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* Remove path to szip header file from AM_CPPFLAGS when configure check of ↵Larry Knox2020-07-101-1/+4
| | | | | | libsz fails. Fix for HDFFV-10830.
* Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib forLarry Knox2020-07-071-1/+1
| | | | junit tests on Macs.
* Merge pull request #2673 in HDFFV/hdf5 from monotonic_timer_fix_01 to developQuincey Koziol2020-07-032-2/+2
|\ | | | | | | | | * commit '13c9b3768e6193db89d06faf59194b77d7747f45': Address CMake and deprecated API build failures from monotonic timer patch.
| * Address CMake and deprecated API build failures from monotonic timer patch.Quincey Koziol2020-07-032-2/+2
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* Merge pull request #2672 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-021-1/+1
|\ | | | | | | | | * commit '870e3ba3f45e90a43ea824d67cc8562aa63a3f6f': Add missing '"'.
| * Add missing '"'.Larry Knox2020-07-021-1/+1
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* Merge pull request #2671 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-07-026-224/+222
|\ | | | | | | | | * commit '88e8597cdef826c1087e4ec1383657a91dcb2a43': Small changes discovered with mingw and windows defines moved
| * Small changes discovered with mingw and windows defines movedAllen Byrne2020-07-026-224/+222
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* | Merge pull request #2670 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-023-1/+20
|\ \ | |/ |/| | | | | * commit 'fc69de0e8ae30e80c1c3c542b156226a75444525': Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
| * Lib files needed are now copied to a subdirectory in the java/testLarry Knox2020-07-023-1/+20
|/ | | | | | directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
* Merge pull request #2668 in HDFFV/hdf5 from monotonic_timer to developQuincey Koziol2020-07-0223-909/+1817
|\ | | | | | | | | | | | | | | | | | | | | | | | | * commit '7371c83f9777b34b31909e99e052398b93c31bed': Remove non-existent example Add new source files to CMake build Clean up warnings va_arg -> HDva_arg Refactor code to remove remaining checks for H5_HAVE_GETTIMEOFDAY scattered around in various places. Also clean up iopipe.c. Correct mistake in H5_now_usec calculation for clock_gettime. Remove detection for mach/mach/time.h, since we're no longer using the time routines from that header. Update H5_now_usec to prefer using clock_gettime. Changes to make timers within the library monotonic.
| * Remove non-existent exampleQuincey Koziol2020-06-301-2/+2
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| * Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-303-7/+17
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| * | Add new source files to CMake buildQuincey Koziol2020-06-282-0/+2
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| * | Clean up warningsQuincey Koziol2020-06-287-54/+53
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| * | va_arg -> HDva_argQuincey Koziol2020-06-271-1/+1
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| * | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-273-54/+134
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| * | | Refactor code to remove remaining checks for H5_HAVE_GETTIMEOFDAY scattered ↵Quincey Koziol2020-06-276-328/+190
| | | | | | | | | | | | | | | | around in various places. Also clean up iopipe.c.
| * | | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-261843-181238/+348913
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| * | | | Correct mistake in H5_now_usec calculation for clock_gettime.Quincey Koziol2017-09-241-1/+1
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| * | | | Remove detection for mach/mach/time.h, since we're no longer using theQuincey Koziol2017-09-243-8/+0
| | | | | | | | | | | | | | | | | | | | time routines from that header.
| * | | | Update H5_now_usec to prefer using clock_gettime.Quincey Koziol2017-09-241-1/+8
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| * | | | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2017-09-0321-889/+846
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| * | | | | Changes to make timers within the library monotonic.Quincey Koziol2017-09-0315-520/+1563
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* | | | | | Merge pull request #2669 in HDFFV/hdf5 from ↵Jake Smith2020-06-301-1/+1
|\ \ \ \ \ \ | |_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/HDftell_macro_typo to develop * commit 'ef05e68c38d2086c6f262744b4087f65a6e58957': Fix typo in HDftell macro definition: 'ftello -> ftell'
| * | | | | Fix typo in HDftell macro definition: 'ftello -> ftell'Jacob Smith2020-06-291-1/+1
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* | | | | Merge pull request #2609 in HDFFV/hdf5 from ~BMRIBLER/hdf5-bmr:develop to ↵Binh-Minh Ribler2020-06-302-1/+15
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop Fix HDFFV-11053 (CVE-2020-10810) * commit 'b155a777629e991374fa2f8609719cb861de4cc2': Changed wording in comment. - added comment to explain a kluge - added the associated entry to release notes Fix HDFFV-11053
| * | | | | Changed wording in comment.Binh-Minh Ribler2020-06-301-2/+2
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| * | | | | - added comment to explain a klugeBinh-Minh Ribler2020-06-292-1/+11
| | | | | | | | | | | | | | | | | | | | | | | | - added the associated entry to release notes
| * | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Binh-Minh Ribler2020-06-29123-4381/+5132
| |\ \ \ \ \ | | |/ / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '30776671fb0a27a98b0640aa968f850241a862ce': (31 commits) * Fix intermittent error with Splitter VFD. Mismatch in time of test file creation was creating false negatives. Added note for HDFFV-10591. Fix HDFFV-10591 Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc. Remove unnecessary version conditions for Clang compilers. Fix for HDFFV-10961: Couple changes to the tests' usage output files for h5clear. Fix for HDFFV-10961: add description to usage for --increment option. Add c++ to --enable-sanitize-checks option. Remove duplicate entries in MANIFEST. Make changes to CMake CompilerFlags.cmake files so extra flags are loaded for non-GNU compilers. Fix MANIFEST 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. Remember the info for the last ID looked up for a given ID type. Eliminate allocating file & memory offset & length arrays when performing I/O on a single element. 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. Remove redundant metadata cache tagging from some low-level internal chunk functions. The metadata cache tagging has already been done by routines further up the call stack. Clean up code to get clang version in config/linux-gnulibc1 Minor normalizations with HDF5 1.10. 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. ...
| * | | | | Fix HDFFV-11053Binh-Minh Ribler2020-05-261-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: A superblock pointer was set to a temporary structure, as a kluge, and meant to be reset back to NULL after the processing was completed. However, in the case of failure before the completion, this setting caused the superblock pointer to be unpinned twice in the error recovery process. As a result, that generated a segfault in h5clear. The fix resets the superblock pointer to NULL after H5F__super_ext_remove_msg fails so that h5clear can fail properly. Note: After the fix, when built in debug mode, there will be an assertion failure with the user's file, which appeared to be corrupted: H5MM_final_sanity_check: Assertion `0 == H5MM_curr_alloc_bytes_s' failed. This did not happen on a good file or on the corrupted file with the library built in production mode. The un-freed memory were allocated during error recovery. Platforms tested: Linux/64 (jelly)
* | | | | | Merge pull request #2667 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-06-301-6/+2
|\ \ \ \ \ \ | |_|/ / / / |/| | | | | | | | | | | | | | | | | * commit '32c483cb86031962a09ecdb49dcb331d28dddee9': Copy lib files for junit.sh to temporary subdirectory of <build directory>/java/test instead of to the prefix/lib directory. Fix for HDFFV-11063.
| * | | | | Copy lib files for junit.sh to temporary subdirectory of <buildLarry Knox2020-06-271-6/+2
|/ / / / / | | | | | | | | | | | | | | | | | | | | directory>/java/test instead of to the prefix/lib directory. Fix for HDFFV-11063.
* | | | | Merge pull request #2665 in HDFFV/hdf5 from ↵Jake Smith2020-06-263-54/+134
|\ \ \ \ \ | |_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/splitter_file_bytes_check to develop * commit 'e1215177b6b87887233a90992a0264f11d78b88c': * Fix intermittent error with Splitter VFD. Mismatch in time of test file creation was creating false negatives.
| * | | | * Fix intermittent error with Splitter VFD.Jacob Smith2020-06-253-54/+134
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Mismatch in time of test file creation was creating false negatives. Add file-duplication routine: `h5_duplicate_file_by_bytes()`. * Change library calls in `h5test.c:h5_compare_file_bytes()` to their HD-prefixed equivalents.
* | | | | Merge pull request #2654 in HDFFV/hdf5 from bmr_HDFFV-10591 to developBinh-Minh Ribler2020-06-224-12/+41
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fixed HDFFV-10591 * commit '7d58d115079d286a566207c529e59bbccc952b03': Added note for HDFFV-10591. Fix HDFFV-10591
| * | | | | Added note for HDFFV-10591.Binh-Minh Ribler2020-06-191-0/+12
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| * | | | | Fix HDFFV-10591Binh-Minh Ribler2020-06-193-12/+29
| |/ / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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) SunOS 5.11 (emu)
* | | | | Merge pull request #2648 in HDFFV/hdf5 from opt_h5open_overhead to developQuincey Koziol2020-06-182-5/+32
|\ \ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | * commit '49fad72f3e003e1e2d7d72edd9b7ec47c802d9f1': Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc.
| * | | | Reduce overhead for H5open, which is involved in the public symbols like ↵Quincey Koziol2020-06-162-5/+32
|/ / / / | | | | | | | | | | | | H5T_NATIVE_INT, etc.
* | | | Merge pull request #2610 in HDFFV/hdf5 from ↵David Young2020-06-166-12/+12
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DYOUNG/werror:hdffv-11060-examples-destdir to develop * commit '4cebd8aa6c965fe2e5dde6dbff36b2be3ca58bf1': Make examples installation respect DESTDIR. Fixes HDFFV-11060.
| * | | | Make examples installation respect DESTDIR. FixesDavid Young2020-05-266-12/+12
| |/ / / | | | | | | | | | | | | HDFFV-11060.
* | | | Merge pull request #2615 in HDFFV/hdf5 from ↵Jake Smith2020-06-152-1/+5
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/splitter_valgrind_patch to develop * commit '6462c67b6578e48c1ef6d847be59c0b5e3598a50': Patch a few holes in the Splitter VFD implementation.
| * | | | Patch a few holes in the Splitter VFD implementation.Jacob Smith2020-05-292-1/+5
| | | | | | | | | | | | | | | | | | | | | | | | | * Missing logfile close on driver-open failure. * Initialize empty string in test/vfd (logfile path in W/O compat check).
* | | | | Merge pull request #2646 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-06-122-28/+6
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '998c6470d78e14228695419c3b514c35ecf3d69e': Remove unnecessary version conditions for Clang compilers.
| * | | | | Remove unnecessary version conditions for Clang compilers.Larry Knox2020-06-122-28/+6
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* | | | | Merge pull request #2643 in HDFFV/hdf5 from ↵Vailin Choi2020-06-113-6/+23
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-10961-h5clear-usage-statement-give to develop * commit '01b632c69ca1c97c2b0e1aaeeab1dd2362b580a6': Fix for HDFFV-10961: Couple changes to the tests' usage output files for h5clear. Fix for HDFFV-10961: add description to usage for --increment option.
| * | | | | Fix for HDFFV-10961:vchoi2020-06-112-4/+16
| | | | | | | | | | | | | | | | | | | | | | | | Couple changes to the tests' usage output files for h5clear.
| * | | | | Fix for HDFFV-10961: add description to usage for --increment option.vchoi2020-06-111-2/+7
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* | | | | Merge pull request #2636 in HDFFV/hdf5 from ↵Larry Knox2020-06-111-4/+126
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~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.
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