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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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Bring r23713 and r23717 from trunk to 1.8 branch:
Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
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Bring r21919-21924 from trunk to 1.8 branch: cleanup FUNC_ENTER macros,
etc.
Also removed Subversion mergeinfo tags from a few directories and files.
These are artifacts from non-root merges using pre-1.6 Subversion clients. (This
should fix the problem of unchanged directories looking "changed" during
checkins.)
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug & production
(daily tested on trunk)
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Purpose: Add generic skip list implementation
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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Purpose: Add generic skip list implementation
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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Bring r18595 from trunk to 1.8 branch:
Clean up compiler warnings
Tested on:
Mac OS X/32 10.6.3 (amazon) w/debug
(too minor to require h5committest)
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Bring r18031 from trunk to 1.8 branch:
Bring r18030 from merge_metadata_journaling branch to trunk:
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling branch.
Also, some other minor cleanups along the way.
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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Bring r17313 from trunk to 1.8 branch:
Bring back various minor code cleanups from the file free space branch
Tested on:
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x,
w/C++ & FORTRAN, in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Description:
Changed Skip list package to use a deterministic skip list. This allows the
skip list package to avoid calling rand() and srand(), even on machines without
rand_r(). There is no longer a p-value or maximum level for skip lists.
Tested: jam, smirom, linew (h5committest)
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Bring back r15510 & r15512 from trunk:
Fix compiler warnings and formatting.
Tested on:
Mac OS X/32 10.5.4 (amazon)
More tests upcoming
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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Clean up some of the warnings on 64-bit Linux...
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
Too minor to require h5committest
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Feature
Description:
Revised Link APIs.
Solution:
New link APIs use H5L*
H5*create_expand do not create links to the objects created; this must
be done manually with H5Llink.
Added APIs to link an object given its ID (H5Llink), to copy links (H5Lcopy),
and changed creation APIs (H5Lcreate_hard and H5Lcreate_soft) and query
API (H5Lget_linkinfo instead of H5Gget_objinfo).
All old APIs are still supported in H5Gdeprec.c .
Platforms tested:
sol, mir, copper
Misc. update:
Forgot to update MANIFEST and release docs. Will do after checkin.
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Bug fix
Description:
Fix "double root open" bug and apply same fix to datasets & named datatypes.
Also fix bug in symbol table entry lookup code that would "transfer" an
object from one file handle to another file handle when the two file handles
were opened on the same actual file.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
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Code optimization
Description:
Begin de-orbital burn of threaded, balanced binary tree code use by
switching file open object code over to using them. Initial benchmarks show
that skip lists are 5-10x faster than our TBBT code...
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
Solaris 2.7 (arabica)
Too minor to require h5committest
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Bug fix
Description:
Correct assertion to check pointer value correctly.
Platforms tested:
AIX 5.1 (copper)
too minor to require h5committest
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Purpose:
Feature
Description:
Datatypes and groups now use H5FO "file object" code that was previously
only used by datasets. These objects will hold a file open if the file
is closed but they have not yet been closed. If these objects are unlinked
then relinked, they will not be destroyed. If they are opened twice (even
by two different names), both IDs will "see" changes made to the object
using the other ID.
When an object is opened using two different names (e.g., if a dataset was
opened under one name, then mounted and opened under its new name), calling
H5Iget_name() on a given hid_t will return the name used to open that hid_t,
not the current name of the object (this is a feature, and a change from the
previous behavior of datasets).
Solution:
Used H5FO code that was already in place for datasets. Broke H5D_t's, H5T_t's,
and H5G_t's into a "shared" struct and a private struct. The shared structs
(H5D_shared_t, etc.) hold the object's information and are used by all IDs
that point to a given object in the file. The private structs are pointed
to by the hid_t and contain the object's group entry information (including its
name) and a pointer to the shared struct for that object.
This changed the naming of structs throughout the library (e.g., datatype->size
is now datatype->shared->size). I added an updated H5Tinit.c to windows.zip.
Platforms tested:
Visual Studio 7, sleipnir, arabica, verbena
Misc. update:
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Bug fix
Description:
Correct problems with "resurrecting" a dataset in a file. (This occurs
when a dataset which is open gets unlinked from the group hierarchy (making it
"dead" and marked for deletion in the file) and then is re-linked to the group
hierarchy). Note that the current solution applies only to datasets, further
work will fix this for groups and named datatypes also.
Also, fix the "debug" routines to be a little more helpful in certain
situations.
Additionally, fix a locking bug in the symbol table node splitting routine
which could be [one of] the cause[s] of the file corruption in flexible
parallel operation.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel
h5committested
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Code cleanup & minor optimization
Description:
Re-work the way interface initialization routines are specified in the
library to avoid the overhead of checking for them in routines where there is
no interface initialization routine. This cleans up warnings with gcc 3.4,
reduces the library binary size a bit (about 2-3%) and should speedup the
library's execution slightly.
Platforms tested:
FreeBSD 4.10 (sleipnir) w/gcc34
h5committest
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Code cleanup
Description:
De-linted more code
Platforms tested:
FreeBSD 4.8 (sleipnir)
too minor to need h5committest
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New feature.
Description:
Mark an object in the "open object list" as deleted when it's reference
count within the file is reduced to zero and it is only being held open by an
ID in the user's application.
Platforms tested:
FreeBSD 4.8 (sleipnir) w/C++
Linux 2.4 (burrwhite) w/FORTRAN
Solaris 2.7 (arabica) w/FORTRAN
IRIX64 6.5 (modi4) w/parallel & FORTRAN
(h5committest not run due to my ongoing difficulties with C++ on burrwhite).
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Update
Description:
Updated copyright statement in files which hadn't been updated yet.
Platforms tested:
Linux (Only comment change)
Misc. update:
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Code cleanup/new feature.
Description:
Split FUNC_LEAVE into API and non-API specific versions. This allows a
solution to compiling this branch with C++, as well as reducing the size
of the binaries produced.
Platforms tested:
FreeBSD 4.7 (sleipnir) w/serial, parallel (including MPE) & thread-safe
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Code cleanup
Description:
Clean up a few more warnings and update dependencies.
Platforms tested:
Linux 2.2.18smp (eirene) serial & parallel
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Lots of performance improvements & a couple new internal API interfaces.
Description:
Performance Improvements:
- Cached file offset & length sizes in shared file struct, to avoid
constantly looking them up in the FCPL.
- Generic property improvements:
- Added "revision" number to generic property classes to speed
up comparisons.
- Changed method of storing properties from using a hash-table
to the TBBT routines in the library.
- Share the propery names between classes and the lists derived
from them.
- Removed redundant 'def_value' buffer from each property.
- Switching code to use a "copy on write" strategy for
properties in each list, where the properties in each list
are shared with the properties in the class, until a
property's value is changed in a list.
- Fixed error in layout code which was allocating too many buffers.
- Redefined public macros of the form (H5open()/H5check, <variable>)
internally to only be (<variable>), avoiding innumerable useless
calls to H5open() and H5check_version().
- Reuse already zeroed buffers in H5F_contig_fill instead of
constantly re-zeroing them.
- Don't write fill values if writing entire dataset.
- Use gettimeofday() system call instead of time() system when
checking the modification time of a dataset.
- Added reference counted string API and use it for tracking the
names of objects opening in a file (for the ID->name code).
- Removed redundant H5P_get() calls in B-tree routines.
- Redefine H5T datatype macros internally to the library, to avoid
calling H5check redundantly.
- Keep dataspace information for dataset locally instead of reading
from disk each time. Added new module to track open objects
in a file, to allow this (which will be useful eventually for
some FPH5 metadata caching issues).
- Remove H5AC_find macro which was inlining metadata cache lookups,
and call function instead.
- Remove redundant memset() calls from H5G_namei() routine.
- Remove redundant checking of object type when locating objects
in metadata cache and rely on the address only.
- Create default dataset object to use when default dataset creation
property list is used to create datasets, bypassing querying
for all the property list values.
- Use default I/O vector size when performing raw data with the
default dataset transfer property list, instead of querying for
I/O vector size.
- Remove H5P_DEFAULT internally to the library, replacing it with
more specific default property list based on the type of
property list needed.
- Remove redundant memset() calls in object header message (H5O*)
routines.
- Remove redunant memset() calls in data I/O routines.
- Split free-list allocation routines into malloc() and calloc()-
like routines, instead of one combined routine.
- Remove lots of indirection in H5O*() routines.
- Simplify metadata cache entry comparison routine (used when
flushing entire cache out).
- Only enable metadata cache statistics when H5AC_DEBUG is turned
on, instead of always tracking them.
- Simplify address comparison macro (H5F_addr_eq).
- Remove redundant metadata cache entry protections during dataset
creation by protecting the object header once and making all
the modifications necessary for the dataset creation before
unprotecting it.
- Reduce # of "number of element in extent" computations performed
by computing and storing the value during dataspace creation.
- Simplify checking for group location's file information, when file
has not been involving in file-mounting operations.
- Use binary encoding for modification time, instead of ASCII.
- Hoist H5HL_peek calls (to get information in a local heap)
out of loops in many group routine.
- Use static variable for iterators of selections, instead of
dynamically allocation them each time.
- Lookup & insert new entries in one step, avoiding traversing
group's B-tree twice.
- Fixed memory leak in H5Gget_objname_idx() routine (tangential to
performance improvements, but fixed along the way).
- Use free-list for reference counted strings.
- Don't bother copying object names into cached group entries,
since they are re-created when an object is opened.
The benchmark I used to measure these results created several thousand
small (2K) datasets in a file and wrote out the data for them. This is
Elena's "regular.c" benchmark.
These changes resulted in approximately ~4.3x speedup of the
development branch when compared to the previous code in the
development branch and ~1.4x speedup compared to the release
branch.
Additionally, these changes reduce the total memory used (code and
data) by the development branch by ~800KB, bringing the development
branch back into the same ballpark as the release branch.
I'll send out a more detailed description of the benchmark results
as a followup note.
New internal API routines:
Added "reference counted strings" API for tracking strings that get
used by multiple owners without duplicating the strings.
Added "ternary search tree" API for text->object mappings.
Platforms tested:
Tested h5committest {arabica (fortran), eirene (fortran, C++)
modi4 (parallel, fortran)}
Other platforms/configurations tested?
FreeBSD 4.7 (sleipnir) serial & parallel
Solaris 2.6 (baldric) serial
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