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* Squashed commit of the following:Larry Knox2020-06-2114-65/+638
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* Merge pull request #2652 in HDFFV/hdf5 from hdf5_1_12_opt_h5open_overhead to ↵Quincey Koziol2020-06-193-5/+37
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '0a091d879133ff5f54199aaeeeb274a5b2883a77': Add info to release notes. Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc.
| * Add info to release notes.Quincey Koziol2020-06-181-0/+5
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| * Reduce overhead for H5open, which is involved in the public symbols like ↵Quincey Koziol2020-06-182-5/+32
|/ | | | H5T_NATIVE_INT, etc.
* Merge pull request #2644 in HDFFV/hdf5 from ↵Vailin Choi2020-06-153-6/+23
|\ | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/112_HDFFV-10961-h5clear-usage-statement-give to hdf5_1_12 * commit 'c2af605d9582a9c0df71c4771d0ec208511ccc3e': Merge pull request #2643 in HDFFV/hdf5 from ~VCHOI/my_third_fork:bugfix/HDFFV-10961-h5clear-usage-statement-give to develop
| * 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.
* Merge pull request #2642 in HDFFV/hdf5 from hdf5_1_12_cache_last_id_info to ↵Quincey Koziol2020-06-112-2/+27
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '38886e95b2f8e6bf84db51ea4f7569295268cff1': Update release notes for last ID caching. Remember the info for the last ID looked up for a given ID type.
| * Update release notes for last ID caching.Quincey Koziol2020-06-111-0/+5
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| * Merge remote-tracking branch 'origin/hdf5_1_12' into ↵Quincey Koziol2020-06-112-28/+39
| |\ | |/ |/| | | hdf5_1_12_cache_last_id_info
* | Merge pull request #2640 in HDFFV/hdf5 from ↵Quincey Koziol2020-06-112-28/+39
|\ \ | | | | | | | | | | | | | | | | | | | | | hdf5_1_12_opt_single_selection_io to hdf5_1_12 * commit 'df31370d45d53f2e8ba10e74791a91e7efdb818f': Add info to release notes about improvement for single element I/O. Eliminate allocating file & memory offset & length arrays when performing I/O on a single element.
| * | Add info to release notes about improvement for single element I/O.Quincey Koziol2020-06-111-1/+7
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| * | Merge remote-tracking branch 'origin/hdf5_1_12' into ↵Quincey Koziol2020-06-112-4/+9
| |\ \ | |/ / |/| | | | | hdf5_1_12_opt_single_selection_io
| * | Eliminate allocating file & memory offset & length arrays when performing ↵Quincey Koziol2020-06-101-27/+32
| | | | | | | | | | | | I/O on a single element.
| | * Remember the info for the last ID looked up for a given ID type.Quincey Koziol2020-06-111-2/+22
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* | Merge pull request #2638 in HDFFV/hdf5 from ↵Quincey Koziol2020-06-112-4/+9
|\ \ | |/ |/| | | | | | | | | | | hdf5_1_12_remove_redundant_chunk_tags to hdf5_1_12 * commit '8e52a143f7dcc7c4c452df32359cae753db8793d': Add info to release notes about improvement to metdata cache tagging for chunked datasets. 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.
| * Add info to release notes about improvement to metdata cache tagging for ↵Quincey Koziol2020-06-101-0/+5
| | | | | | | | chunked datasets.
| * Remove redundant metadata cache tagging from some low-level internal chunk ↵Quincey Koziol2020-06-101-4/+4
|/ | | | functions. The metadata cache tagging has already been done by routines further up the call stack.
* Merge pull request #2628 in HDFFV/hdf5 from hdf5_1_12_tiny_shape_same_opt to ↵Quincey Koziol2020-06-083-7/+21
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit 'b0f921c53fe4aa60bc0ed0fa10942da11ac4a3cd': Add info about optimization to release notes Detect when there's the same-shaped selection of a single block of elements on 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.
| * Add info about optimization to release notesQuincey Koziol2020-06-071-0/+5
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| * Detect when there's the same-shaped selection of a single block of elements onQuincey Koziol2020-06-072-7/+16
|/ | | | | | 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.
* Merge pull request #2627 in HDFFV/hdf5 from hdf5_1_12_h5do_opt to hdf5_1_12Quincey Koziol2020-06-062-14/+9
|\ | | | | | | | | | | * commit '20a8edb705773e6c44d67b952a3dec0a5e0d2c09': Add note about H5DOappend() optimization. Eliminate unneccesary creation of DXPL
| * Add note about H5DOappend() optimization.Quincey Koziol2020-06-051-0/+6
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| * Eliminate unneccesary creation of DXPLQuincey Koziol2020-06-051-14/+3
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* Merge pull request #2600 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to ↵Larry Knox2020-05-201-19/+1
|\ | | | | | | | | | | | | hdf5_1_12 * commit '06dc9c40e7cc0e094f245ceee996e72c0e9ff5b2': Update MANIFEST for removal of older warnings files.
| * Update MANIFEST for removal of older warnings files.Larry Knox2020-05-201-19/+1
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* Merge pull request #2593 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_12 to ↵Larry Knox2020-05-1929-337/+99
|\ | | | | | | | | | | | | hdf5_1_12 * commit '1a9316668131ab84d99a557789bdef9763de5ed2': 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.
| * Revise gnu-*flags and cmake/HDF*CompilerFlags.cmake files to add warningLarry Knox2020-05-1929-337/+99
|/ | | | | | | 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.
* Merge pull request #2583 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-05-162-8/+12
|\ | | | | | | | | | | | | | | hdf5_1_12 * commit '84c3e50cc7f936fe4b892c3c0f7377d6a075422f': Correct mingw paths Correct mingw path
| * Correct mingw pathsAllen Byrne2020-05-152-7/+11
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| * Correct mingw pathAllen Byrne2020-05-151-2/+2
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* Merge pull request #2572 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_12 to ↵Allen Byrne2020-05-13364-5008/+5009
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | hdf5_1_12 * commit '3e628120ceee554636eda775269b4f0ca914c140': Whitespace changes Whitespace updates Whitespace cleanup Whitespace cleanup Whitespace cleanup Whitespace cleanup Whitespace cleanup Whitespace cleanup Whitespace cleanup Whitespace cleanup Whitespace cleanup compared to develop Whitespace cleanup compared to develop
| * Whitespace changesAllen Byrne2020-05-1313-72/+72
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| * Whitespace updatesAllen Byrne2020-05-1366-547/+547
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| * Whitespace cleanupAllen Byrne2020-05-13104-1240/+1242
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| * Whitespace cleanupAllen Byrne2020-05-1348-2020/+2022
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| * Whitespace cleanupAllen Byrne2020-05-1219-188/+187
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| * Whitespace cleanupAllen Byrne2020-05-122-16/+16
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| * Whitespace cleanupAllen Byrne2020-05-128-8/+8
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| * Whitespace cleanupAllen Byrne2020-05-1224-314/+312
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| * Whitespace cleanupAllen Byrne2020-05-1224-191/+191
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| * Whitespace cleanupAllen Byrne2020-05-1221-271/+271
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| * Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_12)Allen Byrne2020-05-125-71/+273
| |\ | |/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'e399be1e9156840aa0664323dfc00a93ac43575c': Complete the comment on thread_main(), explaining why the barrier is used. The first implementation seemed to allow for the possibility that a thread could block at the barrier, wake and exit the barrier, re-acquire the barrier lock and increase `nentered` before the other blocked threads woke and checked `nentered % count == 0`. Then the other blocked threads would check `nentered % count == 0` and, finding it false, go back to sleep in the barrier. This new implementation waits for a looser condition to obtain so that threads don't go back to sleep in the barrier. Test the right condition for the EBUSY return in pthread_barrier_destroy(). s/exit_failure/EXIT_FAILURE/g Implement pthread_barrier(3) for Darwin using a counter, condition variable, and mutex. Untested. Use HD prefix. Provide local copies of err(3)- and errx(3)-alike functions for Visual Studio compatibility. Oops, the test has to return success in the unimplemented case. src/H5Eint.c: #include H5TSprivate.h for H5TS_thread_id() definitions. Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble. Follow HDF5 conventions. Make sure that H5TS_thread_id() is available as either a function or a macro in all configurations. Use a naked pthread_self() call in the HDF5 thread wrappers. If H5_HAVE_THREADSAFE is not #defined, define nothing but a stub implementation of H5TS_thread_id().
* | Merge pull request #2575 in HDFFV/hdf5 from ↵Larry Knox2020-05-125-71/+273
|\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DYOUNG/werror:fix-thread_id-1_12 to hdf5_1_12 * commit 'f0485413e02ebf1117e5b1725f32534e7e26b622': Complete the comment on thread_main(), explaining why the barrier is used. The first implementation seemed to allow for the possibility that a thread could block at the barrier, wake and exit the barrier, re-acquire the barrier lock and increase `nentered` before the other blocked threads woke and checked `nentered % count == 0`. Then the other blocked threads would check `nentered % count == 0` and, finding it false, go back to sleep in the barrier. This new implementation waits for a looser condition to obtain so that threads don't go back to sleep in the barrier. Test the right condition for the EBUSY return in pthread_barrier_destroy(). s/exit_failure/EXIT_FAILURE/g Implement pthread_barrier(3) for Darwin using a counter, condition variable, and mutex. Untested. Use HD prefix. Provide local copies of err(3)- and errx(3)-alike functions for Visual Studio compatibility. Oops, the test has to return success in the unimplemented case. src/H5Eint.c: #include H5TSprivate.h for H5TS_thread_id() definitions. Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble. Follow HDF5 conventions. Make sure that H5TS_thread_id() is available as either a function or a macro in all configurations. Use a naked pthread_self() call in the HDF5 thread wrappers. If H5_HAVE_THREADSAFE is not #defined, define nothing but a stub implementation of H5TS_thread_id().
| * | Complete the comment on thread_main(), explaining why the barrier is used.David Young2020-05-111-1/+9
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| * | The first implementation seemed to allow for the possibility that a threadDavid Young2020-05-111-1/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | could block at the barrier, wake and exit the barrier, re-acquire the barrier lock and increase `nentered` before the other blocked threads woke and checked `nentered % count == 0`. Then the other blocked threads would check `nentered % count == 0` and, finding it false, go back to sleep in the barrier. This new implementation waits for a looser condition to obtain so that threads don't go back to sleep in the barrier.
| * | Test the right condition for the EBUSY return in pthread_barrier_destroy().David Young2020-05-111-1/+1
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| * | s/exit_failure/EXIT_FAILURE/gDavid Young2020-05-111-2/+2
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| * | Implement pthread_barrier(3) for Darwin using a counter, condition variable,David Young2020-05-111-0/+123
| | | | | | | | | | | | and mutex. Untested.
| * | Use HD prefix.David Young2020-05-111-13/+13
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| * | Provide local copies of err(3)- and errx(3)-alike functionsDavid Young2020-05-111-7/+37
| | | | | | | | | | | | for Visual Studio compatibility.
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