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* Hdf5 1 10 merge of printf specifiers and VS2015 min changes (#612)Allen Byrne2021-04-301-17/+16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file * Merge #380 from develop * Finish java merges from develop * Fix java issues with tests and javadoc * Correct use of attribute access plist * Remove debug code * Remove unused variable * Change file access to read only for java tests * Split clang format operations. * More javadoc comments * Remove pre-split setting * format source * Change windows TS to use older VS. * Mostly all javadoc fixes, one argument rename. * synch file * Merge of long double fix and compiler flags * HDFFV-11229 merge changes from develop * HDFFV-11229 correct test script * HDFFV-11229 update autotools test script for two ref files * HDFFV-11229 merge dev changes for long double display in tools * Committing clang-format changes * minor whitespace * remove unneeded macro * Committing clang-format changes * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument Update pkgconfig scripts for parallel builds. Fix install COPYING file reference. Remove unused round defines. Change CMake default setting of BUILD_CPP to off. * Fortran target depends * Remove incorrect source attribute * Revert define removal * printf specifiers and VS2015 min changes * Committing clang-format changes * Add time struct Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Hdf5 merge issue 435 v110 (#462)Larry Knox2021-03-101-3/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. * Fixed clang-tidy readability-misleading-indentation warnings (#427) * Fixed clang-tidy readability-misleading-indentation warnings * Reformatted src/H5Zscaleoffset.c with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Fixed clang-tidy readability-redundant-control-flow warnings (#428) * Fixed clang-tidy readability-redundant-control-flow warnings Just removed useless trailing return statements. * Removed blank lines from h5diffgentest.c with clang-format v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed bad function pointer casts (#434) * Removed bad function pointer casts In one case fixed the actual function signature to be correct. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * fix block coordinate printing example (#437) Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Mike Smith <grimbough@gmail.com>
* 1 10 Merges from develop (#424)Allen Byrne2021-03-041-3/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file
* Hdf5 1 10 Update license url (#403)Larry Knox2021-03-011-1/+1
| | | | | | | | | | | | | | | | | | | | | | | * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Modify temporary rpath for testing in java example scripts. (#230) * Fix undefined left shifting of negative numbers (#338) Undefined Bahavior Sanitizer errored here about left shifting negative numbers. * Update license url (#332) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING file - src and test directories. Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Sean McBride <sean@rogue-research.com>
* Fix spelling of metadataLarry Knox2020-11-131-1/+1
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* Source formattedAllen Byrne2020-10-011-5933/+5444
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* Merge of clang-format changes from developAllen Byrne2020-09-301-999/+998
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* Brings the MDC skiplist optimizations from developDana Robinson2020-08-171-412/+1450
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* Many normalizations with develop.Dana Robinson2020-05-301-18/+15
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* Removed trailing whitespace from source files.Dana Robinson2020-05-261-206/+206
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* Moved H5MM_memcpy and H5MM_xfree_const from developDana Robinson2020-05-151-7/+7
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* Fix some collective metadata read issuesJordan Henderson2019-02-121-42/+13
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* Merge pull request #1522 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to ↵Vailin Choi2019-02-061-0/+4
| | | | | | | | | | | | | develop * commit '7f5741825db0737db5ac46c43009681508a73002': Add release notes information. Modification based on feedback from pull request. Modification based on feedback from pull request. There is performance issue when closing an object. The slow down is due to the search of the "tag_list" to find out the "corked" status of an object. The fix: (1) Add a counter "num_objs_corked" in the cache structure to track the number of "corked" objects. (2) Skip the search of "tag_list" if the counter is zero i.e. no "corked" objects. Conflicts: release_docs/RELEASE.txt
* Merge of logging framework updates.Dana Robinson2018-12-311-7/+8
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* Fixed HDFFV-10404Binh-Minh Ribler2018-07-261-12/+12
| | | | | | | | | Description: Applied the typo fixes from user's report. The previous pull request couldn't be merged because it was too old, and it was too complicated for me to resolve conflicts. Platform tested: Linux/64 (jelly) - very minor
* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-420/+249
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* Better segregate clean & dirty LRU lists so that they are only defined whenQuincey Koziol2017-09-301-0/+8
| | | | the H5C_MAINTAIN_CLEAN_AND_DIRTY_LRU_LISTS macro is defined.
* Style cleanups and misc. bugfixes discovered during full SWMR development.Quincey Koziol2017-09-231-18/+29
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* Updated H5C__flush_single_entry() in H5C.c to correctmainzer2017-08-151-8/+18
| | | | | | | duplicate metadata write bug observed in 1.10.1. Tested parallel/production on jelly parallel/debug & parallel/production on charis (in develop branch)
* Merge pull request #426 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to ↵Larry Knox2017-04-251-6/+4
| | | | | | | | | | hdf5_1_10 * commit '54957d37f5aa73912763dbb6e308555e863c43f4': Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes. Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh. Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1 Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
* Checkin of additions to cache image parallel test code andmainzer2017-03-161-6/+15
| | | | | | | | | | | | associated bug fixes. Also, modifications to H5PB_dest() to flush the page buffer before destroying the page buffer. This is necessary, as when persistant free space managers are enabled, the page buffer will typically contain dirty FSM data at page buffer destroy time. Tested serial/debug, serial/production, serial/check-vfd/debug, parallel/debug, parallel/production on Jelly.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-2/+124
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* Merge in reentrency changes to "make space in cache" from page_buffering branch.Quincey Koziol2017-03-131-0/+20
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* Minor cleanups and bring over "prefetched dirty" fixes for entries loaded fromQuincey Koziol2017-03-121-10/+32
| | | | a cache image.
* Remove some usage of "prefetched_dirty" flag (which hasn't been merged from theQuincey Koziol2017-03-101-1/+0
| | | | | page_buffering branch yet. Also, bring over improvements to flush candidate entries for parallel code.
* Align with incoming page buffering changes: minor cleanups, centralize removingQuincey Koziol2017-03-071-30/+35
| | | | entries from collective metadata read list
* Misc. small cleanups to sync against incoming page buffering changes.Quincey Koziol2017-03-021-47/+17
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* Normalize against incoming page buffering changes.Quincey Koziol2017-03-011-17/+534
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* Corrected version of 4b5e05c084f93c35dae946c2c9e814d565a613b0:Quincey Koziol2017-02-281-5/+5
| | | | | Fix some more signed -> unsigned value issues with cache data structures, also misc. style cleanups. All to align w/incoming page_buffering changes.
* Align w/incoming page buffering changes.Quincey Koziol2017-02-251-93/+25
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* Misc. style cleanups from the page_buffering branch.Quincey Koziol2017-02-181-411/+218
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* Simplify H5C__serialize_single_entry(), using H5C__generate_image()Quincey Koziol2017-02-021-20/+27
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* Cache image feature and testingQuincey Koziol2017-01-291-34/+231
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* Bring change to use array of metadata cache entry classes for H5C_createQuincey Koziol2017-01-281-71/+15
| | | | instead of array of class names from cache image branch.
* Switch list lengths to unsigned integers (to align better w/cache image merge)Quincey Koziol2017-01-281-115/+70
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* Commit Vailin's fix for the h5format_convert test failure.lrknox2017-01-261-0/+5
| | | | | | DAILYTEST-256 #2. Tested on emu, kituo, mayll, ostrich, and osx1011dev with previously failing test configurations.
* Bring changes to metadata cache "get entry status" call and newQuincey Koziol2017-01-061-16/+262
| | | | | "child serialized / unserialized" messages and support from the cache image branch.
* Bring file shutdown code from cache image branchQuincey Koziol2017-01-051-0/+181
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* Merge code from cache image branch to split FSM ring into two types: raw dataQuincey Koziol2017-01-041-7/+5
| | | | and metadata. Also, some more ring reset safeties and minor code cleanups.
* Remove 'const' from cache client pre_serialize callback, to reduce warnings,Quincey Koziol2017-01-031-3/+3
| | | | | and correspondingly remove 'const' from some internal routines. Also rename some H5MF* routines to reflect their static/package usage.
* Align with incoming cache_image branch changes: use the index list (instead ofQuincey Koziol2017-01-021-102/+133
| | | | | the hash buckets) for scanning the entries during a flush, and also add in counters for tracking operations during cache flushes.
* Bring support for doubly-linked list of all entries in cache from incomingQuincey Koziol2016-12-301-6/+15
| | | | cache image branch.
* More normalizations against incoming cache image branch.Quincey Koziol2016-12-291-6/+5
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* Normalize against incoming cache image feature.Quincey Koziol2016-12-281-77/+65
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* Bring over changes from revise_chunks that cleanup recent SWMR changes fromQuincey Koziol2016-12-111-7/+36
| | | | code review feedback.
* Bring SWMR support in to the main development branch. (Finally!) More testsQuincey Koziol2016-12-021-20/+256
| | | | and the tool and API wrappers will be coming in over the weekend.
* Remove "collective write list" parameter from H5C__flush_single_entry() as itQuincey Koziol2016-11-281-22/+17
| | | | | is only used in a couple of places. The collective write list has been moved to be internal to the cache data structure instead.
* Eliminate unnecessary data structure for parallel collective metadata cache I/OQuincey Koziol2016-11-281-16/+1
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* Add a flag for H5C__flush_single_entry() to allow the parallel code to requestQuincey Koziol2016-11-251-27/+31
| | | | | that images for entries be generated, even when not writing the entry from an MPI rank.
* Bring over support for retrying metadata cache entry loads, along with all theQuincey Koziol2016-11-201-172/+201
| | | | supporting metadata cache callback changes, etc.
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