| Commit message (Collapse) | Author | Age | Files | Lines |
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Description:
H5Ocopy could get confused when copying a named datatype containing an
attribute which used that named datatype as its datatype. This happened
because H5Ocopy would recurse into the attribute's datatype before the object
the attribute was in was fully copied (i.e. before the "post-copy" pass).
Modified H5Ocopy to avoid recursing before the post-copy step in this case.
Required many changes, including to how non-committed shared messages are
copied.
Tested: jam, koala, heiwa (h5committest); durandal
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H5close are needed in the corresponding
Fortran wrappers.
Solutions: The calls were not needed and were removed from the C stubs h5open_c and h5close_c for the correspnding
Fortran subroutines h5open_f and h5close_f.
Platforms tested: jam with gcc and gfortran, PGI and Intel
koala with PGI and Intel
linew with the standard Sun compilers
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pending a careful evaluation of enum conversion behavior.
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It was patched
in the config/ibm-aix file.
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use SEC2 as the
default VFD.
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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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entry is suppose to add to the top not the bottom.
Relate to fix for HDFFV-5932 - h5repack.
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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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CLANG compiler's complaints.
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descriptions to correct section.
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memory allocation failed inside the library
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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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getlogin() function for building HDF5 parallel on windows.
Reviewed and tested locally and tested by user.
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Tested: cygwin
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Replaced several old Linux platforms no longer in use with the current Linux test machine information.
No test - doc file only.
M release_docs/RELEASE.txt
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Removed entries of AIX as tested platform.
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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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- 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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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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whole MULTI file saved in the
super block. We took it out in v1.8 library because it's meaningless
for the MULTI file. v1.8 library saves the EOA for the metadata file,
instead. But this caused some backward compatibility problem.
v1.8 library couldn't open the file created with v1.6 library. I
fixed the problem by checking the EOA value to detect the file
created with v1.6 library.
Tested on jam, koala, and 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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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.
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When no conversion is involved in reading or writing the
data, overflowing values are retained. When conversion happens, the values become -1. The conversion function puts -1
when overflow happens. I added two new dataset transfer property to control whether to fill 0xff in the destination
data or convert to the destination data when overflow happens. The two new functions are H5Pset(get)_enum_conv_overflow. I also added test cases in enum.c and dtypes.c.
Tested on jam, koala, and heiwa.
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and variable-length). I also added a test case in dtypes.c.
Tested on jam and linew - relatively simple.
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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)
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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
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