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* Revert incorrect bool type
* Correct grep text for filter test
* Check sizeof type to use correct ref_type
* h5dump reg ref chnages has no error file
* Fix comment
* Remove unneeded files
* Verify the decoded version for "all" and "none" selection.
* Remove double entry
* Add missing include
* Snapshot version 1.8 release 22 (snap4)
Update version to 1.8-snap5
* Fixes for test failures with --disable-tests --disable-tools options.
Don't test ph5diff if tests are disabled.
* Correct conditions for parallel builds with and without tests.
* Snapshot version 1.8 release 22 (snap5)
Update version to 1.8.22-snap6
* TRILAB-192 merging warnings changes from develop
* Autotools reconfigure update
* Restore page ejects.
* Restore page eject chars
* Fix orphaned token
* Update LT files
* Correct extra flags and merge TRILAB-24
* Update release note for CMake warnings
* H5repack bug fixes from develop
* TRILAB-192 - merge changes from develop
Single source, config files, for warnings for both autotools and CMake.
Update CMake libraries, tools, tests to use correct flags.
* Add missing m4 file
* Remove 128bit config check fo 1.8
* TRILAB-192 update LTparse files
* A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails.
The code to fix the problem is the same as what is done in H5D__open_oid().
* Add missing " and update function calls incorrectly
named load_gcc_arguments.
Commit changes to gnu-cxxflags to remove unmatched " and to gnu-fflags
to not add C warnings flags to H5_FCFLAGS.
* TRILAB-192 - cleanup edits and match CMake CXX to autotools
* Fix shadowed type
* TRILAB-192 correct fortran commands
* TRILAB-192 version of std=f2008 special check
* Fix shadow variable
* Add prefix_relto_examplesdir function to set relative path to h5c++.
* TRILAB-192 - parser files cannot handle this warning
* Parallel Fortran tests now use the MPI module instead of including
mpif.h.
* Don't add general warnings flags for unsupported old versions of gcc and
g++ (older than gcc/g++ 4.2).
Correct gnu-cxxflags to determine warnings flags to be added based on
C++ compiler version instead of C compiler version.
* Snapshot version 1.8 release 22 (snap6)
Update version to 1.8.22-snap7
* TRILAB-244 separate CXX warnings and errors from C
* Fix NoFilter build
* Move ADD_H5_FLAGS macro from *CompilerFlags.cmake files to
config/cmake_ext_mod/HDFMacros.cmake for common use.
* Restrict errors to gcc 4.8 and above.
* OESS-65 replace szip with aec szip
* Correct CMake version
* Correct -Werror=unused-variable
* Add -Werror= flags to lists displayed in libhdf5.settings.
* Fix -Werror=unused-variable
* More fixes for unused variable
* Resolve warning errors from -Werror= flags:
-Werror=bad-function-cast
-Werror=bad-function-cast
-Werror=implicit-function-declaration
-Werror=nested-externs
* Remove verbose assignments in smoke_check 3 and 5 functions.
* Update to use optimization flags, C++ error flags, and correct
libhdf5.settings.in to remove unworkable changes.
* Update config/gnu-cxxflags.
* Add missing headers
* Fix ifort warning flag.
Restore AC_DEFUN([PAC_PROG_FC_DEFAULT_REALisDBLE] in m4/aclocal_fc.m4.
Add --enable-symbols, --enable-profiling, and --enable-optimization
options to autotools configure; all configure flags for
--enable-production and --disable-production should match HDF5 1.10 and
1.12 production and debug default flags.
* Add github actions file
* Correct path
* OESS-65 Fix packaging
* Update reference name
* Correct filename
* disable pr action and enable fail fast
* Snapshot 1.8.22-snap7
Update version to 1.8.22-snap8.
* Correct mingw path
* Correct mingw paths
* Revise gnu-*flags and cmake/HDF*CompilerFlags.cmake files to add warning
flags for GCC compilers version 4.8 and above.
Removed files from gnu-warnings that only apply to versions < 4.8.
Consolidated warnings from versions < 4.8 that apply to versions >= 4.8
into the 4.8 warnings files.
* Update MANIFEST for removal of older warnings files.
* Yanked all MPI-1 calls
Added batch scripts in bin/batch.
* Snapshot 1.8.22-snap8.
Update version to 1.8.22-snap9.
* Squashed commit of the following:
commit 45b0cbc71929930a874e1c09e0770aa64d0ae697
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Thu Apr 23 13:14:56 2020 -0500
Add C++ warnings treated as error for autotools builds.
commit 6debcddcc766601799d5bd661bd60946f951a07e
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Fri Jun 19 16:50:03 2020 -0500
Remove tests for develop branch from testh5cc.sh.in.
Add @H5_ECXXFLAGS@ to AM_CXXFLAGS.
commit fed497e7f207313b2a133d3b68c942b7d7104b90
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Fri Jun 12 15:06:39 2020 -0500
Merge pull request #2646 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '998c6470d78e14228695419c3b514c35ecf3d69e':
Remove unnecessary version conditions for Clang compilers.
commit 92e52ce5c211bd1d3991a3b8bb67287ac7b652aa
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Wed Jun 10 18:53:45 2020 -0500
Merge pull request #2639 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'a33667faf226f5d8c9633bf537893e8fce1bf1f6':
Add c++ to --enable-sanitize-checks option.
commit 2e802534fb997b81fa98fdd1c7d97d4310898e0d
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Wed Jun 10 15:18:36 2020 -0500
Merge pull request #2633 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '20eab963899841c9a003baebead8e3bc07d9e127':
Remove duplicate entries in MANIFEST.
Make changes to CMake CompilerFlags.cmake files so extra flags are loaded for non-GNU compilers.
Update new clang files to not pick up clang as vendor for pgCC. Add new files to MANIFEST Temporary demotion of 2 -Werror warning flags that fail on macos 10.12 Remove Production flag unknown to Apple clang.
commit 96ef60a58a23847a7da89a891f2415055ec2ab60
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Mon Jun 8 16:24:49 2020 -0500
Merge pull request #2631 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'b942a4d8a3e27317cac50ce37ff5302d477664d8':
Clean up code to get clang version in config/linux-gnulibc1
commit 8a7c687da568e8b50b38fa53da1ca63759be6ec4
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Mon Jun 8 11:42:37 2020 -0500
Merge pull request #2623 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit 'c7626f79fdee4eee13925e240ef41e61f3367eab':
Add flags from config/clang-warnings/*general files to H5 C and CXX flags for all versions of Clang and Clang++ compilers. Switched from cut to awk in testcheck_version.sh.in to avoid dependence on tab vs. " " in version definitions in H5public.h.
Add files for adding warning flags for clang compilers in autotools configure.
commit db3ef7ff3c1ed79167cecef831501411cff8291f
Merge: 5a0f8d7 f9f1310
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Fri Jun 19 14:46:22 2020 -0500
Merge branch 'hdf5_1_12' of https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into hdf5_1_12
commit 5a0f8d7940ae57b445f545a0abd7e303ce6924ee
Author: Larry Knox <lrknox@hdfgroup.org>
Date: Wed Jun 10 20:15:41 2020 -0500
Merge pull request #2636 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:HDFFV-11000-update-testh5cc.sh.in-for-version to develop
* commit '5c0bd670d6e9919c463fbc05de99e2ba55b0761e':
Add tests for all version to H5_NO_DEPRECATED_SYMBOLS section and to section for current version, with and without default API version flags.
HDFFV-11000: update-testh5cc.sh.in to test sample versioned functions in HDF5 1.10, 1.12 and develop.
* Update configure and Makefile.ins after bin/reconfigure.
* Fix MANIFEST
* Fix HDFFV-10591
Description:
h52gif produced a segfault when a buffer overflow occurred because
the data size was corrupted and became very large. This commit added
a check on the data size against the buffer size to prevent the segfault.
It also added error reporting to h52gif to display an error message
instead of silently exiting when the failure occurred.
Platforms tested:
Linux/64 (jelly)
* Snapshot 1.8.22-snap9. Update version to 1.8.22-snap10.
* Merge pull request #2686 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to develop
* commit '800f93f7c994f88dfa716746153ded4b1e690e3a':
Remove path to szip header file from AM_CPPFLAGS when configure check of libsz fails. Fix for HDFFV-10830.
* Regenerate configure.
* Merge from 1.10-1.12-dev - LT parse needs update
* Incorporate pull request #2693 from develop for the fix to HDFFV-11080:
(1) Patch up the file pointer when reading attribute of variable length datatype
(2) Test to verify the fix when doing multiple threads
(3) Update MANIFEST
(4) Add new test to Cmake
* Switch bison and flex update of LT files from bin/genltanalyse to
bin/genparser, and from automatically updating the LT files whenever
reconfigure is run to running only on man<F12>ual command.
* Update hl/sr/H5LT files.
Add bin/genparser to MANIFEST; remove bin/genltanalyze.
* Fix to the merge of PR #2708 for HDFFV-11080 to the 1.8 branch.
Need to checkin test/Makefile.in for the new file added.
* Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
Description:
When a buffer overflow occurred because a name length was corrupted
and became very large, h5dump produced a segfault on one file and a
memcpy parameter overlap on another file. This commit added checks
that detect a read pass the end of the buffer to prevent these error
conditions.
Platforms tested:
Linux/64 (jelly)
* Fixed typo
* Check for header szlib.h only when libsz passes AC_CHECK_LIB, so that
H5_HAVE_SALIB_H is not defined when szip is not enabled, to prevent
compile failures for incompatible szlib.
* HDFFV-11127 - force RTLD_LOCAL in dlopen
* spelling
* Remove extra parens
* Remove unnecessary assignment freom configure.ac.
* Add hypen to subrelease regex
* Add special case when H5_VERS_SUBRELEASE is 0
* Revert H5_VERS_SUBRELEASE check
* The version string has a second use for packaging
* MinGW uses "MinGW Makefiles"
* Snapshot 1.8.22-snap10. Update version to 1.8.22-snap11.
* Merge clang-format changes from develop
* remove stray file
* Source formatted
* Add options to github actions.
* Add back file, remove py file
* HDFFV-11096 Correct h5dump usage text
* Update formating
* remove autogen for 1.8 branch
* Fix comment whitespace
* Change '==' to 'eq' in test script
* Merge from develop
github updates
bin scripts
parser updates
* Snapshot 1.8.22-snap11. Update version to 1.8.22-snap12.
* Merge from 1.10
Comments, whitespace
Simple init and if block brackets.
Minimal code changes limited to return value and spelling
* Update autotools files
* Update FD source
* More merges from 1.10 comments and inits
* Comment fixes
* Fix macro argument
* Remove autogen file and cache dir
* Revert autotools files to previous version
* Correct boolean value and missing define
* URL and options corrections
* revert autoconf files
* Fix compile issues with vfd drivers.
* Fix HDFS test
* Remove extra #endif
* Move init above execution
* Multiple changes to bring branch up-to-date (#87)
Correct TARGET variable and CMake config file location.
Add option to allow filter plugins to be built inline.
Update CMake tools macros.
* hdf5 1 8 release text (#113)
* Multiple changes to bring branch up-to-date
Correct TARGET variable and CMake config file location.
Add option to allow filter plugins to be built inline.
Update CMake tools macros.
* release text updates - mostly whitespace
* Fixed HDFFV-10480 and HDFFV-11159 (#145)
* Fixed HDFFV-10480 and HDFFV-11159
Description
Checked against buffer size to prevent segfault, in case of data corruption.
+ HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
+ HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode and
A user's patch was applied to this previously, but it is redone
for a more correct fix, that is the check now accounted for the
previous advance of the buffer pointer.
Platforms tested:
Linux/64 (jelly)
* Fixed typo
* Update HDF5 1.8 copyright headers with updated copyright URL (#148)
* Update URL for COPYING file in copyright headers.
* Make fortran copyright headers uniformly spaced.
* Update url for Copyright file in c++/src/footer.html.
* OESS-98 Update plugin build option (#171)
* 1.8 has extra fortran CMake option (#176)
* 1.8 has extra fortran CMake option
* Update license URL
* OESS-98 fix tools test for plugins (#180)
* Hdf5 1 8 (#169)
* Fixed HDFFV-10480 and HDFFV-11159
Description
Checked against buffer size to prevent segfault, in case of data corruption.
+ HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
+ HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode and
A user's patch was applied to this previously, but it is redone
for a more correct fix, that is the check now accounted for the
previous advance of the buffer pointer.
Platforms tested:
Linux/64 (jelly)
* Fixed typo
* Fixed HDFFV-11150
Description
Replaced an HDassert with a check for null pointer in H5O_dec_rc() to
catch null pointer in corrupted data situation.
Reversed the fix in svn-r24463 in which a check for null pointer prior
to calling H5O_dec_rc()
Platforms tested:
Linux/64 (jelly)
* HDF5 1 8 fix fortran build on macs (#186)
* Correct fortran and shared libs option
* Fix for no shared fortran build
* OESS-98 fix hdf5 link target (#191)
* Partial changes to RELEASE.txt for release. (#185)
* Partial changes to RELEASE.txt for release.
* Update supported and tested platforms.
* Update version to 1.8.22-12.
* close #195. (#196)
* Update HDF5PluginMacros.cmake
* Update HDF5PluginMacros.cmake
* Update directory for SZ filter in HDF5PluginMacros.cmake.
Updates for release:
Switch configure default to production mode.
Set HDF5_GENERATE_HEADERS to OFF.
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Restores maintainer mode in the autotools (#200) (#203)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Hdf5 1 8 22 (#212)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Brings ttsafe_attr_vlen.c changes from develop (#214)
Fixes exposed pthread problem on Windows.
* Update SO numbers for Hdf5 1 8 22 (#215)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Hdf5 1 8 22 (#224)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Update CMake/HDF5Examples version in bin/release
* Update CMake/HDF5Examples version number in bin/release (#225)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Fixed typo in an error message. (#228)
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* Bring 3 small changes from Hdf5 1.8 to 1.8.22 (#241)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Stat st blocks fix 1822 (#251)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* Fixes Autotools detection of the st_blocks field in stat (#246)
* Fixes Autotools detection of the st_blocks field in stat
The Autotools and CMake will now both correctly determine if the
stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS
appropriately.
* Fixes a typo in configure.ac
* Restore lines in RELEASE.txt.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Stat st blocks fix 1822 (#256)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* Fixes Autotools detection of the st_blocks field in stat (#246)
* Fixes Autotools detection of the st_blocks field in stat
The Autotools and CMake will now both correctly determine if the
stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS
appropriately.
* Fixes a typo in configure.ac
* Restore lines in RELEASE.txt.
* Updated configure with reconfigure.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* RELEASE.txt cleanup.
* Hdf5 1 8 22 (#261)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Hdf5 1 8 22 (#266)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Hdf5 1 8 22 - Reverts lock/unlock callback signature to 1.8.21 version (#267)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Update version in H5public.h
* Hdf5 1 8 22 (#269)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Update version in H5public.h
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Set version 1.8.22 for release.
* dd RELEASE.txt entry for HDFFV-10741.
* Hdf5 1 8 22 (#279)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Update version in H5public.h
* Set version 1.8.22 for release.
* dd RELEASE.txt entry for HDFFV-10741.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) (#277)
* Cache the pointer to the next point to process after the last call to
H5S__get_select_elem_pointlist. This allows the normal process of
iterating over the points in batches to be much more efficient, as the
library does not need to traverse the entirety of the preceding points
every time the funciton is re-entered.
* Update RELEASE.txt for point selection iteration performance fix.
* Hdf5 1 8 22 (#281)
* Restores maintainer mode in the autotools (#200)
Maintainer mode should be enabled in development branches.
Also adds helpful commenting.
Add bin/switch_maint_mode
Disable maintainer mode for release.
Fix incomplete merge for stub functions in H5Fdhdfs.c
* Update configure for Restores maintainer mode in the autotools (#200).
* Update MANIFEST for switch_maint_mode script.
* Update so numbers for 1.8.22 release.
* Add so numbers changes in Makefile.ins for 1.8.22 release.
* Update pkgconfig settings with version - #218 (#223)
* Add notice of final HDFF5 1.8 release.
Add solaris 64bit alignment issue to "Known Problems".
* Update 1.8 final release notice.
* Update CMake/HDF5Examples version in bin/release
* Fixed typo in an error message. (#227)
* Remove duplicate setting (#239)
* RELEASE.txt cleanup.
* Add macOS Big Sur to tested machines, also missing entries for macOS 10.13 and 10.14.
* )Update version.
* Reverts lock/unlock callback signature to 1.8.21 version (#254)
* Reverts lock/unlock callback signature to 1.8.21 version
This callback is unused in 1.8. The ros3 and hdfs VFDs are the only VFDs
that have the lock callback implemented and that is just as no-op stubs.
These stubs were removed so the callbacks are now NULL pointers, like
the other VFDs in 1.8.
* Trivial whitespace fix
* Update version to 1.8.22-14.
* Update version in H5public.h
* Set version 1.8.22 for release.
* dd RELEASE.txt entry for HDFFV-10741.
* Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270) (#277)
* Cache the pointer to the next point to process after the last call to
H5S__get_select_elem_pointlist. This allows the normal process of
iterating over the points in batches to be much more efficient, as the
library does not need to traverse the entirety of the preceding points
every time the funciton is re-entered.
* Update RELEASE.txt for point selection iteration performance fix.
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
* Hdf5 1 8 22 (#284)
* Fixed typo in an error message.
* Updated for HDFFV-11150, HDFFV-10480, and HDFFV-11159
* Update "Support for New Platforms and Compilers" section in RELEASE.txt;
add check_version workaround for binary compatibility to "Known
Problems".
* Add SUSE Linux to tested platforms.
* Update numbers in config/lt_vers.am and run bin/reconfigure for so
numbers.
* Update version in 3 files missed by merge.
Co-authored-by: Allen Byrne <byrn@hdfgroup.org>
Co-authored-by: Vailin Choi <vchoi@hdfgroup.org>
Co-authored-by: vchoi <vchoi@jelly.ad.hdfgroup.org>
Co-authored-by: hdftest <hdftest@hdfgroup.org>
Co-authored-by: Jordan Henderson <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <derobins@hdfgroup.org>
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Neil Fortner <nfortne2@hdfgroup.org>
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removed and replace it with new url for COPYING file.
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fix for HDFFV-9412:
- Check for mpi is_initialized and is_finalized before making MPI calls in init/terminate of HDF5.
- Add a test to make sure we can make serial HDF5 calls from rank 0 after MPI_Finalize is called.
tested with h5committest
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HDFFV-883: attach callback to terminate HDF5 library when MPI_COMM_SELF is destroyed on MPI_Finalize.
tested h5committest.
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Tested: h5committest
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Bring r24864 from trunk to 1.8 branch:
Remove all traces of MPI-POSIX VFD and GPFS detection/code.
Remove remaining traces of stream VFD.
Remove testpar/t_posix_compliant test (it's not actually verifying anything).
Clean up H5D__mpio_opt_possible() further.
Moved environment variable that disables MPI collective operations into
MPI-IO VFD (instead of it being in src/H5S.c).
A few other small code cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
(daily tested on trunk)
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Bring r22219 from trunk to 1.8 branch: (with release manager's blessing)
Merge "file image" changes from feature branch back to trunk.
Tested on:
h5committested
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Moved the two shape same tests from testphdf5 to a separated executables,
named t_shapesame. The shape same tests runs too long for testphdf5.
In a separated executalbe, it will be easier to separate any errors in
testphdf5 sub-tests from the shape same tests.
t_shapesame.c:
Contains the shape same tests (cloned from t_rank_projection.c) plus
a duplicate of "testphdf5.c" for now. After verifying it is correct, more
cleanup is needed.
testphdf5.c:
Removed the two shape same tests (chsssdrpio & cbhsssdrpio).
Makefile.am:
Makefile.in:
Added t_shapesame as a new test executable.
Removed t_rank_projections.c from part of testphdf5.
testph5.sh.in:
Temporary added the "t_shapesame -p" test for testing shape same tests
with MPIO-Posix VFD.
Tested: h5committested, plus serial jam.
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Bring r19092 from trunk to 1.8 branch:
Bring "shape same" changes from LBL branch to trunk. These changes
allow shapes that are the same, but projected into dataspaces with different
ranks to be detected correctly, and also contains code to project a dataspace
into greater/lesser number of dimensions, so the I/O can proceed in a faster
way.
These changes also contain several bug fixes and _lots_ of code
cleanups to the MPI datatype creation code.
Many other misc. code cleanup are included as well...
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
(h5committested on trunk)
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and removed the redundant cleaning of Makefile.
Tested: jam parallel.
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Added them to the clean list.
Tested: kagiso, serial and parallel.
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Ran reconfigure to generate the Makefile.in files.
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Description:
Preliminary test of H5Fflush to verify that it still works when using MPIO collective mode.
Platforms:
Linux (heping)
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Configuration feature
Description:
'make install' now tests both static and shared libraries if both are installed.
Solution:
Previously, shared libraries were only tested when static libraries were not installed.
Also cleaned up line in commence.am that was including HL library in all Makefiles.
Platforms tested:
mir (Makefile change only)
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Code maintenance
Description:
Remove flexible parallel code
Platforms tested:
FreeBSD 4.11 (sleipnir)
Linux 2.4 (heping)
Solaris 2.9 (shanti)
Linux 2.4/64 (mir)
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new feature
Description:
1) separated the HL library into "public" and "private" header files, with the same caracteristics as the basic library
2) added the public headers to hdf5.h (with a conditional include macro, defined in configure.in)
3) added the path to HL in all Makefile.am 's , because of the inclusion in hdf5.h
Solution:
Platforms tested:
linux 32, 64
AIX
solaris
with fortran and c++
(one packet table example fails)
Misc. update:
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Improvement.
Description:
The t_cache takes a long long time to run and it tests HDF5 calls.
Move it to the back and let more basic tests to run first so that
basic features are tested first.
Platforms tested:
Tested in heping with pp.
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1) Add parallel test for metadata cache
2) Split serial test for metadata cache into two parts
3) Fix bug in which cache was flushed needlessly when the
cache wasn't full.
4) Performance improvements
5) Update API for parallel cache coherency bug fix.
Description:
See above.
Solution:
See above.
Platforms tested:
h5committest
Misc. update:
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Added t_posix_compliant to the rest of the build and patched up minor
compile bugs/warnings encountered on other platforms.
Description:
It seems that <getopt.h> needs to be included to get the file to build, even though the man page
seems to indicate that <unistd.h> should be sufficient.
Solution:
Platforms tested:
copper, colonelk, sol
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Bug fix
Description:
Building with --disable-static seems to have been broken on several platforms.
Fixed this.
Configure will now disable shared libraries automatically when using pgf90
or when building on Cygwin.
Solution:
To avoid errors when using shared libraries with pgf90 (which I had not
realized were compiler-specific), I had manually set convenience libraries
to use the -static linking flag. Apparently, this is not necessary, and
caused these libraries to be created as empty archives when --disable-static
was used.
Also, some libraries were including other libraries, which was not
necessary.
I also fixed code in configure.in to correctly detect whether shared
or static libraries are enabled, and moved code that disables shared libraries
to before libtool is created (rather than editing libtool after the fact).
Despite repeated warnings that only one shared library can be linked at a
time, I have yet to have shared libraries break the linking of tests on
any system. We'll see if the Daily Tests turn up anything.
Platforms tested:
mir (fortran, C++), sleipnir (C++), modi4 (fortran, C++, parallel),
sol (fortran, C++), cygwin
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tidy up.
Description:
MPE option created *.clog file whenever it is executed in MPI.
The cleanup of *.clog files were done in individual Makefile.in.
Often, it is forgotten.
Solution:
Moved the cleaning of *.clog files to CHECK_CLEANFILES in commence.am
so that it is applied whenever check-clean is called.
Platforms tested:
heping pp using MPE.
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Bug #281
Description:
A dataset created in serial mode with H5D_ALLOC_TIME_INCR allocation setting
was not extendible, either explicitly by H5Dextend or implicitly by writing
to unallocated chunks. This was because parallel mode expects the allocation
mode be H5D_ALLOC_TIME_INCR only.
Solution:
Modified library to allocate more space when needed or directed if the
file is opened by parallel mode, independent of what the dataset allocation
mode is.
Platforms tested:
Heping pp.
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bug fix
Description:
Previous commit contained an extra bin (t_chunk_alloc) that is not
ready yet. It was a mistake. Removed it.
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Bug fix and code minor cleanup.
Description:
The attempt to redirect stderr together to the log files were
done in the wrong order such that stderr output goes to where
stdout WAS. Fixed that.
Code minor cleanup--use shell variables to hold the name of the
log file and the test instead of generating them repeatedly. This
makes easier code reading, less crowded and avoid typos.
Only conclude.in is changed. The Makefile.in changes are all
derived from automake.
Platforms tested:
h5committested.
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Makefile feature
Description:
'make check-clean' now cleans *.h5 files created by tests as well as
.log and .chkexe files.
Solution:
check-clean is now a separate target in its own right, which cleans less
than mostlyclean (check-clean < mostlyclean < clean < distclean).
Platforms tested:
mir, heping, modi4 (serial and parallel)
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Feature: tests now use parallel make and only run once
Description:
When make is invoked in parallel (using the -j option), several tests will
now be run simultaneously. This should speed up testing on a number of
systems.
When a test passes, it creates a foo.chkexe or foo.chksh file, which prevents
the test from running again unless the test or library changes.
Solution:
Most of the changes live in config/conclude.am. Added *.chkexe and *.chksh
files to the list of files to be cleaned at "make mostlyclean" time.
Parallel tests still run one at a time, but use the same make instructions
as serial tests.
Platforms tested:
mir, eirene, sleipnir, pommier, copper, modi4 (some errors occurred, probably
due to the test being run before updating hdf5. Will re-run tests after
checkin.)
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Added check-s and check-p targets.
Description:
Added check-s and check-p targets to 1.7 branch to match changes to 1.6
branch. Now parallel and serial tests can be run separately.
Platforms tested:
mir, modi4, copper
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Bug fix
Description:
Arabica exhibited strange errors when linker found wrong versions of
header files. This happened because include directories were
given to linker in the wrong order.
Solution:
Move include directories from AM_CFLAGS variable to INCLUDES
variable to put them before CPPFLAGS variable. Trust me, it works.
This bug may also have contributed to strange errors on other platforms
(kelgia?).
Platforms tested:
copper, sleipnir, arabica.
(h5dump broke while building on arabica, but this happened in
a clean checkout, too).
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Configuration feature
Description:
HDF5 now uses automake to generate Makefiles
Solution:
Makefile.in files are now generated from Makefile.am files.
To reconfigure (after chaning a Makefile.am or configure.in):
/bin/sh bin/reconfigure.sh
Platforms tested:
Many
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