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* Hdf5 merge issue 487 v112 (#491)Larry Knox2021-03-261-23/+92
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. * Simplified hl parsing (#399) * Stop using global variables to share parse context with the lexer. The lexer uses an unconventional strategy for parsing lexical categories NUMBER (decimal numbers) and STRING (double-quoted strings) that involves sharing the parse context with the lexer using global variables. There are a couple of problems with that. First, the lexer is too complicated for the simple tokenization it performs—it's hard to tell if it is correct. Second, as @seanm points out, the shared global variables spill into the namespace shared by other libraries and application programs—e.g., VTK. * Regenerate source files from *.[yl]. * Replace strndup, which isn't available on Windows, with a custom routine, `trim_quotes`, that produces a copy of its `const char *` argument with leading and trailing double quotes ('"') removed. While I am here, remove the unnecessary statement `BEGIN INITIAL;`, which I should have deleted in a previous commit. * Regenerate .c from .l. * You haven't programmed in C until you have programmed in High-Definition (HD) C. * \#include "H5private.h" for HD* definitions. * Regenerate *.[ch] from *.[yl]. * Removed workarounds for pre-standard inline keyword (#423) Fixes -Wreserved-identifier warnings due to multiple underscores in H5_HAVE___INLINE. * Replaces checks for fork, etc. with checks for unistd.h (#457) * Replaces checks for fork, etc. with H5_HAVE_UNISTD_H Code previously checked for individual POSIX API calls using H5_HAVE_FORK, etc. The calls we use have been standardized for decades and available via unistd.h. Some test messages that were missing when tests are skipped due to a lack of unistd.h were also added. The configure checks for individual POSIX API calls will be removed in a later commit. * Stupid formatter * develop JNI export references and java updates (#467) * 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 * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix display of long double in tools (#469) * 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 * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace * GH #359 implement and fix tools 1.6 API usage * remove excessive comments * Flip inits to correct ifdef section * rework ifdef to be simpler * format issue * Reformat ifdef inits * remove static attribute * format compliance * Update names * Revert because logic relies on float not being int * Changes noticed from creating merge of #412 * Double underscore change * Correct compiler version variable used * Remove header guard underscores * Whitespace cleanup * Split format source and commit changes on repo push * remove pre-split setting * Change windows TS to use older VS. * correct window os name * HDFFV-11212 JNI export util and Javadoc * Suggested review changes * Another change found * Committing clang-format changes * HDFFV-11113 long double in tools * HDFFV-11113 add note Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Update clang config (#473) * Update clang config to put H5E_BEGIN_TRY / H5E_END_TRY on separate lines, empty C++ methods on separate lines, understand that ALL_MEMBERS / UNIQUE_MEMBERS are foreach macros, and properly skip the 'config' directory in the find command without emiting a warning * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Correct syntax error. (#474) a Fortran compile -> a Fortran compiler * Cleans up a couple of MSVC warnings in testhdf5 (#475) * Fixes a few testhdf5 warnings raised in Visual Studio Visual Studio is grumpier about treating pointers like integers than gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix typos and grammar errors. (#476) * Suppresses the tcheck_version test's abort dialog on Windows (#477) * Suppresses the tcheck_version test's abort dialog on Windows Windows raises a modal abort/retry/ignore dialog box when CRT calls abort(). This change installs a report hook that suppresses the dialog so that the CMake tests don't time out waiting for a nonexistent user to click a dialog box. * Committing clang-format changes * Removes __cdecl from callback Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Rerun genparser. * Fix merge issues and rerun genparser. 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: David Young <dyoung@hdfgroup.org> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Quincey Koziol <koziol@lbl.gov>
* Hdf5 merge issue #458 to hdf5_1_12 (#463)Larry Knox2021-03-121-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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. 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>
* 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 Byrne2021-01-291-2/+2
| | | | | | | | | | | | | | | | | | | | | * 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 Koziol2020-11-301-2/+2
| | | | | | | * 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
* Manual sync with develop (#95)Dana Robinson2020-11-171-2/+2
| | | | Brings all features from develop. Note that RELEASE.txt has not been updated (will be done in a future PR).
* Cleanup comments in tests, align comments better, update vfd testAllen Byrne2020-10-051-1/+1
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* Source formattedAllen Byrne2020-10-011-3024/+2984
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* Clean up private / package / static namespace issues (function naming, whichQuincey Koziol2020-08-221-6/+6
| | | | | | 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.
* Add HD prefix to testsAllen Byrne2019-08-151-604/+604
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* VOL FEATUREDana Robinson2018-10-101-16/+16
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* Normalize with vol_integration.Dana Robinson2018-05-291-31/+31
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* Cleanup API context function usage.Quincey Koziol2018-03-191-5/+11
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* Add API context interface and use it throughout the library.Quincey Koziol2018-03-151-937/+895
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* Rework of the POSIX file open permissions and macros to clean upDana Robinson2017-04-281-4/+4
| | | | | | HDopen() calls. Also fixed a minor const warning in the core VFD.
* Changed the Windows POSIX open() file permissions to be correctDana Robinson2017-04-281-4/+4
| | | | according to MSDN. Partial fix for HDFFV-9630.
* 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.
* [svn-r29081] - merge in the phdf5_metadata_opt/ branch with the collective ↵Mohamad Chaarawi2016-02-101-49/+49
| | | | | | | | metadata optimizations. - rename H5AC_dxpl_id to H5AC_ind_read_dxpl_id and update all usage in the library tested on bb-8 with parallel and serial.
* [svn-r29057] added dxpl type checking when debug mode is enabled ↵Mohamad Chaarawi2016-02-071-49/+49
| | | | | | (H5_DEBUG_BUILD) tested on bb-8 with Serial and Parallel, debug and production builds.
* [svn-r28843] Description:Quincey Koziol2016-01-081-1/+1
| | | | | | | | Bump number of records for random update test again. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28765] Description:Quincey Koziol2016-01-021-1/+1
| | | | | | | | | Bump the nunmber of v2 B-tree records for the random 4-level B-tree update test by another 25,000 records. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (Too minor to require h5committest)
* [svn-r28759] Description:Quincey Koziol2015-12-311-1/+1
| | | | | | | | Bump number of records for level 4 update test, to cut down on number of random failures. Tested on: None - trivial
* [svn-r28748] Description:Quincey Koziol2015-12-301-1/+1
| | | | | | | | | Bump number of records for level 4 B-tree test, so that it's more likely to always get to level 4. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28742] Description:Quincey Koziol2015-12-291-187/+2439
| | | | | | | | | Add 'update' operation to v2 B-trees, which will insert a new record, or modify an existing one, depending on if the record exists or not. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel (h5committest forthcoming)
* [svn-r28710] Description:Quincey Koziol2015-12-191-25/+157
| | | | | | | | | | | | Bring r28708 from revise_chunks branch: Fix earray, farray and btree2 use of incorrect file pointer when two files are opened and used to access the data structure. Misc. minor code cleanups as well. Tested on: MacOSX/64 10.11.2 (amazon) w/serial & parallel h5committest forthcoming
* [svn-r28138] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-10-201-1/+1
| | | | | | | | | | | | | | available Fix tests accordingly and fix misuse of hbool_t in various places Fix initialization of H5Pgcpl/ocpl structs in property decoding routines Tested on: Linux/32 (jam) Linux/64 (platypus) Linux/PPC64 (ostrich) MacOSX/64 10.11
* [svn-r27768] Description:Quincey Koziol2015-09-141-1/+1
| | | | | | | | | | | | | | | | | | | | | | Complete revamp of package initialization/shutdown mechanism in the library. Each package now has a single init/term routine. This new way should avoid packages being re-initialized during library shutdown and is also be _much_ more proactive about giving feedback for resource leaks internal to the library. Introduces a new "module" header file for packages in the library (e.g src/H5Fmodule.h) which sets up some necessary package configuration macros for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly modified version of this header, src/H5FDdrvr_module.h) Also cleaned up a bunch of resources leaks all across the library and tests, along with addressing many warnings, as I encountered them. Tested on: MacOSX/64 10.10.5 (amazon) w/serial & parallel Linux/64 3.10.x (kituo) w/serial & parallel Linux/64 2.6.x (ostrich) w/serial
* [svn-r27548] Revert r27545Jerome Soumagne2015-08-211-1/+1
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* [svn-r27545] Add first support for _Bool and make hbool_t a "real" _Bool if ↵Jerome Soumagne2015-08-211-1/+1
| | | | | | available Fix tests accordingly
* [svn-r20529] Purpose: Add testing for bug 1864Neil Fortner2011-04-151-0/+3
| | | | | | | | | Description: Added internal tesitng routines to traverse a file and verify that symbol table information is *always* cached, whenever possible. Added this check to the end of many tests to check all the test files, right before the call to h5_cleanup. Tested: jam, amani, heiwa (h5committest)
* [svn-r19005] Purpose:Mike McGreevy2010-06-151-0/+60
| | | | | | | | | | | | | | | | | | | | | | | Commit metadata tagging framework. Description: This check-in contains a new framework whose goal is to apply a tag value to each new entry in the metadata cache as it is created. This tag value is such that it relates each piece of metadata to the HDF5 object that it belongs to (dataset, group, et cetera). This changeset includes the framework that applies the tags as well as a suite of tests to verify correct tag application, though does not yet make use of the tag values to flush/evict individual objects. Please refer to the "flush/evict individual objects" RFC for further discussion of these changes. Tested: jam, amani, linew (h5committest) liberty, abe, blue print
* [svn-r17980] Description:Quincey Koziol2009-12-101-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring Coverity changes into the trunk: (also other minor cleanups) r17955: Fix Coverity item 24. Add missing error condition to H5AC_ext_config_2_int_config. r17956: Fix Coverity item 24. Improve error checking in H5A_compact_build_table_cb. r17957: Fix Coverity item 150. Fix warning in H5A_compact_build_table_cb. r17958: Fix Coverity item 117. Fix error handling in H5B_shared_new. r17959: Fix Coverity item 209. Added an assertion for leaf->shared in H5B2_cache_leaf_dest. r17960: Fix Coverity item 208. Added an assertion for internal->shared in H5B2_cache_internal_dest. r17961: Fix Coverity item 89. Reworked the code to avoid array overrun in H5C__autoadjust__ageout__insert_new_marker. r17962: Fix for coverity Resource_leak 195,203,204,205. r17963: Fix Coverity item 44. Prevented potential NULL dereference in H5D_btree_debug. r17964: Fix Coverity issues #197, 198 & 199: memory not being released. (Also clean up other resource leaks in nearby and/or similar code). r17965: Fix Coverity issue #151: release resources on error r17966: Fix Coverity issue #187: Remove leftover code remnant from prior bugfix which was causing resource leak of open files. r17967: Fixed Coverity issues # 193 & 194. Removed unnecessary memory allocation and added comparison of length of path parameter to the size of the destination buffer in h5import.h/h5import.c. r17968: Fix Coverity item 144. Fixed memory leak on error in H5D_chunk_copy. r17969: Fix for coverity Resource_leak #196. r17970: Coverity 167-173: Initialized pointer of buffers. In error handling, closed types and free memory. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17943] Description:Quincey Koziol2009-12-011-11/+11
| | | | | | | | | | | | | | | | | | | | | | Finish refactoring v2 B-trees so that they can have client callback context provided to the encode/decode callbacks. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17893] Descrption:Quincey Koziol2009-11-151-367/+367
| | | | | | | | | | | | | | | | | | | | | | | | | Remove old shim H5B2 routines from refactoring, rename new routines to old routine names and switch all users of the H5B2 interface back to the old routine names now that the switch to using the more current open -> <operation> -> pattern is used for all the H5B2 code. This is the final change before adding a context to the H5B2 client encode/decode callbacks. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.2 (amazon) in debug mode Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17848] Description:Quincey Koziol2009-11-071-2283/+2339
| | | | | | | | | | | | | | | | | | | | | | | | Further refactoring v2 B-trees so that they can get context to the encode/decode client callbacks: - Switch tests to using refactored routines Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17842] Description:Quincey Koziol2009-11-051-55/+55
| | | | | | | | | | | | | | | | | | | | | | | | | | Further refactor v2 B-tree code toward being able to pass context info down to encode/decode client callbacks: - Separate H5B2_create call to return H5B2_t structure - Make loading the v2 B-tree header pick up the client class from the ID stored in the file. Simplify some internal API calls as a result. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17785] Description:Quincey Koziol2009-10-291-127/+158
| | | | | | | | | | | | | | | | | | | | | | | | | | Further refactor v2 B-tree code to bring it closer to modern data structure designed in the library, mainly by introducing a H5B2_t type so that the v2 B-tree could be held open, but not require the B-tree header to be protected the whole time. A few other minor tweaks as well. Also, remove unused 'dirty' flag from fractal heap header. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17740] Description:Quincey Koziol2009-10-241-47/+50
| | | | | | | | | | | | | | | | | | | | | | | Refactor v2 B-tree code to take creation parameters to H5B2_create() as a struct (instead of individual arguments), call the client's class "cls" instead of "type" internally, and add client class name to client class struct. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r17657] Description:Quincey Koziol2009-10-151-43/+43
| | | | | | | | | | | | | | | | | | | | | | | Refactor the v2 B-tree code to use an open & close call internally, in preparation for making those part of the library private APIs for dealing with v2 B-trees. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode Mac OS X/32 10.6.1 (amazon) in debug mode Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode
* [svn-r15868] Description:Quincey Koziol2008-10-151-161/+224
| | | | | | | | | | | | | | | | | | | | | | | | | | | Correct a minor error in file free space allocation which was affecting the 'multi' VFD and preventing some tests from fully working with it. Wholesale revisitation of all the places where tests were disabled with various VFDs and remove or correct all these so that _only_ the tests which _really_ can't work with particular VFDs are skipped during a 'make check-vfd' test. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15825] Description:Quincey Koziol2008-10-091-97/+97
| | | | | | | | | | | | | | | | | | | | | | | | Fix various problems with a the core & sec2 VFDs. Improve the h5_get_file_size() routine to handle files created with VFDs that use multiple files. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15800] Description:Quincey Koziol2008-10-071-52/+30
| | | | | | | | | | | | | | | | | | | | | | | Bring file free space branch changes through r15795 into trunk, which includes a fair bit of code cleanup & rearrangement along with a couple of bug fixes also. Tested on: Mac OS X/32 10.5.5 (amazon) in debug mode Mac OS X/32 10.5.5 (amazon) w/C++ & FORTRAN, w/threadsafe, in production mode FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (smirom) w/Intel compilers w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, in production mode Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN, in production mode Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
* [svn-r15628] Description:Quincey Koziol2008-09-161-2/+2
| | | | | | | | | | | | | Remove trailing whitespace from C/C++ source files, with the following script: foreach f (*.[ch] *.cpp) sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f end Tested on: Mac OS X/32 10.5.5 (amazon) No need for h5committest, just whitespace changes...
* [svn-r13871] Description:Quincey Koziol2007-06-151-1/+1
| | | | | | | | | | | | | Fix problems with 'check-vfd' target, that were [mostly] introduced with the recent "unique, but sharable" ISOHM optimization. The problems were mostly with using the 'core' VFD, so the H5Pset_fapl_core() API call was changed to re-open existing files (therefore operating more list the sec2, stdio, etc. VFDs). This allows many more of the tests to run using the 'core' VFD, so those were enabled also. Tested on: Linux/64 2.6 (chicago2) w/check-vfd
* [svn-r13253] Updated all C and C++ style source code files with the THG ↵Albert Cheng2007-02-071-2/+3
| | | | | | | | | copyright notice. Tested platform: Kagiso only since it is only a comment block change. If it works in one machine, it should work in all, I hope. Still need to check the parallel build on copper.
* [svn-r12949] Description:Quincey Koziol2006-11-201-2/+2
| | | | | | | | | | | | | | | | Finish implementation of H5Literate() [still needs real tests] Clean up datatype macro warnings a bit more. Unify iterator callback macros and put up in public header file, with the iterator directions. Tested on: Mac OS X/32 10.4.8 (amazon) FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12915] Description:Quincey Koziol2006-11-151-110/+179
| | | | | | | | | | Finish adding "delete by index" feature to v2 B-trees. Tested on: FreeBSD/32 4.11 (sleipnir) Linux/32 2.4 (heping) Linux/64 2.4 (mir) AIX/32 5.? (copper)
* [svn-r12914] Description:Quincey Koziol2006-11-141-9/+178
| | | | | | | | Checkpoint partially working v2 B-tree delete by index code (ifdef'ed out) for further work. Tested on: Linux/32 2.6 (chicago)
* [svn-r12877] Description:Quincey Koziol2006-11-071-2/+2
| | | | | | | Clean up more compiler warnings. Tested on: Linux/64 2.6 (chicago2)
* [svn-r12873] Decription:Quincey Koziol2006-11-071-20/+59
| | | | | | | | Add support for reverse index lookup to v2 B-trees (needed for reverse index lookup of links in groups) Tested on: Linux/64 2.6 (chicago2)
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