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* Merge pull request #2693 in HDFFV/hdf5 from ↵Vailin Choi2020-07-171-0/+4
|\ | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-11080-heap-use-after-free-by-the-call to develop * commit '3023b34272cc6ada84aebfa7441a6a55afa3621c': Update MANIFEST. Add new test to Cmake. Fix for jira issue 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
| * Fix for jira issue HDFFV-11080:vchoi2020-07-141-0/+4
| | | | | | | | | | (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
* | Minor normalization with 1.10Dana Robinson2020-07-174-31/+30
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* | H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-163-25/+66
| | | | | | | | Update trefer.c with vlen test case
* | Fallback to older time functions in new timer code.Dana Robinson2020-07-141-23/+8
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* 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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* | Small changes discovered with mingw and windows defines movedAllen Byrne2020-07-025-223/+221
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* | Merge pull request #2668 in HDFFV/hdf5 from monotonic_timer to developQuincey Koziol2020-07-0210-568/+1064
|\ \ | |/ |/| | | | | | | | | | | | | | | | | | | | | * 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.
| * Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-301-0/+6
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| * | Clean up warningsQuincey Koziol2020-06-282-3/+7
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| * | va_arg -> HDva_argQuincey Koziol2020-06-271-1/+1
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| * | Refactor code to remove remaining checks for H5_HAVE_GETTIMEOFDAY scattered ↵Quincey Koziol2020-06-272-32/+41
| | | | | | | | | | | | around in various places. Also clean up iopipe.c.
| * | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-26427-53399/+111938
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| * | | Correct mistake in H5_now_usec calculation for clock_gettime.Quincey Koziol2017-09-241-1/+1
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| * | | Update H5_now_usec to prefer using clock_gettime.Quincey Koziol2017-09-241-1/+8
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| * | | Changes to make timers within the library monotonic.Quincey Koziol2017-09-0310-513/+991
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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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* | | Changed wording in comment.Binh-Minh Ribler2020-06-301-2/+2
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* | | - added comment to explain a klugeBinh-Minh Ribler2020-06-291-0/+2
| | | | | | | | | | | | - added the associated entry to release notes
* | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Binh-Minh Ribler2020-06-2938-608/+664
|\ \ \ | |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. ...
| * | Merge pull request #2654 in HDFFV/hdf5 from bmr_HDFFV-10591 to developBinh-Minh Ribler2020-06-221-0/+5
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fixed HDFFV-10591 * commit '7d58d115079d286a566207c529e59bbccc952b03': Added note for HDFFV-10591. Fix HDFFV-10591
| | * | Fix HDFFV-10591Binh-Minh Ribler2020-06-191-0/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
| * | | 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 #2615 in HDFFV/hdf5 from ↵Jake Smith2020-06-151-0/+3
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | ~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 Smith2020-05-291-0/+3
| | | | | | | | | | | | | | | | | | | | * Missing logfile close on driver-open failure. * Initialize empty string in test/vfd (logfile path in W/O compat check).
| * | | Merge pull request #2635 in HDFFV/hdf5 from cache_last_id_info to developQuincey Koziol2020-06-101-2/+22
| |\ \ \ | | | | | | | | | | | | | | | | | | | | * commit '0ef32f07fb9e8fb6063f3318425506047454d6f4': Remember the info for the last ID looked up for a given ID type.
| | * | | Remember the info for the last ID looked up for a given ID type.Quincey Koziol2020-06-091-2/+22
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| * | | | Merge pull request #2634 in HDFFV/hdf5 from opt_single_selection_io to developQuincey Koziol2020-06-101-27/+32
| |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'a8a4e9f27b67ae2e22970e42859225adcc2e5cbb': Eliminate allocating file & memory offset & length arrays when performing I/O on a single element.
| | * | | | Eliminate allocating file & memory offset & length arrays when performing ↵Quincey Koziol2020-06-091-27/+32
| | |/ / / | | | | | | | | | | | | | | | I/O on a single element.
| * | | | Remove redundant metadata cache tagging from some low-level internal chunk ↵Quincey Koziol2020-06-091-4/+4
| |/ / / | | | | | | | | | | | | functions. The metadata cache tagging has already been done by routines further up the call stack.
| * | | Merge pull request #2630 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-06-086-46/+38
| |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '87695c999ad7ea348ee6dc03b46b0bd345f7d7df': Minor normalizations with HDF5 1.10.
| | * | | Minor normalizations with HDF5 1.10.Dana Robinson2020-06-076-46/+38
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| * | | | Detect when there's the same-shaped selection of a single block of elements onQuincey Koziol2020-06-051-0/+9
| |/ / / | | | | | | | | | | | | | | | | | | | | both selections, but with different selection types (i.e. one selection defined as an 'all' type and the other as a hyperslab or point type), without falling into the generic selection iteration case.
| * | | Normalization of H5T.c with 1.10.Dana Robinson2020-06-041-24/+24
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| * | | Normalization of H5D.c with 1.10.Dana Robinson2020-06-041-11/+10
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| * | | Normalizations with 1.10 branch.Dana Robinson2020-06-023-16/+19
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| * | | Normalization with hdf5_1_10Dana Robinson2020-06-0124-473/+466
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* | | 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)
* | Replaced a few calls to HDmemcpy with H5MM_memcpy, which does overlapDana Robinson2020-05-152-8/+8
| | | | | | | | checking.
* | Removed HDgets macros since gets was deprecated in C99 and removedDana Robinson2020-05-101-2/+5
| | | | | | | | in C11 (gets() is not used in our repo).
* | Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-012-3/+5
| | | | | | | | the dataset is extended.
* | Merge pull request #2542 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:warning_fixes ↵Dana Robinson2020-04-271-15/+17
|\ \ | | | | | | | | | | | | | | | | | | to develop * commit 'c3367e6634d4dee88ff855da08e312f6685c23af': Moved -Woverlength-strings to the developer flags.
| * | Moved -Woverlength-strings to the developer flags.Dana Robinson2020-04-261-15/+17
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* | | Fix `src/H5FDdirect.c:1346:5: error: ISO C90 forbids mixed declarationsDavid Young2020-04-241-4/+1
|/ / | | | | | | and code [-Werror=declaration-after-statement]`.
* | Merge pull request #2525 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-04-231-1/+1
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '43424a1392b662a29542bb70014c253162ccfe48': Add missing ')'. Add C++ warnings treated as error for autotools builds. Move macro ADD_H5_CFLAGS to cmake_ext_mod/HDFMacros.cmake and remove duplicate versions. Address PR suggestions and add overlooked GCC compiler version flags. 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.
| * | Add C++ warnings treated as error for autotools builds.Larry Knox2020-04-231-1/+1
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* | | Trim trailing whitespaceQuincey Koziol2020-04-20147-2473/+2473
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* | Fixed some minor cmp callback bugs and cleaned warnings.Dana Robinson2020-04-171-3/+5
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