| Commit message (Collapse) | Author | Age | Files | Lines |
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Merged from trunk.
Tested: local linux
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1-byte integer. I used the macro H5_VMS
to choose the correct format in the initialization of ls_dataformat.
Tested with h5committest.
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Change printfs in perform output and h5dump to prevent overflow.
This fixes: https://jira.hdfgroup.uiuc.edu/browse/HDFFV-8450
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initialization of h5tools_dataformat.
Tested on jam and OpenVMS - simple change.
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Found and removed two more "//" comments.
Tested: in Koala by
$ env CFLAGS="-ansi" ../hdf5/bin/buildhdf5 -fortran -cxx -config # enable fortran and cxx, configure only
$ make AM_CFLAGS=-ansi # compile all source file by setting HDF5 build CFLAGS as "-ansi" only
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removal line.
Tested: local linux
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HDFFV-8465: corrected DTD reference path
Merged from trunk
Tested: local linux with cmake
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Tested: local linux
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Bring r23695 from trunk to 1.8 branch:
Clean up warnings in H5Tconv.c (down to _only_ 9000 lines of output now!)
Merge changes from Coverity branch back to trunk:
r20684:
Fix for coverity bug #1721 which was due to the fix for coverity bug #943.
r20685:
Use HDstrncpy. --gh
r20761:
Purpose: Fix valgrind issues
Description:
Free image_data and data as appropriate in test_image.
r20762:
Purpose: Fix coverity issue 600
Description:
Add check for return value of H5O_close in H5Ocopy. Also cleaned up various
warnings.
r20763:
Purpose: Fix valgrind issues with h5stat
Description:
Modified h5stat to free "iter" before exit, and free "hand" before exit if
parse_command_line exits directly.
r20764:
fixed coverity issues:
69, 327, 614, 684, 685, 696, 697, 1681, 967, 826, 660, 80
r20765:
Fixed coverity bug 668
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program but I did add a check that n_elements is >= 1.
I also changed an error condition from doing its own close and returning -1 to "goto out;" like the rest of the program.
r20766:
Fixed coverity bug 667
Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning.
No actual integer overflow tests are performed since it's just a test program.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
(h5committest upcoming)
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These are
often added by Windows text editors.
Tested on: jam (just tested to make sure it builds - no code changes)
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Tested: local linux - with and without valgrind
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The previous change set exec_prefix, libdir and includedir to actual values.
That removed the option for user to hand edit just the first prefix=...
to make "everything" to work.
Changed h5redeploy to do this by default:
## Installation directories: ##
## prefix architecture-independent files. ##
## exec_prefix architecture-dependent files, default is <prefix>. ##
## libdir libraries, default is <exec_prefix>/lib. ##
## includedir header files, default is <prefix/include>. ##
############################################################################
This allows users to just change the first line of prefix=<...> and the
effect will change libdir and includedir too.
This was also try to accommodate the -prefix option of h5XX. Unfortunately,
after changing h5redeploy, I found out the h5XX code to support -prefix
actually does not provide the stated efffect. This will be fixed in the
release.
Tested: h5committested plus hand test.
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into this 1.8 DESY branch.
Tested with h5committest (duck failed with CMake because I don't know how to change test/CMakeLists.txt. I'll wait for Allen to do it).
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Change h5redeploy to change all 4 lines, prefix=..., exec_prefix=...,
libdir=..., and includedir=... This way, it reset all 4 lines. Should work
for both version of h5cc created by configure or by rpm.
Tested: hand tested in jam.
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Tested: local linux
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HDFFV-8214 - h5repack failed converting small chunked dataset (size < 1K) to contiguous layout.
Description:
h5repack failed converting small chunked dataset (size < 1K) to contiguous layout.
The first case was when chunk dim is bigger than the dataset dim (at leat one), h5repack failed with displaying error stacks.
The other case is when chunk dim is smaller than the dataset dim, h5repack failed to change layout.
Merged from HDF5 trunk 23407
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), emu (solaris-BE), fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
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Bring r23415 from trunk to 1.8 branch:
Avoid using fpclassify() for detecting zero/non-zero values.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/debug
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Bring r23395 from trunk to 1.8 branch:
Bring Coverity changes from branch to trunk:
r20682:
fixed coverity:
76, 77, 635, 636, 1164, 1165, 1166, 1121, 1122, 1117, 1343
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
(too minor to require h5committest)
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filter in h5dump
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Tested: local linux
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HDFFV-7643 - h5diff - incorrect exit-code returns for extra attribute exist
Description:
h5diff: Fixed to return correct exit code 1 when detect unique
attribute. Prior to this fix, h5diff returned exit code 0 indicating
two files are identical.
Merged from HDF5 trunk r23304.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), emu (solaris-BE), Windows (32-LE cmake), cmake (jam)
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Purpose:
Revert back one of the coverity updates from previous (r23220) checkin. "r20457: Coverity issue 691" in previous svn log. Only revert the change about using "STDOUT_FILENO".
Description:
Using "STDOUT_FILENO" caused error on Windows. On unix it's defined in <unistd.h>, but not in Windows. After a little discussion with Allen, he remembered how the similar case were handled for h5dump redirecting those streams. (in h5dump.c) However it would requires more attention to apply, so this issue is entered as a separate task in jira HDDFV-8306.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE)
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Bring r23219 from trunk to 1.8 branch:
Bring reviewed changes from Coverity branch back to trunk (QK & JK):
r20457:
Coverity issue 691: return of H5duo could be negative. Fixed by using
STDOUT_FILENO and redesign parse_command_line and main to cleanup file
allocations. The output_file var is null when using stdout. In cleanup do not
close output_file if NULL.
r20510:
Initialize ufid = -1 and predicate HDclose call on ufid != -1
r20511:
Purpose: Fix coverity issue 1715
Description: Free "file" and nested data on failure in H5FD_core_open.
r20512:
Initialize ifid = -1 and predicate HDclose call on ifid != -1
r20514:
Initialize h5fid = -1 and predicate HDclose call on h5fid != -1
r20516:
Added else branch to the if (ret_value < 0) check.
r20522:
Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor
potential buffer overwrite bugs, or coverity errors. Fixed by replacing
strcpy and sprintf with strncpy and snprintf.
r20523:
fixed coverity issues 68, 1120, 1116i
r20524:
Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence.
r20601:
Purpose: Fix coverity issues 1703-1705
Description: Modified the cleanup code in test_free in accum.c to reset
allocated buffers to NULL after they are freed, and modified the error cleanup
code to check if these buffers are NULL before freeing them. Also fixed some
unrelated warnings in accum.c.
r20602:
Use HDsnprintf and HDstrncat
r20603:
Purpose: Fix coverity issues 808-809
Description: Modified test_core in vfd.c to check the returns from malloc, and
keep track of whether points and check are allocated by setting them to NULL
when they are not. Added code to free points and check on error if they are
not NULL. Also fixed unrelated warnings in vfd.c.
r20604:
Use HDstrncpy.
r20605:
Use HDstrncpy and HDstrncat.
r20606:
Purpose: Fix coverity issue 807
Description: Modified long_compact in stab.c to keep track of whether objname is
allocated by setting it to NULL when it is not. Added code to free objname on
error if it is not NULL.
r20607:
Changed string function calls to use versions that specify the string length
to fix coverity issues 832 and 839.
Tested on:
Mac OSX/64 10.8.2 (amazon)
(Too minor to require h5committest)
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This was prompted by HDFFV-8227, OS X requires latest version of cmake for proper support.
Tested: local linux
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Merge from trunk
Add testfiles.
Tested: local linux
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Merge from trunk
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testh5stat.sh fails in LLNL uDawn. The test actually ran as expected
but it did not prepare for the extra error messages from the MPI
process.
Solution:
This sort of problem has been fixed by using the output filters in
output_filter.sh. testh5stat.sh is updated to use the output filters.
Tested:
uDawn.
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Bring r22998 from trunk to 1.8 branch:
Clean up warnings and bring changes from Coverity branch back to trunk:
r20451:
Fixed coverity 810
r20454:
Purpose: Fix coverity issue 816
Description: Modified various file drivers to always check the return value from
H5P_get_driver_info.
r20455:
Purpose: Cleanup fix for coverity issue 816
Description: Removed redundant check for "fa" in H5FD_core_open.
Tested on:
Mac OSX/64 10.8.2 (amazon) w/debug
(Too minor to require h5committest)
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HDFFV-8145 h5diff slowness with version >= 1.8.7
Description:
Improved speed when comparing HDF5 files with lots of attributes. Much slower performance was identified with release version from 1.8.7 to 1.8.10 compared to 1.8.6.
Merged from HDF5 trunk r22933.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), cmake (jam)
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Bring r22921 from trunk to 1.8 branch:
Review Coverity changes and bring them back to trunk. (QK & JK)
r20402:
Added #includes for h5tools.y or h5tools_utils.h as required to remedy implicit
function declarations which caused compiler warnings and coverity issues 703-4
and 708-11.
r20414:
This is related to the previous checkin r20399. There were incorrect updates
which caused incorrect behavior when no file was given. Also possible segfault
when handling hyperslab options. Simplify the code changes.
r20449:
Description: Modified H5E_walk2_cb to check return value of H5I_object_verify.
r20450:
fixed coverity 813
Tested on:
Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, debug & threadsafe
(too minor to require h5committest)
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Bring r22915 from trunk to 1.8 branch:
Bring Coverity changes back to trunk:
r20399:
Change parse_command_line to free hand structure on error and only "leave()" at end of main.
r20400:
Purpose: Fix coverity issue 592
Description: Added void cast to call to H5F_sfile_assert_num() in
H5F_term)interface(). There is no need to check the return value of this
function in general, and there would be nothing to do even if it did fail.
r20401:
Added free(src_sizes) and free(src_offset). --gh
Tested on:
Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, threadsafe
(too minor for h5committest)
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HDFFV-8012 - h5repack changes max dims and cause failure if only "-f none" is used without changing layout for chunked dataset when a chunk dim is bigger than a dataset dim
Description:
"h5repack -f <obj>:NONE <file.h5> out.h5" command failed if source file contains chunked dataset and a chunk dim is bigger than a dataset dim.
Another issue is that the command changed max dims if chunk dim is smaller than the dataset dim.
These issue occurred when dataset size is smaller than 64k (compact size limit)
Fixed them.
Merged from HDF5 trunk r22805
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
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variable. Use ADD_DEFINITIONS (${HDF5_EXTRA_C_FLAGS}) in non-fortran CMakeLists.txt folders
Tested: local
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HDFFV-5919 - GMQS: h5diff - The number of object difference is not consistent between dataset and group/type when attribute(s) have differences
Description:
Object differences are not consistent between dataset and group/datatype when their attribute(s) have differences. This is because attribute(s) differences is not accumulated to group or datatype object’s difference, but accumulated to dataset difference.
To fix, do not accumulate attribute difference to dataset difference. This is referred to h5diff’s default behavior and also past report from users that users were confused by the accumulated behavior. (also can’t figure out only for dataset difference , also hard to spot dataset difference when it has lots of attributes or differences)
This also lead to fix inconsistent format indicating difference between dataset and group/datatype object.
Merged from HDF5 trunk r22751.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
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Convert configure.in to configure.ac.
Align TESTS usage with autotools convention.
Update all references from configure.in to configure.ac
Tested: h5committest
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subsetting.
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Tested: windows
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libtool 2.4.2
Tested THG machines.
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