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* Minor normalization with 1.10Dana Robinson2020-07-174-31/+30
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* Merge pull request #2694 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:fix_vlen_ref to ↵Jerome Soumagne2020-07-164-25/+336
|\ | | | | | | | | | | | | develop * commit 'aa9d2bd9bcce7a1a53c9d9cf519df5401041bb74': H5R: fix type conversion of references within vlen type
| * H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-164-25/+336
|/ | | | Update trefer.c with vlen test case
* Merge pull request #2692 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-07-142-29/+8
|\ | | | | | | | | | | | | | | to develop * commit 'b8013380792a3503003f0a2bd60d7541656b03c7': Removed POSIX #defines from configure on Solaris. Fallback to older time functions in new timer code.
| * Removed POSIX #defines from configure on Solaris.Dana Robinson2020-07-141-6/+0
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| * Fallback to older time functions in new timer code.Dana Robinson2020-07-141-23/+8
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* Merge pull request #2686 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-111-1/+4
|\ | | | | | | | | * commit '800f93f7c994f88dfa716746153ded4b1e690e3a': Remove path to szip header file from AM_CPPFLAGS when configure check of libsz fails. Fix for HDFFV-10830.
| * Merge branch 'develop' of ↵Larry Knox2020-07-1023-1079/+1078
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| * | 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.
* | | Merge pull request #2684 in HDFFV/hdf5 from ↵Allen Byrne2020-07-116-4/+90
|\ \ \ | |_|/ |/| | | | | | | | | | | | | | ~BYRN/hdf5_adb:feature/HDFFV-11116-trilabs-mod-location to develop * commit '07a52ecb2ffa1d8d32f06db23470833899db3deb': HDFFV-11116 Add option for install location of Fortran MOD files
| * | HDFFV-11116 Add option for install location of Fortran MOD filesAllen Byrne2020-07-096-4/+90
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| * | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-083-6/+24
| |\ \ | | | | | | | | | | | | | | | | | | | | * commit '188c43b8ee78d830c22f30fb9adb802e46722fcd': Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib for junit tests on Macs. Fixes Autotools builds on Solaris after monotonic timer changes
| * \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-032-2/+2
| |\ \ \ | | | | | | | | | | | | | | | | | | | | * commit 'd52b27ad1d8142945a92310b79ab79171e76a3c3': Address CMake and deprecated API build failures from monotonic timer patch.
| * \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-031-1/+1
| |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '7443e5d53d1c6f15e095de7c44bcc3a5a46d9cf7': Add missing '"'.
| * \ \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-023-1/+20
| |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '4c2071bfd3270dc3a688914b4a058147b94b7023': 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
* | \ \ \ \ \ Merge pull request #2683 in HDFFV/hdf5 from ↵Dana Robinson2020-07-0921-1074/+1055
|\ \ \ \ \ \ \ | |_|_|_|_|/ / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:develop_normalization to develop * commit '127d1cfdf06e9c1cd264595c496a063848358a0a': Minor changes from normalization with 1.10
| * | | | | | Minor changes from normalization with 1.10Dana Robinson2020-07-0921-1074/+1055
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* | | | | | | Merge pull request #2680 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-07-072-5/+23
|\ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit 'd9105b2fcf04f36ea348bf9726a49c05cacc0b78': Fixes Autotools builds on Solaris after monotonic timer changes
| * | | | | | | Fixes Autotools builds on Solaris after monotonic timer changesDana Robinson2020-07-072-5/+23
| | |_|_|_|/ / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | clock_gettime() wasn't being found, so some configure changes were needed to set an appropriate POSIX level and use a C99 compiler. This required several compiler flag changes. Autotools only
* | | | | | | Merge pull request #2677 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-071-1/+1
|\ \ \ \ \ \ \ | |/ / / / / / |/| | | | | / | | |_|_|_|/ | |/| | | | * commit 'da607fe4638c9cc08f717fbe65e799c1676c17ff': Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib for junit tests on Macs.
| * | | | | 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)
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