)
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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.
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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.
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Tested: local linux (after clearing old testfiles)
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Tested: local linux
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- 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)
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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
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H5_SIZEOF_LONG_LONG. This is set if 64-bit integers are supported.
Tested: local linux
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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)
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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)
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status of check
Tested: heiwa
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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)
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inside the test macro. Allows individual tests to be independently executed.
Tested: local linux
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