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* Update copyright headers (#2184)Larry Knox2022-11-011-1/+0
| | | | | * Updated source file copyright headers to remove "Copyright by the Board of Trustees of the University of Illinois", which is kept in the top-level COPYING file.
* Misc clang production warning fixes (#1932)Dana Robinson2022-07-271-5/+5
| | | | | | | * Misc clang production warning fixes * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Develop clang 13 format (#1933)Allen Byrne2022-07-261-12/+13
| | | | | * Update format source to clang 13 * More format changes
* Be a bit safer with signed arithmetic, thus quieting some signed-overflow ↵David Young2022-04-301-2/+3
| | | | | | | | | | | | | | | | | | | | | | | warnings from GCC (#1706) * Avoid a signed overflow: check the range of `entry_ptr->age` before increasing it instead of increasing it and then checking the range. This quiets a GCC warning. * Avoid the potential for signed overflow by rewriting expressions `MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`. This change quiets some GCC warnings. * Change some local variables that cannot take sensible negative values from signed to unsigned. This quiets GCC warnings about potential signed overflow. * In a handful of instances, check the range of a signed integer before increasing/decreasing it, just in case the increase/decrease overflows. This quiets a handful of GCC signed-overflow warnings. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Removes the STATIC flavor of FUNC_ENTER macros (#1622)Dana Robinson2022-04-081-19/+19
| | | | | * Removes the STATIC flavor of FUNC_ENTER macros
* Parallel rank0 deadlock fixes (#1183)jhendersonHDF2022-01-221-0/+3
| | | | | | | * Fix several places where rank 0 can skip past collective MPI operations on failure * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed Spelling Errors (#1166)Scot Breitenfeld2021-12-071-6/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * fixed missed closing of a dataset * fixed missed closing of a dataset * fixed typo in error return * Committing clang-format changes * minor edits * code format * Committing clang-format changes * code format * minor edit * switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging * Committing clang-format changes * changed size_i in printf to reflect the I/O. * Committing clang-format changes * Fixed seg fault with xlf on BE with -qintsize=8 * fixed error function string * spelling corrections via codespell, added new spell check github actions * Committing clang-format changes * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * misc * misc * misc * misc * misc * Committing clang-format changes * misc * work around for https://github.com/codespell-project/codespell/issues/2137 * misc * added missing file * misc * misc. * misc * switch to using Codespell with GitHub Actions * misc. * misc. * fixed more sp errors * Fix new typos found by codespell. * fixed proceed with precede * fixed variable in fortran test * fixed minnum * updated spelling list Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removes gratuitous (double)x.yF casts (#632)Dana Robinson2021-05-071-5/+4
| | | | | | | | | * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)Sean McBride2021-03-101-1/+1
| | | | | | | | | * Fixed all clang-tidy bugprone-suspicious-string-compare warnings This change was generated entirely by clang-tidy itself. * Reformat code with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Patches from vtk (#358)Sean McBride2021-02-251-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Drop the export attribute on forward declaration They don't mean anything on forward declarations anyways. * Fixed -Wunused-parameter warnings in some C++ files Allowed all the attribute #defines to work in C++ also. * Fixed -Wunused-variable warnings by removing dead code * Fixed all -Wshorten-64-to-32 warnings by adjusting casts There was no truncation in fact, since the unsigned result was upcast to size_t then implicitly downcast to uint32_t. * Fixed all -Wcomma warnings by spliting statements onto own lines * Fixed all -Wself-assign warnings with different unused param suppression * Fixed all -Wextra-semi warnings * Fixed all -Wswitch-enum warnings Just added new explicit cases with the existing default case. * Fixed all -Wmissing-prototypes warnings Just made functions static. Moved them into an extern "C" block. * Reformatted source with bin/format_source using clang version 10.0.1 Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Update license url (#332)Larry Knox2021-02-171-1/+1
| | | | | | * 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.
* develop revert source to clang-format version 11 (#293)Allen Byrne2021-01-291-8/+8
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction
* Basic alignment with async branch (#115)Quincey Koziol2020-11-231-8/+8
| | | | | | | * Basic alignment with async branch - trivial changes to reduce clutter in overall diff. * Update minor error code to reflect change within library * Update the error output to match library
* Clang-format of source filesAllen Byrne2020-09-301-926/+885
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* Merge branch 'develop' into mdc_sl_optmainzer2020-08-151-48/+0
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| * Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-061-48/+0
| | | | | | | | | | | | 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.
* | Tab to space conversions.mainzer2020-08-141-79/+79
| | | | | | | | | | | | | | | | 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.
* | When flushing, the metadata cache attempts to flush entries in increasingmainzer2020-08-051-2/+11
|/ | | | | | | | | | | | | | | | 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.
* Trim trailing whitespaceQuincey Koziol2020-04-201-269/+269
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* Added an H5MM_memcpy call that checks for buffer overlap.Dana Robinson2019-03-161-6/+6
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* Fix some collective metadata read issuesJordan Henderson2019-02-121-2/+2
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* Normalization with vol_integration (misc internal and datatype)Dana Robinson2018-09-201-7/+7
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* Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-2/+2
| | | | | | | | | 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
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-1/+4
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
| * Fix bounds check for the generation of cache image.Vailin Choi2018-01-221-1/+4
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* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-41/+34
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* Better segregate clean & dirty LRU lists so that they are only defined whenQuincey Koziol2017-09-301-0/+2
| | | | the H5C_MAINTAIN_CLEAN_AND_DIRTY_LRU_LISTS macro is defined.
* 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.
* Omnibus checkin for several relatively minor modifications:mainzer2017-03-281-23/+50
| | | | | | | | | | | | | | | | | | | | 1) Added code test/page_buffer.c to verify that page buffering is disabled in parallel builds. 2) Added code to test/cache_image.c to verify correct interaction between evict on close and cache image -- in particular management of a file containing a cache image containing dirty metadata that has been opened R/O. Also fix for the bug exposed. 3) Added code to testpar/t_cache_image.c to verify expected procedure for reading cache images, and also supporting stats collection code needed for the test. 4) Repair of an overactive sanity check in H5C__reconstruct_cache_contents(). 5) Other minor tidies in passing. Tested serial and parallel, debug and production on Jelly.
* Final merge of page buffering branch to developQuincey Koziol2017-03-141-1/+96
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* Minor cleanups and bring over "prefetched dirty" fixes for entries loaded fromQuincey Koziol2017-03-121-0/+2
| | | | a cache image.
* Remove some usage of "prefetched_dirty" flag (which hasn't been merged from theQuincey Koziol2017-03-101-2/+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 Koziol2017-03-071-39/+95
| | | | entries from collective metadata read list
* Normalize against incoming page buffering changes.Quincey Koziol2017-03-011-707/+184
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* Align w/incoming page buffering changes.Quincey Koziol2017-02-251-2/+3
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* Misc. style cleanups from the page_buffering branch.Quincey Koziol2017-02-181-8/+8
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* Optimize loading cache image, removing lots of memory allocations and copies.Quincey Koziol2017-02-031-201/+150
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* Simplify H5C__serialize_single_entry(), using H5C__generate_image()Quincey Koziol2017-02-021-179/+45
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* Add missing filesQuincey Koziol2017-01-291-0/+4100
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