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* Merge branch 'develop' into develop_minorDana Robinson2020-08-1717-1847/+3640
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| * Merge pull request #2769 in HDFFV/hdf5 from mdc_sl_opt to developJohn Mainzer2020-08-1715-1837/+3630
| |\ | | | | | | | | | | | | | | | | | | * commit 'd00bab96fb4da12a18b5de528c96469978c4c927': Minor copy edits to comments -- no code changes. Tab to space conversions. When flushing, the metadata cache attempts to flush entries in increasing 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.
| | * Minor copy edits to comments -- no code changes.inactive/mdc_sl_optmainzer2020-08-173-3/+3
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| | * Merge branch 'develop' into mdc_sl_optmainzer2020-08-15364-10247/+6767
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| | * | Tab to space conversions.mainzer2020-08-147-465/+463
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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_optmainzer2020-08-13196-3757/+5236
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| | * | | When flushing, the metadata cache attempts to flush entries in increasingmainzer2020-08-0515-1857/+3651
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
| * | | | Merge pull request #2784 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-08-172-10/+10
| |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '0d14414ddd860f24f1386771ed3ba8d2f5e2710d': 1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] after AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
| | * | | | 1. HDFFV-10830 part 2, move AC_CHECK_HEADERS([szlib.h] afterLarry Knox2020-08-162-10/+10
| |/ / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress] to avoid compiling H5Z.c with szlib.h after its path is removed from AM_CPPFLAGS. 2. Remove unnecessary links to ${HDF5_TOOLS_LIB_TARGET} in utils/mirror_vfd/CMakeLists.txt that prevent building HDF5 with tools disabled.
* | | | | Trivialities noticed while normalizing 1.10Dana Robinson2020-08-172-2/+2
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* | | | Merge pull request #2771 in HDFFV/hdf5 from ↵Binh-Minh Ribler2020-08-165-14/+199
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~BMRIBLER/hdf5_bmr:hdf5_bmr_HDFFV-10933 to develop Fixed HDFFV-10933 * commit '16349c5fddce8a74644e18d01d7ea8186aaaa255': Fixed HDFFV-10933
| * | | | Fixed HDFFV-10933Binh-Minh Ribler2020-08-145-14/+199
| | |_|/ | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: Updated the original fix by Kent Y. in commit 200a77d8c3e51663c375aafffff607ae9b438f4e - used internal functions instead of public API - moved some code into the subroutine for a cleaner look. - added test to dsets.c Platforms tested: Linux/64 (jelly)
* | | | Merge pull request #2779 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-08-161-0/+4
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | * commit '31673041d8342002d11ced2a7def938438dd912d': Fix javadoc warning
| * | | | Fix javadoc warningAllen Byrne2020-08-161-0/+4
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* | | | Merge pull request #2776 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-08-165-4/+57
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | * commit '6a344232f641135e6bc5f89d66a01c68d29bfa00': Add testfiles TRILABS-277 Use JIRA number as #ifdef
| * | | | Add testfilesAllen Byrne2020-08-151-0/+7
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| * | | | TRILABS-277 Use JIRA number as #ifdefAllen Byrne2020-08-155-4/+50
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* | | | Merge pull request #2768 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-08-1537-120/+2079
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '2d659de898f23b78bbbb47a1dbd5ffb5d9f953a6': HDFFV-9984 fix test logic HDFFV-9984 - correct name of ref files HDFFV-9984 add missing ref file HDFFV-9984 - add missing ref files HDFFV-9984 Add options to merge/prune external links during repack
| * \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-08-1511-66/+65
| |\ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | * commit '40bf112b56c90b7e90c9ec3d7a35a78d1d12288b': Trivialities noticed while merging things to 1.10
* | | | | Merge pull request #2773 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-08-1511-66/+65
|\ \ \ \ \ | |_|/ / / |/| | | | | | | | | | | | | | | | | | | | | | | | to develop * commit 'c5b176594082f6e5a8b6d9140f9db1f13530e087': Trivialities noticed while merging things to 1.10
| * | | | Trivialities noticed while merging things to 1.10Dana Robinson2020-08-1511-66/+65
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| * | | HDFFV-9984 fix test logicAllen Byrne2020-08-142-6/+5
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| * | | HDFFV-9984 - correct name of ref filesAllen Byrne2020-08-145-0/+0
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| * | | HDFFV-9984 add missing ref fileAllen Byrne2020-08-141-0/+28
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| * | | HDFFV-9984 - add missing ref filesAllen Byrne2020-08-147-0/+541
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| * | | HDFFV-9984 Add options to merge/prune external links during repackAllen Byrne2020-08-1431-120/+1511
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* | | Merge pull request #2765 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-08-141-10/+10
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit '3feeb8ec20a7b08acdcd77f3e10c8c93818d890e': Fixes naming issues in H5VM inline functions
| * | | Fixes naming issues in H5VM inline functionsDana Robinson2020-08-141-10/+10
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* | | Merge pull request #2753 in HDFFV/hdf5 from ~EPOURMAL/hdf5_ep:develop to developElena Pourmal2020-08-142-54/+70
|\ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'c6248cfb6975a6ecadf0259390247ce05dc13c4b': Addresseda Dana's comments from the pull request. Fixed several typos in the comments found by Larry during the review. The H5DSis_scale function was updated to return "not a dimension scale" (0) instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification (HDFFV-10436).
| * | | Addresseda Dana's comments from the pull request.Elena2020-08-141-29/+32
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| * | | Fixed several typos in the comments found by Larry during the review.Elena2020-08-121-3/+3
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| * | | Merge branch 'develop' of ↵Elena2020-08-122-6/+6
| |\ \ \ | | | | | | | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~epourmal/hdf5_ep into develop
| * | | | The H5DSis_scale function was updated to return "not a dimension scale" (0)Elena2020-08-122-42/+55
| | | | | | | | | | | | | | | | | | | | | | | | | instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification (HDFFV-10436).
* | | | | Merge pull request #2744 in HDFFV/hdf5 from remove_unneeded_tagging to developQuincey Koziol2020-08-148-46/+54
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit 'cb5de74ac26158f6f541eed2e0dddb50d4d197d6': Remove redundant calls to set the metadata cache tag
| * \ \ \ \ Merge remote-tracking branch 'origin/develop' into remove_unneeded_taggingQuincey Koziol2020-08-14364-10201/+6708
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* | | | | | Merge pull request #2739 in HDFFV/hdf5 from namespace_cleanup_01 to developQuincey Koziol2020-08-14359-10156/+6651
|\ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '3f46a380e084d83a84783383bdfbbd9a443e9f27': Correct typos w/HGOTO_DONE & HGOTO_ERROR Move H5T_vlen_reclaim to package scope Switch H5VM inline routines back to single underscope and put a comment in their header about this naming Clean up private / package / static namespace issues (function naming, which header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
| * \ \ \ \ \ Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01Quincey Koziol2020-08-122-6/+6
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| * | | | | | Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01Quincey Koziol2020-08-113-24/+32
| |\ \ \ \ \ \ | | | |_|/ / / | | |/| | | |
| * | | | | | Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01Quincey Koziol2020-08-104-8/+9
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| * | | | | | | Correct typos w/HGOTO_DONE & HGOTO_ERRORQuincey Koziol2020-08-107-50/+47
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| * | | | | | | Move H5T_vlen_reclaim to package scopeQuincey Koziol2020-08-074-6/+6
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| * | | | | | | Merge remote-tracking branch 'origin/develop' into namespace_cleanup_01Quincey Koziol2020-08-07147-952/+1997
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| * | | | | | | | Switch H5VM inline routines back to single underscope and put a comment in ↵Quincey Koziol2020-08-0640-166/+214
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | their header about this naming
| * | | | | | | | Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-06362-10270/+6711
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email addresses from library source code (still needs cleaned from other directories). Misc. warning, style, and whitespace cleanup.
* | | | | | | | | Merge pull request #2762 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-08-131-2/+2
|\ \ \ \ \ \ \ \ \ | |_|_|_|_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit 'b806f3e9acad6261438dacecbb11a87bcd644e72': Tweak to hide unused threadsafe callback in non-threadsafe builds
| * | | | | | | | Tweak to hide unused threadsafe callback in non-threadsafe buildsDana Robinson2020-08-131-2/+2
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* | | | | | | | Merge pull request #2756 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-08-132-4/+13
|\ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'c5cb9534b27760596bfd0c4cdf1db31fd2bac2a7': spelling HDFFV-11127 - force RTLD_LOCAL in dlopen
| * \ \ \ \ \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-08-131-13/+14
| |\ \ \ \ \ \ \ \ | |/ / / / / / / / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit 'baf7ebc4ca4eeecb11a607f420a5d5b95169eed5': Cleans warnings and cruft from ttsafe_attr_vlen.c Fixes Windows issues due to exposed pthread code
* | | | | | | | | Merge pull request #2760 in HDFFV/hdf5 from ↵Dana Robinson2020-08-131-13/+14
|\ \ \ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:ttsafe_windows_fix to develop * commit '04b24163f7f08248a58d256371e088c8cc7816c8': Cleans warnings and cruft from ttsafe_attr_vlen.c Fixes Windows issues due to exposed pthread code
| * | | | | | | | | Cleans warnings and cruft from ttsafe_attr_vlen.cDana Robinson2020-08-121-11/+9
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