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* Fix shutdown errors when using the HDF5_VOL_CONNECTOR environmentDana Robinson2020-03-184-2/+28
| | | | | variable to set a dynamically loaded plugin as the default VOL connector. Fixes HDFFV-11057
* Merge branch 'develop' into develop_minorDana Robinson2020-03-185-5/+23
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| * Merge pull request #2451 in HDFFV/hdf5 from ↵Vailin Choi2020-03-165-5/+23
| |\ | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/develop_seg_fault_sel_compat to develop * commit '81b1ed4e1724b8a6a731ab2b8fb03234a8b49d15': Fix issues when deserializing point/all/none selection with version beyond the library's supported version: (1) Verify the decoded version before proceeding further with deserialization (2) Close the dataspace if errors occurred after opening the dataspace
| | * Fix issues when deserializing point/all/none selection with version beyond ↵Vailin Choi2020-03-135-5/+23
| | | | | | | | | | | | | | | | | | | | | the library's supported version: (1) Verify the decoded version before proceeding further with deserialization (2) Close the dataspace if errors occurred after opening the dataspace
| | * Merge pull request #26 in ~VCHOI/my_third_fork from develop to ↵Vailin Choi2020-03-11143-975/+1423
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | bugfix/develop_seg_fault_sel_compat * commit '9abbdeaa66c70a00b6a7bedee9c76d2493a8e947': (31 commits) Remove system command from valgrind reports Whitespace Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG). Add semicolons to more PASSED() invocations. So that I can use PASSED(); anywhere a statement can go, #define PASSED() with a do-while wrapper. revert type cast Switch the 'get offset' operation from a dataset 'get' callback to a [native] dataset 'optional' operation. Modfy expression to match mpicc build with Intel as intel compiler, not gcc. Complete the comment on thread_main(), explaining why the barrier is used. Fixed issue building HDF5 with NAG Fortran 7.0. 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. Add java version and reference libsettings 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. Update examples and fix old version references. Move MODEL check to before usage in CTestScript.cmake. Copy generated files instead creating twice Fix standalone link Fix Fortran macro use and jni comment ...
* | | | Very minor comment change in H5VLconnector.h.Dana Robinson2020-03-121-1/+1
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* | | Merge pull request #2378 in HDFFV/hdf5 from ↵David Young2020-03-121-5/+5
|\ \ \ | |_|/ |/| | | | | | | | | | | | | | ~DYOUNG/werror:dont-crash-on-close to develop * commit '093c2c7e69bc4a40e9d49eece1d6fdcf54e8ecb0': Avoid a crash, don't check if we're flushing when the file is closing: there's no need to check if the metadata cache is flushing if we already know the file is closing, because the condition we rely on is "closing OR flushing." Further, the cache may have already gone away, so sometimes calling into the cache to see if it's flushing will crash the program.
| * | Avoid a crash, don't check if we're flushing when the file is closing:David Young2020-02-131-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | there's no need to check if the metadata cache is flushing if we already know the file is closing, because the condition we rely on is "closing OR flushing." Further, the cache may have already gone away, so sometimes calling into the cache to see if it's flushing will crash the program.
* | | Merge pull request #2351 in HDFFV/hdf5 from ↵David Young2020-03-052-6/+2
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | ~DYOUNG/werror:b-bye-HDpthread_self to develop * commit '224cb4a03406ed72e02d026efeab47fdf7f6b33b': Use a naked pthread_self() call in the HDF5 thread wrappers.
| * | | Use a naked pthread_self() call in the HDF5 thread wrappers.David Young2020-02-062-6/+2
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* | | | Merge pull request #2424 in HDFFV/hdf5 from ~DYOUNG/hdf5:passed-do-while to ↵David Young2020-03-0519-254/+253
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit 'b53eb6fb29e556c482ce20fa7a21485c99beea74': Add semicolons to more PASSED() invocations. So that I can use PASSED(); anywhere a statement can go, #define PASSED() with a do-while wrapper.
| * | | | Add semicolons to more PASSED() invocations.David Young2020-02-284-5/+5
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| * | | | So that I can use PASSED(); anywhere a statement can go, #define PASSED() withDavid Young2020-02-2815-249/+248
| | | | | | | | | | | | | | | | | | | | a do-while wrapper.
* | | | | Merge pull request #2434 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-03-042-16/+16
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '24298a031f0b7f6a04364cfbfbdd9c8b6cc1a038': Remove system command from valgrind reports Whitespace
| * | | | | Remove system command from valgrind reportsAllen Byrne2020-03-021-2/+2
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| * | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-03-012-3/+3
| |\ \ \ \ \ | |/ / / / / |/| | | | | | | | | | | | | | | | | * commit 'a01ac97ba509e51905b816e8a29b5d0b2bc8be87': Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).
* | | | | | Merge pull request #2427 in HDFFV/hdf5 from ~JAKE.SMITH/hdf5:develop to developJake Smith2020-03-012-3/+3
|\ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '2d9a81878d05732725f96d7d9b20ada8dfd2a146': Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).
| * | | | | | Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).Jacob Smith2020-02-282-3/+3
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| | * | | | WhitespaceAllen Byrne2020-02-291-14/+14
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* | | | | Merge pull request #2431 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/type_cast to ↵Kimmy Mu2020-02-291-2/+2
|\ \ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | | | | | | | | | | | develop * commit 'b5cf422799797cf0b573cc9992f866381bd63054': revert type cast
| * | | | revert type castkmu2020-02-281-2/+2
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* | | | | Merge pull request #2419 in HDFFV/hdf5 from revise_get_offset to developQuincey Koziol2020-02-285-37/+21
|\ \ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | * commit '38af6ee3d59a8e836f4c62dd533ddabd914c7abb': Switch the 'get offset' operation from a dataset 'get' callback to a [native] dataset 'optional' operation.
| * | | | Switch the 'get offset' operation from a dataset 'get' callback to a [native]Quincey Koziol2020-02-285-37/+21
|/ / / / | | | | | | | | | | | | dataset 'optional' operation.
* | | | Merge pull request #2411 in HDFFV/hdf5 from ~DYOUNG/werror:darwin-barriers ↵Larry Knox2020-02-281-1/+139
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '803d805c74466a9d736455930b17de2d9f5cb02d': 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.
| * | | | Complete the comment on thread_main(), explaining why the barrier is used.David Young2020-02-271-1/+9
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| * | | | The first implementation seemed to allow for the possibility that a threadDavid Young2020-02-271-1/+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 Young2020-02-271-1/+1
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| * | | | s/exit_failure/EXIT_FAILURE/gDavid Young2020-02-271-2/+2
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| * | | | Implement pthread_barrier(3) for Darwin using a counter, condition variable,David Young2020-02-271-0/+123
| | | | | | | | | | | | | | | | | | | | and mutex. Untested.
* | | | | Merge pull request #2415 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-02-282-2/+2
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '811988f82c182012704942d333ee7800f4a78349': Modfy expression to match mpicc build with Intel as intel compiler, not gcc.
| * | | | | Modfy expression to match mpicc build with Intel as intel compiler, notLarry Knox2020-02-272-2/+2
|/ / / / / | | | | | | | | | | | | | | | gcc.
* | | | | Merge pull request #2414 in HDFFV/hdf5 from ~BRTNFLD/hdf5_msb:develop to developScot Breitenfeld2020-02-271-6/+19
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'dde7e73d9fe8cc3b849767790aa9b13ee2d600cd': Fixed issue building HDF5 with NAG Fortran 7.0.
| * | | | | Fixed issue building HDF5 with NAG Fortran 7.0.M. Scot Breitenfeld2020-02-271-6/+19
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Accounted for the additon of half precision floating-point with a KIND=16. HDFFV-11033
* | | | | | Merge pull request #2412 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-02-271-2/+3
|\ \ \ \ \ \ | |/ / / / / |/| | | | | | | | | | | | | | | | | * commit '6686cac564f5d0015a32b92e4478002069c973ee': Add java version and reference libsettings
| * | | | | Add java version and reference libsettingsAllen Byrne2020-02-271-2/+3
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* | | | | Merge pull request #2409 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-02-2716-266/+257
|\ \ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | | | | | | * commit '13f5b3aee20d1d65f56dc08f088e0f218da5cf37': Update examples and fix old version references. Move MODEL check to before usage in CTestScript.cmake.
| * | | | Update examples and fix old version references.Allen Byrne2020-02-2615-259/+249
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| * | | | Move MODEL check to before usage in CTestScript.cmake.Allen Byrne2020-02-262-7/+8
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* | | | Merge pull request #2405 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-02-255-15/+40
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | * commit '2af8a87af0d7a1589a4df22d16b2d2513876e7a9': Copy generated files instead creating twice Fix standalone link
| * | | | Copy generated files instead creating twiceAllen Byrne2020-02-251-8/+32
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| * | | | Fix standalone linkAllen Byrne2020-02-254-7/+8
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* | | | Merge pull request #2398 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-02-254-16/+12
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | * commit '04e67af8f968b2c6f50cb42990d3dfa79aa353d9': Fix Fortran macro use and jni comment
| * | | | Fix Fortran macro use and jni commentAllen Byrne2020-02-254-16/+12
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* | | | Merge pull request #2394 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-02-246-22/+172
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'cf58730177d60fd7311582a29539d87f10a7d88e': Update Windows platforms HDFFV-11036 add release note HDFFV-11036 add file compare test process Correct usage of add_compile_definitions
| * | | | Update Windows platformsAllen Byrne2020-02-241-5/+1
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| * | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-02-241-0/+2
| |\ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | * commit 'd24afb233383aa6c945fad430eb1b66edc4d6c63': Add missing MANIFEST entry, ./doc/code-conventions.md .
* | | | | Merge pull request #2385 in HDFFV/hdf5 from manifest-repair to developDavid Young2020-02-241-0/+2
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '921278c604b3129c1ff5066f0a2b94abcb3aa8f7': Add missing MANIFEST entry, ./doc/code-conventions.md .
| * | | | | Add missing MANIFEST entry, ./doc/code-conventions.md .David Young2020-02-201-0/+2
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| | * | | | HDFFV-11036 add release noteAllen Byrne2020-02-241-1/+8
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| | * | | | HDFFV-11036 add file compare test processAllen Byrne2020-02-244-13/+162
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