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* 1.8/master (#317)hdf5-1_8_22Larry Knox2021-02-081-78/+110
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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>
* Fix for HDFFV-9947Vailin Choi2017-09-071-0/+3
| | | | Fix to return error when encoding dataspace selection exceeds 32 bit integer limit.
* Change copyright headers to replace url referring to file to belrknox2017-05-161-6/+4
| | | | removed and replace it with new url for COPYING file.
* [svn-r19093] Description:Quincey Koziol2010-07-191-0/+6
| | | | | | | | | | | | | | | | | | | | 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)
* [svn-r15629] Description:Quincey Koziol2008-09-161-1/+1
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r14326] Description:Quincey Koziol2007-12-061-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | - Keep skip list for tracking chunks with dataset (instead of creating/ destroying it for each I/O operation) and just delete the skip list nodes. - Avoid computations for normalizing selection offset when offset not set. - Avoid updating object modification time twice during dataset creation. - Avoid updating dataset layout message (and object modification time) until dataset is closed. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14307] Description:Quincey Koziol2007-11-291-1/+4
| | | | | | | | | | | | | | | | | | | | | | | | - Extracted common code from H5D_select_read/H5D_select_write into single routine (H5D_select_io) and made H5D_select_read/H5D_select_write "gateway" routines, passing I/O buffer to operate on in "op" struct. - Create optimized pathway in H5D_select_io for I/O operations on single elements. - Make "get linear offset of first element" callback for each type of selection (used in "optimized pathway", above) Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14278] Description:Quincey Koziol2007-11-201-0/+3
| | | | | | | | | | | | | | | | | | | | - Remember # of elements in file selection, instead of querying more than once - Handle building chunk map for single element as special case Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14271] Description:Quincey Koziol2007-11-201-1/+2
| | | | | | | | | | | | | | | | | | | Avoid copying maximum dimensions for temporary dataspaces used for describing chunks during raw data I/O. Tested on: FreeBSD/32 6.2 (duty) in debug mode FreeBSD/64 6.2 (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/default API=1.6.x, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Mac OS X/32 10.4.10 (amazon) in debug mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
* [svn-r14010] Description:Quincey Koziol2007-07-241-0/+16
| | | | | | | | | | | | | | | Fix problem with dataspace messages where the version of the format for a dataspace message could depend on the "use the latest format" flag from the file after it was initially created. Also, move debuging routine into separate file. Tested on: FreeBSD/32 6.2 (duty) FreeBSD/64 6.2 (liberty) Linux/32 2.6 (kagiso) Mac OS X/32 10.4.10 (amazon) Solaris/32 2.10 (linew)
* [svn-r13750] Description:Quincey Koziol2007-05-141-1/+1
| | | | | | | | | Various minor cleanups found while working on the "unique, but sharable" ISOHM changes. Tested on: Mac OS X/32 10.4.9 (amazon) FreeBSD/32 6.2 (duty)
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | 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.
* [svn-r13156] Description:Quincey Koziol2007-01-191-6/+7
| | | | | | | | | Begin refactoring code to straighten out the contorted code that handles shared messages. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
* [svn-r13002] Description:Quincey Koziol2006-11-301-2/+2
| | | | | | | | | | | | Fix problem with copying objects when the dataset to copy has an "older" version of the layout message and needs to compute the size of the dataset's storage after the dataspace information is available. Minor random cleanups also... Tested on: FreeBSD/32 4.11 (sleipnir) Too minor/weird to test w/h5committest...
* [svn-r12902] Checkin of Shared Object Header Message work.James Laird2006-11-131-0/+1
| | | | | | | | | | | | This feature is still in progress; Shared Object Header Messages are not complete as a feature and are not thoroughly tested. There are still "TODO" comments in the code (comments with the word "JAMES" in them, so as not to be confused with other TODO comments). Hopefully this checkin will reduce the liklihood of conflicts as I finish implementing this feature. All current tests pass on juniper, copper (parallel), heping, kagiso, and mir.
* [svn-r11966] Purpose:Quincey Koziol2006-02-271-1/+2
| | | | | | | | | | | | Code cleanup Description: Style fixes for consistency & other minor cleanups Platforms tested: FreeBSD 4.11 (sleipnir) Mac OSX (amazon) Linux 2.4
* [svn-r11712] Purpose:Quincey Koziol2005-11-151-3/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | New feature Description: Check in baseline for compact group revisions, which radically revises the source code for managing groups and object headers. WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! This initiates the "unstable" phase of the 1.7.x branch, leading up to the 1.8.0 release. Please test this code, but do _NOT_ keep files created with it - the format will change again before the release and you will not be able to read your old files!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! WARNING!!!! Solution: There's too many changes to really describe them all, but some of them include: - Stop abusing the H5G_entry_t structure and split it into two separate structures for non-symbol table node use within the library: H5O_loc_t for object locations in a file and H5G_name_t to store the path to an opened object. H5G_entry_t is now only used for storing symbol table entries on disk. - Retire H5G_namei() in favor of a more general mechanism for traversing group paths and issuing callbacks on objects located. This gets us out of the business of hacking H5G_namei() for new features, generally. - Revised H5O* routines to take a H5O_loc_t instead of H5G_entry_t - Lots more... Platforms tested: h5committested and maybe another dozen configurations.... :-)
* [svn-r11558] Purpose:Quincey Koziol2005-10-131-0/+1
| | | | | | | | | | | | | | | | Bug fix Description: Check in Kent's fixes to hyperslab rebuilding code that should correctly detect situation when different sub-hyperslabs exist in a higher dimension. Solution: Remember previous sub-hyperslab information and compare that with newly generated sub-hyperslab to make certain they are the same. Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r11245] Purpose:Quincey Koziol2005-08-131-3/+3
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Trim trailing whitespace, which is making 'diff'ing the two branches difficult. Solution: Ran this script in each directory: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Platforms tested: FreeBSD 4.11 (sleipnir) Too minor to require h5committest
* [svn-r9727] Purpose:Quincey Koziol2004-12-291-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-) Description: Generally speaking, this is the "signed->unsigned" change to selections. However, in the process of merging code back, things got stickier and stickier until I ended up doing a big "sync the two branches up" operation. So... I brought back all the "infrastructure" fixes from the development branch to the release branch (which I think were actually making some improvement in performance) as well as fixed several bugs which had been fixed in one branch, but not the other. I've also tagged the repository before making this checkin with the label "before_signed_unsigned_changes". Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel & fphdf5 FreeBSD 4.10 (sleipnir) w/threadsafe FreeBSD 4.10 (sleipnir) w/backward compatibility Solaris 2.7 (arabica) w/"purify options" Solaris 2.8 (sol) w/FORTRAN & C++ AIX 5.x (copper) w/parallel & FORTRAN IRIX64 6.5 (modi4) w/FORTRAN Linux 2.4 (heping) w/FORTRAN & C++ Misc. update:
* [svn-r9354] Purpose:Quincey Koziol2004-10-011-11/+0
| | | | | | | | | | | | | | | | Bug fix & code cleanup Description: More dataset cleanups to get to a point where we can fix the chunked I/O bug. Also fix a couple of errors in the recent file object resurrection changes which should hopefully address the recent daily test failres (H5T.c) Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel Solaris 2.7 (arabica) h5committest
* [svn-r8932] Purpose:Quincey Koziol2004-07-221-15/+1
| | | | | | | | | | | | | | | | | | | | Code cleanup Description: Clean up collective chunking code a bit. Also, add '--enable-instrument' configure flag to have a mechanism for determining that optimized operations happened correctly in the library (instead of just the "normal" way) by allowing 'flag' properties to be set outside the library and set when the "right" thing happens. This is mainly for debugging and regression checks, so we make certain we don't break optimized I/O by accident. It's enabled by default when --enable-debug is on (which is on by default in the development branch and off by default in the release branch), but can also be independently controlled with its own configure flag. Platforms tested: FreeBSD 4.10 (sleipnir) w/parallel IBM p690 (copper) w/parallel
* [svn-r8906] Purpose:MuQun Yang2004-07-201-2/+2
| | | | | | | | | | | | | | | | | | | | | | | Adding the first round of patches about supporting collective chunk IO in HDF5 Description: The current HDF5 library doesn't support collective MPIO with chunk storage. When users set collective option in their data transfer with chunk storage, the library silently converted the option to INDEPENDENT and that caused trememdous performance penalty. Some application like WRF-parallel HDF5 IO module has to use contiguous storage for this reason. However, chunking storage has its own advantage(supporting compression filters and extensible dataset), so to make collective MPIO possible inside HDF5 with chunking storage is a very important task. This check-in make collective chunk IO possible for some special cases. The condition is as follows(either case is fine with using collective chunk IO) 1. for each process, the hyperslab selection of the file data space of each dataset is regular and it is fit in one chunk. 2. for each process, the hyperslab selection of the file data space of each dataset is single and the number of chunks for the hyperslab selection should be equal. Solution: Lift up the contiguous storage requirement for collective IO. Use H5D_isstore_get_addr to get the corresponding chunk address. Then the original library routines will take care of getting the correct address to make sure that MPI FILE TYPE is built correctly for collective IO> Platforms tested: arabica(sol), copper(AIX), eirene(Linux) parallel test is checked at copper. Misc. update:
* [svn-r8677] Purpose:Quincey Koziol2004-06-141-14/+4
| | | | | | | | | | | | | | | | | | | Code cleanup & optimization Description: Remove old structures that used a union to store information about the dataspace extent and just store the information directly in the dataspace extent itself. Remove ifdef'd references to permutation ordering in dataspaces. We'll definitely need more than this code if/when we implement this feature. Change allocation of dataspace information from calloc() to malloc(). Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8673] Purpose:Quincey Koziol2004-06-131-81/+71
| | | | | | | | | | | | | | | | | | Code optimization Description: Revised dataspace selections to use a more "object oriented" mechanism to set the function pointers for each selection and selection iterator. This reduces the amount and number of times that dataspace selection info has to be copied. Additionally, change hyperslab selection information to be dynamically allocated instead of an inline struct. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8613] Purpose:Quincey Koziol2004-06-051-8/+8
| | | | | | | | | | | | | | | | | Refactor code Description: Move chunk and contiguous cached raw data from file information to dataset information. This simplifies a number of internal interfaces, aligns the code with it's purpose better and should allow more optimizations to the chunked data I/O performance. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.10 (sleipnir) h5committest Misc. update:
* [svn-r8544] Purpose:Quincey Koziol2004-05-201-7/+2
| | | | | | | | | | | | | | Code optimization Description: Expand the use of macros to inline trivial function pointer lookup and calls to reduce the overall number of functions invoked during normal operation of the library. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel Too minor to require h5committest
* [svn-r8520] Purpose:Quincey Koziol2004-05-131-1/+1
| | | | | | | | | | | | Code optimization Description: Don't make a separate allocation for the selection offset - incorporate it into the selection structure as a fixed size array. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel
* [svn-r8496] Purpose:Quincey Koziol2004-05-081-1/+1
| | | | | | | | | | | | | Code optimization Description: Further reduce the number of copies we make of a hyperslab selection for chunked I/O, especially when we are only going to throw the old selection away for a new one. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel
* [svn-r8462] Purpose:Quincey Koziol2004-05-011-2/+2
| | | | | | | | | | | | | Code optimization Description: Reduce the number of times the number of elements in a selection is computed. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) w/parallel too minor to require h5committest
* [svn-r8460] Purpose:Quincey Koziol2004-05-011-11/+11
| | | | | | | | | | | | | | | Code optimization Description: Move the element size for the selection into the selection iterator instead of always passing it as a parameter. Also, eleminate another 64-bit multiply for "all" selections. Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) too minor to require h5committest
* [svn-r8408] Purpose:Quincey Koziol2004-04-221-14/+3
| | | | | | | | | | | | | | Code optimization Description: Instead of dynamicly allocating various arrays for various pieces of information about a selection or selection iterator, just use fixed size array of size H5S_MAX_RANK (as the rest of the library does). Platforms tested: Solaris 2.7 (arabica) FreeBSD 4.9 (sleipnir) h5committest
* [svn-r8376] Purpose:Quincey Koziol2004-04-171-2/+1
| | | | | | | | | | | | | | | | | Code cleanup Description: Update null dataspace changes to try to write older version of dataspace information whenever possible. Refactor common code to only one location. Allow I/O operations to succeed on null dataspaces. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest
* [svn-r8314] Purpose: Progressive check-inRaymond Lu2004-04-061-1/+2
| | | | | | | | | | Description: NULL dataspace. This step is mainly for dataspace header message and a test. Solution: The test mainly checks NULL dataspace features. Backward compatibility is tested in the fill value test. Platforms tested: h5committest
* [svn-r8158] Purpose:Quincey Koziol2004-02-061-14/+10
| | | | | | | | | | | | | | | | | Code cleanup/optimization Description: Query property list values once, at the beginning of the I/O routines, instead of querying the property list values multiple (lots!) of times in lower level routines. Solution: Create "property list caches" for internal library queries of the property list values. Platforms tested: IBM p690 (copper) w/parallel & fphdf5 h5committest
* [svn-r6957] Purpose:Quincey Koziol2003-06-041-23/+10
| | | | | | | | | | | | | | | | Code cleanup & performance improvements Description: Optimize hyperslabs that are built to detect situations where "regular" hyperslabs can be recovered from span tree descriptions. Also, improve "same shape" routine to correctly work with all the different combinations of selections. Platforms tested: FreeBSD 4.8 (sleipnir) w/C++ FreeBSD 4.8 (sleipnir) w/parallel h5committested
* [svn-r6843] Purpose:Quincey Koziol2003-05-091-9/+2
| | | | | | | | | | | | Code cleanup Description: Clean up warnings exposed by compiling on O2K. Also, revert some of Bill and my changes to the H5S_mpi_opt_types_g, etc. and settle them back into their original location. Platforms tested: h5committested.
* [svn-r6837] Purpose:Quincey Koziol2003-05-081-4/+47
| | | | | | | | | | | | | | | Code cleanup. Description: Move many package or internal function prototypes and macro definitions into tighter scope according to their current use. Added more comments where appropriate. Eliminate ancient, unused functions. Added a couple "accessor" functions to get parts of data structures which were moved out of scope. Platforms tested: h5committested
* [svn-r6825] Purpose:Quincey Koziol2003-05-071-28/+41
| | | | | | | | | | | | | | | | | | | | | | | | | New feature/enhancement Description: Chunked datasets are handled poorly in several circumstances involving certain selections and chunks that are too large for the chunk cache and/or chunks with filters, causing the chunk to be read from disk multiple times. Solution: Rearrange raw data I/O infrastructure to handle chunked datasets in a much more friendly way by creating a selection in memory and on disk for each chunk in a chunked dataset and performing all of the I/O on that chunk at one time. There are still some scalability (the current code attempts to create a selection for all the chunks in the dataset, instead of just the chunks that are accessed, requiring portions of the istore.c and fillval.c tests to be commented out) and performance issues, but checking this in will allow the changes to be tested by a much wider audience while I address the remaining issues. Platforms tested: h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)
* [svn-r6546] Purpose:Bill Wendling2003-03-311-3/+14
| | | | | | | | | | | | Update Description: Updated copyright statement in files which hadn't been updated yet. Platforms tested: Linux (Only comment change) Misc. update:
* [svn-r6252] Purpose:Quincey Koziol2003-01-091-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* [svn-r5931] MuQun Yang2002-09-201-62/+62
| | | | | | | | | | | | Purpose: __DLL__ is a keyword in some platforms and __DLL__ is also defined as a macro for windows DLL applications. That causes problems. Description: Solution: Use H5_DLL*** to replace __DLL***__ at all header files. Change the macro defination at H5api_adpt.h. Platforms tested: linux2.2.18smp, irix64, solaris 2.7 and windows 2000
* [svn-r5839] Purpose:Quincey Koziol2002-07-311-46/+102
| | | | | | | | | | | | | | | Code cleanup Description: Move operations on each type of selection into the source code file for each selection type (all->H5Sall.c, hyperslab->H5Shyper.c, etc.) Remove central H5S_select_<foo> operations, instead calling the operations through function pointers in each selection (a much more object-oriented approach). Platforms tested: FreeBSD 4.6 (sleipnir)
* [svn-r5834] Purpose:Quincey Koziol2002-07-241-26/+23
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Large code cleanup/re-write Description: This is phase 1 of the data I/O re-architecture, with the following changes: - Changed the selection drivers to not actually do any I/O, they only generate the sequences of offset/length pairs needed for the I/O (or memory access, in the case of iterating or filling a selection in a memory buffer) - Wrote more abstract I/O routines which get the sequence of offset/ length pairs for each selection and access perform the I/O or memory access. Benefits of this change include: - Removed ~3400 lines of quite redundant code, with corresponding reduction in the size of library binary. - Any selection can now directly access memory when performing I/O, if no type conversions are required, instead of just "regular" hyperslab and 'all' selections, which speeds up I/O. - Sped up I/O for hyperslab selections which have contiguous lower dimensions by "flattening" them out into lesser dimensional objects for the I/O. No file format or API changes were necessary for this change. The next phase will be to create a "selection driver" for each type of selection, allowing each type of selection to directly call certain methods that only apply to that type of selection, instead of passing through dozens of functions which have switch statements to call the appropriate method for each selection type. This will also reduce the amount of code in the library and speed things up a bit more. Phase 3 will involve generating an MPI datatype for all types of selections, instead of only "regular" hyperslab and 'all' selections. This will allow collective parallel I/O for all I/O operations which don't require type conversions. It will also open up the door for allowing collective I/O on datasets which require type conversion. Phase 4 will involve changing the access pattern to deal with chunked datasets in a more optimal way (in serial). Phase 5 will deal with accessing chunked datasets more optimally for collective parallel I/O operations. Platforms tested: FreeBSD 4.6 (sleipnir) w/ parallel & C++ and IRIX64 6.5 (modi4) w/parallel
* [svn-r5543] Purpose:Quincey Koziol2002-06-061-3/+0
| | | | | | | | | | Bug fix. Description: Return H5S_all_opt_possible() prototype to original position in H5Spkg.h, it is not related to parallel I/O. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5530] Purpose:Bill Wendling2002-06-041-0/+3
| | | | | | | | | | | | | | | Code Cleanup Description: Removed some compiler warnings. Solution: In a few cases, NULL was being returned when a FAIL was supposed to be returned instead. There were some header files which needed to be included in a few of the sources. A couple of if-then statements had assignments in the conditional part. The compiler warned that they should have extra "()"s around them. Made the code check the values instead. Platforms tested: Linux (parallel) Modi4 (parallel)
* [svn-r5259] Purpose:Quincey Koziol2002-04-251-6/+2
| | | | | | | | | | | | | | | | Code cleanup Description: Previously, the I/O pipeline (pline), external file list (efl) and fill- value (fill) structs were passed down the raw data function call chain, even into and/or through functions which didn't use them. Since all three of these pieces of information are available from the dataset creation property list, just pass the dataset creation property list down the function call chain and query for the information needed in a particular function. Platforms tested: FreeBSD 4.5 (sleipnir)
* [svn-r5196] Purpose:Quincey Koziol2002-04-171-1/+1
| | | | | | | | | | Code cleanup Description: Fix incorrect include from <H5Sprivate.h> to "H5Sprivate.h" Platforms tested: Just eyeballed it.
* [svn-r5170] Raymond Lu2002-04-111-3/+3
| | | | | | | | | | | Purpose: New feature Description: Fill-value's behaviors for contiguous dataset have been redefined. Basicly, dataset won't allocate space until it's necessary. Full details are available at http://hdf.ncsa.uiuc.edu/RFC/Fill_Value, at this moment. Platforms tested: Linux 2.2.
* [svn-r5152] Purpose:Quincey Koziol2002-04-091-0/+6
| | | | | | | | | | | | | | | New Feature Description: Added new H5Dfill() routine to fill the elements in a selection for a memory buffer with a fill value. This is a user API wrapper around some internal routines which were needed for the fill-value modifications from Raymond as well as Pedro's code for reducing the size of a chunked dataset. Platforms tested: FreeBSD 4.5 (sleipnir) [and IRIX64 6.5 (modi4) in parallel, in a few minutes]
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