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* Merge pull request #2461 in HDFFV/hdf5 from ↵Vailin Choi2020-04-021-2/+12
|\ | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/dtype_close_on_error to develop * commit 'afdcac28b85d690eebc80ab568fa5266081baaaa': A fix in the cleaning up code for datatype when datatype initialization via H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
| * A fix in the cleaning up code for datatype when datatype initialization via ↵vchoi2020-03-231-2/+12
| | | | | | | | | | | | | | | | | | | | H5D__init_type() fails. This is triggered by the tests for revised references when the libver bounds setting does not allow version 4 datatype message to be created. The test failure is abort core dumped. This is due to the datatype initialization fails before the datatype ID is registered. The datatype cleanup code should provide for the above situation. The code to fix the problem is the same as what is done in H5D__open_oid().
* | Changed default dataset shared struct to initialize hid_t IDs toDana Robinson2020-04-021-0/+3
| | | | | | | | H5I_INVALID_HID.
* | Merge pull request #2363 in HDFFV/hdf5 from ~DYOUNG/werror:thread_id to developDavid Young2020-04-011-39/+77
|\ \ | | | | | | | | | | | | | | | * commit '63c95faf49559ea66e3066427961095b69fdb213': Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble. Follow HDF5 conventions.
| * | Remove tongue-in-cheek credit for Rusty Shackleford and Dale Alvin Gribble.David Young2020-02-101-21/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Delete the comment questioning whether pthread_mutex_lock is allowed in a key destructor, since pthread_key_create(3) provides the answer: There is no notion of a destructor-safe function. If an application does not call pthread_exit() from a signal handler, or if it blocks any signal whose handler may call pthread_exit() while calling async-unsafe functions, all functions may be safely called from destructors. Delete redundant comment.
| * | Follow HDF5 conventions.David Young2020-02-071-30/+89
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* | | TRILAB-192 restrict extensive warnings to librariesAllen Byrne2020-03-241-0/+6
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* | | Merge pull request #2445 in HDFFV/hdf5 from alloc_stats to developQuincey Koziol2020-03-238-212/+439
|\ \ \ | | | | | | | | | | | | | | | | | | | | * commit 'b51585a9110c4322c52f9dcdc60cd26c3ea44546': Revise API for H5get_alloc_stats() to take a struct instead of separate values. Add routines to query the library's free list sizes and allocation stats.
| * | | Revise API for H5get_alloc_stats() to take a struct instead of separate values.Quincey Koziol2020-03-204-61/+33
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| * | | Merge remote-tracking branch 'origin/develop' into alloc_statsQuincey Koziol2020-03-204-3/+17
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| * | | Merge remote-tracking branch 'origin/develop' into alloc_statsQuincey Koziol2020-03-185-5/+23
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| * \ \ \ Merge remote-tracking branch 'origin/develop' into alloc_statsQuincey Koziol2020-03-121-5/+5
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| * | | | | Add routines to query the library's free list sizes and allocation stats.Quincey Koziol2020-03-108-212/+467
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* | | | | | Merge pull request #2402 in HDFFV/hdf5 from ↵David Young2020-03-231-1/+1
|\ \ \ \ \ \ | |_|_|_|/ / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DYOUNG/werror:break-out-warnings to develop * commit '2f09d8f3c8a4a44932c1b8ffb0f6ea2219059a5c': Move the GNU warnings configuration under config/gnu-warnings/ and trim the filename prefixes. Update config/gnu-flags to suit. By default, demote warnings promoted to errors back to warnings. Incorporate the H5_ECFLAGS into the library CFLAGS. Now a bunch of errors will occur. Next commit will demote the warnings promoted to errors back to warnings again. Break out warnings into more files that autoconf and CMake can share. This change temporarily disables the warnings that were promoted to errors, but I will add those warnings back as warnings, not errors, in the next commit.
| * | | | | Incorporate the H5_ECFLAGS into the library CFLAGS. Now a bunch of errors willDavid Young2020-02-251-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | occur. Next commit will demote the warnings promoted to errors back to warnings again.
* | | | | | Fix shutdown errors when using the HDF5_VOL_CONNECTOR environmentDana Robinson2020-03-183-2/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* | | | | 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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* | | | Fix incorrect FUNC_LEAVE macro (should match FUNC_ENTER_*_TAG).Jacob Smith2020-02-282-3/+3
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* | | | Switch the 'get offset' operation from a dataset 'get' callback to a [native]Quincey Koziol2020-02-285-37/+21
| |_|/ |/| | | | | | | | dataset 'optional' operation.
* | | TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-211-1/+1
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* | | Merge developJordan Henderson2020-02-21208-6115/+17611
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| * | | Replace the old H5F_DECODE_LENGTH() implementation with one thatDavid Young2020-02-191-1/+1
| | | | | | | | | | | | | | | | initializes the variable it's loading on every path.
| * | | Merge pull request #2367 in HDFFV/hdf5 from ~DYOUNG/werror:unused to developDavid Young2020-02-198-23/+53
| |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '50aac126d7c4082c2aeb0f3a68cad26bd1cd9783': Start to document the function/parameter/variable attribute macros. Filter all of the new _USED / _UNUSED type modifiers. H5_HAVE_PARALLEL, _DEBUG_API, etc. Add attributes to some variables and parameters that are unused under some configurations.
| | * | | H5_HAVE_PARALLEL, _DEBUG_API, etc. Add attributes to some variables andDavid Young2020-02-108-23/+53
| | |/ / | | | | | | | | | | | | parameters that are unused under some configurations.
| * | | Merge pull request #2369 in HDFFV/hdf5 from ~DYOUNG/vs2010:develop to developDavid Young2020-02-173-13/+41
| |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Merged per discussion with Elena. * commit 'b4697f969295245840350e17d75d92a0fdd7e7a9': Use HD prefix. Delete unhelpful comment per Jordan's question. Make sure that H5TS_thread_id() is available as either a function or a macro in all configurations. Provide local copies of err(3)- and errx(3)-alike functions for Visual Studio compatibility. Provide C99/POSIX.1 format strings PRI[doux]{8,16,32,64,MAX,PTR} on systems that are missing <inttypes.h>.
| | * \ \ Make sure that H5TS_thread_id() is available as either a function or a macro inDavid Young2020-02-102-12/+2
| | |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | all configurations. (Merge remote-tracking branch 'origin/thread_id_everywhere' into vs2010-develop)
| | | * | | Delete unhelpful comment per Jordan's question.David Young2020-02-101-3/+0
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| | | * | | Make sure that H5TS_thread_id() is available as either a function or a macro inDavid Young2020-02-072-12/+5
| | | |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | all configurations. Previously it was neither declared nor defined in --disable-threadsafety builds. The compiler's warning got lost in the noise---I first saw the issue because my -Werror branch stopped compiling cold---and the tests still linked and ran.
| | * | | Provide C99/POSIX.1 format strings PRI[doux]{8,16,32,64,MAX,PTR} on systemsDavid Young2020-02-071-1/+39
| | |/ / | | | | | | | | | | | | that are missing <inttypes.h>.
| * | | Merge pull request #2325 in HDFFV/hdf5 from ~DYOUNG/werror:h5t_copy to developDavid Young2020-02-1715-194/+480
| |\ \ \ | | |_|/ | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Merged per discussion with Elena. * commit '3f903a441ad84001ea66589728bd8b036b6fdfca': Take out the temporary performance tests. Make calls through a function pointer. Use the same number of arguments, always. Increase iterations, provide a baseline for no-op, simplify the overhead case a bit. Temporarily add some code that measures the time to run the simplest possible H5T__copy_all()-like routine 10 million times and then measures the version with FUNC_ENTER_STATIC/_LEAVE_NOAPI and a HGOTO_ERROR() statement. H5T_copy() constification plus Quincey's contributions.
| | * | H5T_copy() constification plus Quincey's contributions.David Young2020-01-2915-194/+480
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| * | | Fix improper S3 signing key null check (HDFFV-11015).Jacob Smith2020-02-071-2/+2
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| * | If H5_HAVE_THREADSAFE is not #defined, define nothing but a stub implementationDavid Young2020-02-051-0/+7
| | | | | | | | | | | | of H5TS_thread_id().
| * | src/H5Eint.c: #include H5TSprivate.h for H5TS_thread_id() definitions.David Young2020-02-031-0/+1
| | | | | | | | | | | | test/thread_id.c: move threads_failure() inside #ifdefs.
| * | Change thread IDs to uint64_t from unsigned long, per Quincey's suggestion.David Young2020-02-034-13/+13
| | | | | | | | | | | | | | | Fix a typo in the H5TS_thread_init() comment and reword some ID properties.
| * | Replace pthread_self_ulong() with H5TS_thread_id(). The POSIX ThreadsDavid Young2020-02-036-21/+124
| | | | | | | | | | | | | | | implementation ought to be portable to any system that has POSIX Threads. On Windows, I use the same API call as before.
| * | Merge pull request #2329 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:H5MM_const to ↵Dana Robinson2020-01-3110-50/+67
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit '10301154215fb6a22590e80f7b5ed0005f3e1786': Minor refactoring to the VFD info free call. Updated the 'const memory free' changes based on PR feedback. Added a free wrapper that lets us free constant pointers without generating warnings.
| | * | Minor refactoring to the VFD info free call.Dana Robinson2020-01-311-10/+8
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| | * | Updated the 'const memory free' changes based on PR feedback.Dana Robinson2020-01-319-45/+27
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| | * | Added a free wrapper that lets us free constant pointers withoutDana Robinson2020-01-308-25/+62
| | | | | | | | | | | | | | | | | | | | | | | | | | | | generating warnings. Also, brought the const-ness of the VOL connector info in line with the VFD info (not visible externally).
| * | | VS2010 needs an underscoreAllen Byrne2020-01-301-0/+6
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| * | Merge pull request #2318 in HDFFV/hdf5 from ↵David Young2020-01-2915-127/+125
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | ~DYOUNG/werror:reduce-werror-diffs-1 to develop * commit 'fa1b2f6ef35c459c9f74ead885c119ae7f61c056': Reduce differences between my -Werror branch and `develop`:
| | * | Reduce differences between my -Werror branch and `develop`:David Young2020-01-2915-127/+125
| | |/ | | | | | | | | | | | | | | | | | | | | | Rename index -> idx, fileno -> fnumber, fileno -> fno to avoid GCC shadowed declaration warnings about index(3). Convert #pragma GCC diagnostic push/pop/ignored to the HDF5 library's H5_GCC_DIAG_OFF()/H5_GCC_DIAG_ON() macros.
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