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* Tab to space conversions.mainzer2020-08-141-4/+4
| | | | | | | | Re-applied tab to space conversions accidentally reverted in the commit of the metadata cache skip list optimization, and performed some additional tab to space conversions in passing. Tested parallel / debug on Jelly.
* Merge branch 'develop' into mdc_sl_optmainzer2020-08-1375-713/+1096
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| * Cleans warnings and cruft from ttsafe_attr_vlen.cDana Robinson2020-08-121-11/+9
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| * Fixes Windows issues due to exposed pthread codeDana Robinson2020-08-121-4/+7
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| * Fixes a size mismatch when copying old-style to new-style referencesDana Robinson2020-08-121-4/+4
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| * Fixes memory leads in trefer.cDana Robinson2020-08-121-20/+22
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| * Merge pull request #2752 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-08-122-6/+6
| |\ | | | | | | | | | | | | | | | | | | to develop * commit '78c6be05a84f854074a4df2e10c15a56444e4015': Fixes the splitter VFD test on Windows.
| | * Fixes the splitter VFD test on Windows.Dana Robinson2020-08-122-6/+6
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| * | Fixes flock Windows failureDana Robinson2020-08-071-6/+6
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| * Removes staff email addresses from the repositoryDana Robinson2020-08-0765-70/+66
| | | | | | | | Removes redundant C library headers from hl library
| * Merge pull request #2730 in HDFFV/hdf5 from ↵Dana Robinson2020-08-063-64/+185
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:file_locking_squash_2 to develop * commit '47ad0ac7237b464e939fe54dd129a151944d9706': Renames BEST-EFFORT to BEST_EFFORT for file locking env var Updated the file locking Fortran property list wrappers and added a test. Fixed missing parens in VFDs Minor change to header comments in file locking C++ changes. Squash merge of file locking fixes
| | * Merge branch 'develop' into file_locking_squash_2Dana Robinson2020-08-064-14/+18
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| | * | Squash merge of file locking fixesDana Robinson2020-08-033-64/+185
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| * | | Merge pull request #2715 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:fix_vlen_ref to ↵Jerome Soumagne2020-08-061-0/+303
| |\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop * commit 'ef6db167a86e6c065d46963dbd75cd325fe83813': H5R: fix encoding of references that are part of compound types
| | * | | H5R: fix encoding of references that are part of compound typesJerome Soumagne2020-07-281-0/+303
| | | | | | | | | | | | | | | | | | | | Add corresponding test and some debug information
| * | | | Fixes warnings in the splitter VFD and testsDana Robinson2020-08-061-109/+148
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| * | | Warning fixes in tools and h5test.cDana Robinson2020-08-061-8/+15
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| * | | Minor normalizations with 1.12 branchDana Robinson2020-08-013-6/+3
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| * | Minor normalizations with hdf5_1_10Dana Robinson2020-07-319-414/+331
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* | When flushing, the metadata cache attempts to flush entries in increasingmainzer2020-08-055-1046/+1320
|/ | | | | | | | | | | | | | | | address order. To facilitate this, the metadata cache needs a list of of dirty entries in increasing address order. This is implemented via a skip list of all dirty entries in the cache. To date this skip list has been maintained at all times. However, profiling indicates that we can avoid significant overhead by constructing the skip list of dirty entries just before a flush, taking it down afterwareds, and not maintaining it during normal operation. This commit implements this optimization for both serial and parallel. Tested serial and parallel, debug and production on charis and jelly.
* Fixed additional typos in tselect.c comments.Dana Robinson2020-07-281-2/+2
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* Fixes typo in tselect.cDana Robinson2020-07-281-1/+1
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* Updates H5Sset_extent_none() to set H5S_NULLDana Robinson2020-07-281-2/+78
| | | | | | | | The API call used to set the internal H5S_NO_CLASS value which produced errors when such a dataspace was passed to many other API calls. Fixes HDFFV-11027
* Merge pull request #2693 in HDFFV/hdf5 from ↵Vailin Choi2020-07-175-1/+181
|\ | | | | | | | | | | | | | | ~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
| * Update MANIFEST.vchoi2020-07-161-0/+1
| | | | | | | | Add new test to Cmake.
| * Fix for jira issue HDFFV-11080:vchoi2020-07-144-1/+180
| | | | | | | | | | (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
* | H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-161-0/+270
|/ | | | Update trefer.c with vlen test case
* Add new source files to CMake buildQuincey Koziol2020-06-281-0/+1
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* Clean up warningsQuincey Koziol2020-06-281-21/+20
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* Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-273-54/+134
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| * * Fix intermittent error with Splitter VFD.Jacob Smith2020-06-253-54/+134
| | | | | | | | | | | | | | | | Mismatch in time of test file creation was creating false negatives. Add file-duplication routine: `h5_duplicate_file_by_bytes()`. * Change library calls in `h5test.c:h5_compare_file_bytes()` to their HD-prefixed equivalents.
* | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-26226-49539/+88368
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| * Merge pull request #2615 in HDFFV/hdf5 from ↵Jake Smith2020-06-151-1/+2
| |\ | | | | | | | | | | | | | | | | | | ~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 Smith2020-05-291-1/+2
| | | | | | | | | | | | | | | * Missing logfile close on driver-open failure. * Initialize empty string in test/vfd (logfile path in W/O compat check).
| * | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2020-06-071-7/+7
| |\ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'aa338c3a87a4544ccb164832422e3e2462a57b88': 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. Normalization of H5T.c with 1.10. Normalization of H5D.c with 1.10.
| | * | Detect when there's the same-shaped selection of a single block of elements onQuincey Koziol2020-06-051-7/+7
| | | | | | | | | | | | | | | | | | | | | | | | 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 flags from config/clang-warnings/*general files to H5 C and CXX flags ↵Larry Knox2020-06-061-3/+3
| |/ / | | | | | | | | | | | | | | | | | | 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.
| * | Normalizations with 1.10 branch.Dana Robinson2020-06-021-4/+4
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| * Minor tweaks to testhdf5 code after normalization with 1.10.Dana Robinson2020-05-282-45/+45
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| * Misc warning fixes.Dana Robinson2020-05-104-18/+39
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| * Align contents of CMake and autotools testfile cleanup lists.Quincey Koziol2020-05-032-90/+49
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| * Avoid allocating a chunk index for datasets with 0-sized dimensions, untilQuincey Koziol2020-05-012-20/+214
| | | | | | | | the dataset is extended.
| * Merge pull request #2541 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-04-271-0/+59
| |\ | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit 'c03ee563f46013d22f36a1895664a9ba876558e9': Further updates to the tools warnings fixes from code review. Updates to tools warning PR from code review. Fixes for warnings in the tools code.
| | * Updates to tools warning PR from code review.Dana Robinson2020-04-261-4/+4
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| | * Fixes for warnings in the tools code.Dana Robinson2020-04-251-0/+59
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| * | For compatibility with non-C99 Visual Studio versions, use "%" PRIuMAXDavid Young2020-04-241-2/+2
| | | | | | | | | | | | instead of "%ju".
| * | Fix `test/swmr_sparse_reader.c:118:77: error: cast from pointerDavid Young2020-04-241-2/+2
| |/ | | | | | | | | | | | | to integer of different size [-Werror=pointer-to-int-cast]` and `test/snapshots-hdf5/current/test/swmr_sparse_reader.c:129:100: error: cast from pointer to integer of different size [-Werror=pointer-to-int-cast]`.
| * Trim trailing whitespaceQuincey Koziol2020-04-2067-517/+517
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| * Merge branch 'develop' of ↵Jacob Smith2020-04-074-352/+1096
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~jake.smith/hdf5 into feature/vfd_splitter_mirror_a
| | * Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-04-071-0/+553
| | |\ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'f6514c35ea3786206a8db73e1cad8fce8fe6a715': Updated test ddl files so CMake passes after h5dump failures. Modifications based on PR review feedback. Add two routines gen_ref_files() and gen_sel_files() to generate test files related to references and selections. These test files will be copied to 1.12, 1.10 and 1.8 for compatibility testing.
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