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* Update Copyright headers. (#2534)Larry Knox2023-03-131-1/+0
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* clang 13 format #1933 (#1939)Allen Byrne2022-07-271-7/+8
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* Hdf5 1 12 merges (#1528)jhendersonHDF2022-03-251-27/+39
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Add support for parallel filters to h5repack (#832) * Allow parallel filters feature for comm size of 1 (#840) * Avoid popping API context when one wasn't pushed (#848) * Fix several warnings (#720) * Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201) * Fix free list tracking and cleanup cast alignment warnings (#1288) * Fix free list tracking and cleanup cast alignment warnings * Add free list tracking code to H5FL 'arr' routines * Fix usage of several HDfprintf format specifiers after HDfprintf removal (#1324) * Use appropriate printf format specifiers for haddr_t and hsize_t types directly (#1340) * Fix H5ACmpio dirty bytes creation debugging (#1357) * Fix documentation for H5D_space_status_t enum values (#1372) * Parallel rank0 deadlock fixes (#1183) * 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> * Fix a few issues noted by LGTM (#1421) * Fix cache sanity checking code by moving functions to wider scope (#1435) * Fix metadata cache bug when resizing a pinned/protected entry (v2) (#1463) * Disable memory alloc sanity checks by default for Autotools debug builds (#1468) * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Cherry-pick 3 merge commits from develop to hdf5_1_12 (#629)Larry Knox2021-05-061-7/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. * close #195. (#196) * Update HDF5PluginMacros.cmake * Update HDF5PluginMacros.cmake * Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer. Update test to be more thorough with using compound datatype fields everywhere. (#206) * 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. * Fixes various warnings noticed on Windows (#425) * Fixes various warnings noticed on Windows - Adds a prototype for our implementation of vasprintf - Return type of H5_get_utf16_str() is now non-const - Fixes possible uninitialized return type in Wremove_utf8 - Better isolation of fork() code in accum.c:test_swmr_write_big() - Better isolation of non-zlib code in dsets.c:test_filter_delete() - Removed unused variable in trefer.c:test_reference_cmpnd_obj() * Fixes clang-format issues * Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429) * Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes Removes useless const declarations. * Fixed most readability-non-const-parameter warnings These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature. * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Added C++11 override keyword where appropriate (#433) Added H5_OVERRIDE macro for compatibility with both C++11 and older. * Various clang tidy warning fixes (#448) * Fixed clang-tidy bugprone-reserved-identifier warnings * Fixed clang-tidy bugprone-assert-side-effect warnings * Fixed clang-tidy bugprone-copy-constructor-init warning * Fixed clang-tidy readability-redundant-preprocessor warning For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block. Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing. Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS. * Fixed clang-tidy readability-redundant-string-init warnings * Fixed some clang-tidy performance-type-promotion-in-math-fn warnings * Fixed clang-tidy performance-unnecessary-value-param warnings * Reformat source with clang v10.0.1. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Removed checks/workarounds for pre-C++89 compatibility (#449) After 30+ years, just assume that the following exist: - extension-less includes - namespaces - std:: - static_cast - bool * Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451) * 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> * Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451. * Minor parallel improvements (#519) * Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up MPI-IO VFD tracing support (#520) * Clean up tracing support * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Brings the native implementation of H5Fdelete() from Bitbucket (#524) * Committing clang-format changes * Brings the native VFD H5Fdelete() implementation from Bitbucket Only brings the 'del' callbacks, not the 'open/close' scheme. * Formatter changes * Committing clang-format changes * Fixes direct VFD callback name * Removes UNUSED macro from family API call * Adds barrier and rank 0 check to MPI-I/O VFD delete * Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete" This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143. * Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"" This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702. * Adds a second barrier after the delete in MPI-I/O VFD * Only delete files in the core VFD when the backing store flag is set * Fixes string issues in multi VFD Also, h5test.c cleanup code now uses H5Fdelete(). * Formatted source * Rework fapl checks for MPI-I/O VFD delete callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Minor warning fixes in develop (#526) * Committing clang-format changes * Minor warning fixes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes implementation of my_strdup() from the multi VFD (#527) * Committing clang-format changes * Removes my_strdup() from the multi VFD * Use strdup directly when memory sanity checks are off Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes dead H5ST package from the library (#528) * Committing clang-format changes * Removes the unused H5ST package from the library Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix HDFFV-11232 (#530) * 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 * added H5fortkit dependency for H5VLff.F90, HDFFV-11232 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes incorrect usage of H5I_BADID (#554) * Committing clang-format changes * Fixes incorrect use of H5I_BADID Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601) * Committing clang-format changes * Fixes a segfault when H5Pset_mdc_log_options() is called multiple times An internal string is incorrectly freed when the API call is invoked multiple times on a property list, which will usually cause a segfault to occur. On the first call the log location is NULL so the problem doesn't occur. Fixes HDFFV-11239 * Fixes typos Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607) * Committing clang-format changes * Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid fapl ID This was due to a pointer-containing struct being memset after the first internal API call. If the first call failed, the error condition would check if the pointer was not NULL and then attempt to free it if not. This would lead to the freeing of a wild pointer if an invalid fapl ID were passed in. This was fixed by reordering the memset and adding a test to ensure the problem stays fixed. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611) * Committing clang-format changes * Fixes incorrect size_hint handling in H5Gcreate1 * Updates the size hint type for group creation * Updates the RELEASE.txt note * Revert "Updates the RELEASE.txt note" This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff. * Reverts previous behavior to use a uint32_t struct field * Updates RELEASE.txt Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)" This reverts commit 38d1b121ae428138b8863c2a319518c7363c2d94. * Removed mentions of Wdeclaration-after-statement now that C99 is requ… (#447) * Removed mentions of Wdeclaration-after-statement now that C99 is required * Remove -Werror=declaration-after-statement from error-general file. Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Made private my_yyinput function static (#618) This prevents it being exported as a public symbol. * Adds const to a few global variables (#623) * Committing clang-format changes * Adds consts to a few global variables Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org> Co-authored-by: Quincey Koziol <quincey@koziol.cc> Co-authored-by: Sean McBride <sean@rogue-research.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* Hdf5 1 12 whitespace changes (#606)Allen Byrne2021-04-291-174/+174
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards * Merge #380 from develop * Correct date entry * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * Some Javadoc warning fixes * Committing clang-format changes * Updated javadoc fixes * HDFFV-11228/9 merges from develop * remove obsolete debug comment * Fix conflict * HDFFV-11229 merge changes from develop * HDFFV-11229 merge second compare from develop * HDFFV-11229 fix reference file * 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 * Update with changes from develop * 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. * Whitespace changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* 1 12 Merges from develop (#421)Allen Byrne2021-03-041-10/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version * Merge workflow and minor changes from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge serval small changes from dev * fix typo * Minor non-space formatting changes * GH #386 copyright corrections for java folder * revert because logic requires false return * Merges from develop #358 patches from vtk #361 fix header guard spelling * Remove case statement for H5I_EVENTSET * Correct call with versioning * Remove tabs * Double underscore change * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings Remove more underscores from header guards
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - src and test directories.
* 1 12 Whitespace changes after clang-format run (#288)Allen Byrne2021-01-291-5/+5
| | | | | | | | | | | | | | | | | | | | | * OESS-98 fix tools test for plugins * sync fork * Merge of changes from dev * Move problem option to bottom of the list until fixed * HDFFV-11106 - fix parsing optional args * HDFFV-11106 add note * grammer fix * Whitespace after clang formatting * Undo format version 11 changes * Update check to working version
* Basic alignment with async branch (#115) (#137)Quincey Koziol2020-11-301-5/+5
| | | | | | | * 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
* Merge changes from developAllen Byrne2020-10-081-0/+4
| | | | | Comments and whitespace Skip file-locking and cache changes
* Source formattedAllen Byrne2020-10-011-808/+799
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* Add clang-format changes from develop.Allen Byrne2020-09-281-3/+3
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* Remove redundant calls to set the metadata cache tagQuincey Koziol2020-08-271-22/+22
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* Switch H5VM inline routines back to single underscope and put a comment in ↵Quincey Koziol2020-08-221-1/+1
| | | | their header about this naming
* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-22/+14
| | | | | | 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.
* Sync with developDana Robinson2020-08-011-2/+3
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* Whitespace cleanupAllen Byrne2020-05-131-104/+104
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* Merge pull request #2094 in HDFFV/hdf5 from ~KMU/hdf5:bugfix/unused to developKimmy Mu2020-01-281-1/+1
| | | | | | | | | | | * commit '145ef3ceee20c28a443bd11507c58858bea3f889': more cleanup change it back pick up missing piece fix unused related warnings removed unused parameter more fix and address comments remove unsed var,function,macro, etc
* Yanked -Wc++-compat from the flags used to build the C library in bothDana Robinson2019-12-161-24/+24
| | | | the Autotools and CMake.
* Switch shared file struct name from 'H5F_file_t' to 'H5F_shared_t', to matchQuincey Koziol2019-08-221-9/+9
| | | | naming convention for shared structs in rest of library data structures.
* Small tidy up.Quincey Koziol2019-08-211-10/+8
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* Progress toward movig H5MF* API to use shared file pointers instead of topQuincey Koziol2019-08-211-37/+34
| | | | file pointers.
* Progress on moving the H5MF* interface to using shared file pointers instead ofQuincey Koziol2019-08-211-39/+38
| | | | top file pointers.
* Begin converting the H5MF interface to use shared file pointers insteadQuincey Koziol2019-08-211-50/+54
| | | | of top file pointers.
* Finish converting H5PB_* routines to use shared file pointer, instead of topQuincey Koziol2019-08-201-1/+1
| | | | file pointer.
* Rest of changes for 'top' file pointer to 'shared' file pointer for H5F__accumQuincey Koziol2019-08-191-3/+2
| | | | routines.
* (1) Add/remove comments.Vailin Choi2019-06-271-92/+32
| | | | | | | | | | | (2) A temporary fix to address the test/objcopy.c: test_copy_group_deep() test failure with the family driver. The test failure occurs with these configurations in objcopy.c: --with shared src messages (CONFIG_SHARE_SRC) --without shared dst messages (CONFIG_SHARE_DST) --with latest format for source file (CONFIG_SRC_NEW_FORMAT) --without dense attributes (CONFIG_DENSE) --with latest format for destination file (CONFIG_DST_NEW_FORMAT) The temporary fix is in src/H5MFaggr.c (see comments above #ifdef REPLACE/#endif).
* Merge branch 'develop' of ↵Vailin Choi2019-06-261-0/+3
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~vchoi/my_third_fork into bugfix/new_shutdown_fsm
| * Fix for HDFFV-10808 H5Pset_file_space_strategy succeeds when using ↵Vailin Choi2019-06-241-0/+3
| | | | | | | | | | | | | | H5Pset_libver_bounds v18,v18. Fails file creation when non-default free-space info is set in fcpl and the library version high bound is less than v110 because free-space info message is introduced in library release v110.
* | Checkin for new shutting down free-space manager.Vailin Choi2019-06-201-374/+108
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* Normalization with vol_integration (test code and H5Xtest.c)Dana Robinson2018-09-201-0/+3
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* Merge branch 'develop' of ↵Larry Knox2018-07-181-11/+11
|\ | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| * Fixed HDFFV-10404Binh-Minh Ribler2018-07-131-11/+11
| | | | | | | | | | | | | | | | | | 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
* | Apply Cygwin pathches from Marco Atzeri.Larry Knox2018-07-181-9/+9
|/ | | | Commit Joe Lee's typo corrections for src/H5MF.c.
* Normalize with vol_integration.Dana Robinson2018-05-291-93/+106
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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-03-181-3/+1
|\ | | | | | | | | | | merge_func_enter_vol Plus initial steps toward merging API context push into FUNC_ENTER_API* macros
* | Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-474/+336
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* Fixed misc Warnings flagged by VS2017.Dana Robinson2017-11-271-1/+4
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* Style cleanups and misc. bugfixes discovered during full SWMR development.Quincey Koziol2017-09-231-0/+1
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* Changes made based on RFC review commentsVailin Choi2017-07-181-1/+1
| | | | Test the changes in a branch via daily testing.
* 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 andmainzer2017-03-161-0/+6
| | | | | | | | | | | | 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 Koziol2017-03-141-965/+2517
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* Bring changes to I/O parameters from page_buffering branch.Quincey Koziol2017-03-131-3/+13
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* Align w/incoming page buffering changes.Quincey Koziol2017-02-251-66/+67
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* Switch major error code from H5E_FSPACE [back] to H5E_RESOURCEQuincey Koziol2017-02-181-99/+99
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* Misc. style cleanups from the page_buffering branch.Quincey Koziol2017-02-181-70/+70
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* Cache image feature and testingQuincey Koziol2017-01-291-2/+2
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* Bring file shutdown code from cache image branchQuincey Koziol2017-01-051-70/+654
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* Merge code from cache image branch to split FSM ring into two types: raw dataQuincey Koziol2017-01-041-42/+226
| | | | and metadata. Also, some more ring reset safeties and minor code cleanups.
generated by cgit v0.12 at 2024-07-17 05:27:58 (GMT)