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* Reverts PR 906 and 907 due to binary compatibility issues (#918)Dana Robinson2021-08-171-2/+1
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* Merge2 839 issue PRs to hdf5 1 12 (#906)Larry Knox2021-08-131-1/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Use internal version of H5Eprint2 to avoid possible stack overflow (#661) * Reduces overly-pedantic casting in the public headers (#644) * Committing clang-format changes * Fixes overly pedantic casting in public headers Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes (#699) * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes pre-C99 build and header cruft (#700) * Committing clang-format changes * Removes pre-C99 build and header cruft * Assumes ANSI C headers exist * Assumes stdbool.h, stdint.h, and inttypes.h are present * Assumes the C++ compiler can handle stdint.h * Removes all work-arounds for missing functionality, especially stdbool.h * Formats source Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up type size checks in configure.ac (#702) * Removes some DEC Alpha cruft from H5detect and H5private.h (#708) * Updates bin/trace script to correctly wrap H5TRACE macros near clang-format column limit (#719) * Removes clang-format comments from H5O.c call * Fixes bin/trace to correctly wrap lines near the clang-format limit * Removed unused variable from bin/trace * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ (#726) * Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ Allows C++ library to be built on older versions of gcc. * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Moves H5PacketTable default ctor inside source file (#731) * Remove private H5_GCC_DIAG_OFF/ON from standalone program (#734) * Organize and align compiler flags (#741) * 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 * Disable long double tests for now * HDFFV-11228 remove arbitrary CMake warning groups. * Make each flag a string * Some Javadoc warning fixes * Updated javadoc fixes * # WARNING: head commit changed in the meantime HDFFV-11229 Fix long double usage in tools and java Changed h5dump and h5ls to just print 128-bit for long double type. Added test and file for dataset and attributes with all three float types. * Committing clang-format changes * HDFFV-11229 Add release note * HDFFV-11229 windows testfile needed * fix typo * Remove non supported message text * HDFFV-11229 - change ldouble test to check both native and general * HDFFV-11229 add second file compare * HDFFV-11229 fix reference file * HDFFV-11229 autotools check two refs * HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output * Committing clang-format changes * Update release note * Update attribute type of ref file * Change source of ninja for macs * try port instead of brew * Recommended is to use brew. * Undo non long double changes * remove unneeded file * Fix perl and doxygen CMake code * Add "option" command for clang options * Rework CMake add_custom to use the BYPRODUCTS argument * Add stamp files to BYPRODUCTS * Only one copy of file exists * Fix custom cmmand depends targets * Fix fortran custom command DEPENDS * Add LD_LIBRARY_PATH to tests * Add custom target for DEPENDS * Add h5detect conditionaly to generated target DEPENDS * Correct DEPENDS targets * Parallel builds need the mpi compiler for pkgconfig scripts. * install only if MPI build * Fortran target depends * Remove incorrect source attribute * doxygen adjustments * doxygen build updates * Correct version * Correct function version - function has been merged to 1.12 * Correct version string for map functions * Cleanup warnings for tools debug builds * TRILAB-227 - fix indexing for h5diff selections * Correct location of pos to index function call * TRILAB-227 Enable test * Quote subset args * Use MATCHES because of AppleClang * if blocks needed for build modes * Update list of DT platforms * VS2019 correctly displays float values * revert VS2019 change * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Java reference functions updated enabled fortran in cmake gcc action yaml file java reference test changed to correctly test refs jni reference functions that create ids changed to use jni id logging * Correct BYPRODUCTS argument * Correct more genereated files BYPRODUCTS * BYPRODUCTS must have unique locations * Fix typo * Fix fortran configure checks * Rework H5_PAC_C_MAX_REAL_PRECISION setting logic * Add note about fortran configure change * Adds a quick for for some egregious chunk_info badness (#722) * Fixes issue with ccmake that prevents building Fortran (#723) ccmake runs iteratively, and the check_fortran_source_runs macros were clobbering a single output file that did not get updated on further configure iterations * Fix conflicts with merge * Move MAX_PRECISION back to HDF5UseFortran.cmake * Use STREQUAL to test macro argument * Move C language test to ConfigureChecks from HDF5UseFortran * MAX_PRECISION defines must be defined * Organize flags and align autotools and cmake * Fix comment in no-error-general warnings files. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> * Fixes C++ warnings when passing hsize_t values to printf in test code (#745) * Normalization of H5_nanosleep() with VFD SWMR branch (#746) * Normalization of H5_nanosleep() with VFD SWMR branch * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Correct missing variable declaration. * Fixes some H5SL include statements (#758) * Fixes non-C99 format strings in tarray test code (#766) * Cleans up some POSIX header bits in H5private.h (#783) * Further simplifies Autotools type size checks (#789) Also fixes an issue where clock_gettime and difftime are not detected due to earlier simplifications of this code. * Normalization of CMake H5pubconf.h with Autotools (#791) Mostly just moving things around and changing the comments to keep the delta small. The only symbol change is that for curl/curl.h which I changed to H5_HAVE_CURL_CURL_H to match the Autotools. This symbol is not used in the library and is just an artifact of the checks. Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
* Hdf5 1 12 fix warnings files (#755)Allen Byrne2021-06-151-21/+57
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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 * Rework CMake add_custom to use the BYPRODUCTS argument * Revert CMake configure checks for round defines * With VS 2015 minimum strdup is supported * Doxygen comments merged from develop * doxygen build updates * Correct version string for map functions * TRILAB-227 and tools debug merge from develop * TRILAB-227 Enable test * Quote subset args * Use MATCHES in compiler id compare, merge from dev * Revert test enable * Add file to list * doxygen version errors * if blocks needed for build modes * Update list of test platforms * Issue #669 remove version from pkgcfg filename * remove version from h5cc script * Merge CMake and java refs from dev * Reworked CMake Fortran configure macros to allow multiple runs. * Fix CMake issue with tests not comparing test argument properly. * MAX_PRECISION defines must be defined with a value * Fix warnings files and -std * remove std for c++11 * Replace file Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Update URL in source file Copyright headers for web copy of COPYINGLarry Knox2021-02-201-1/+1
| | | | file - files not in src or test.
* TRILAB-192 - merge changes from developAllen Byrne2020-04-071-11/+21
| | | | Single source, config files, for warnings for both autotools and CMake. Update CMake libraries, tools, tests to use correct flags.
* Create common warnings for build systemsAllen Byrne2020-01-201-2/+17
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* 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.
* Updated the icc flags (C flags only).derobins2016-12-021-10/+10
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* [svn-r29142] Updated the Intel files in config to use the new NO_SYMBOLS flagsDana Robinson2016-02-171-5/+2
| | | | | and modified the failsafe configure flags in ibm-aix to use the new scheme.
* [svn-r29023] Fixed typos in symbols flags that prevented using -g, etc.Dana Robinson2016-02-011-2/+2
| | | | | Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial autotools
* [svn-r28996] Autotools configure updates to allow separation of build type, ↵Dana Robinson2016-01-271-5/+15
| | | | | | | | | | | | | | debug symbols, asserts, profiling, and optimization. Also much refactoring, improved help, and --enable-<foo> options will now emit errors on nonsense (e.g.: --enable-foo="asdfasdf"). The libhdf5.settings.in file was also reformatted. Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1 serial and parallel autotools w/ various options
* [svn-r24997] Added compiler versions for mpich to settings file and ↵Larry Knox2014-04-091-5/+6
| | | | | | | | | | | | | configure summary. For make installcheck, compile and run installed examples using the installed scripts. They were being compiled but not run. Add Fortran2003 examples to the run-ex-fortran script when fortran2003 is enabled. Set flag to -O3 in production mode for Intel compilers other than those with specified other settings. Gentoo patches: Remove unnecessary setting of LD_LIBRARY_PATH from configure. Prevent potential array subscript out of bounds error in perform/pio_engine.c and sio_engine.c. Tested with h5committest on jam, koala, ostrich and platypus, on emu and kite, and parallel tests on jam, koala and platypus with mpich built with gnu 4.8.2 and with intel compilers.
* [svn-r22020] Fix for HDFFV-7878.Larry Knox2012-03-031-1/+1
| | | | | | | gnu-flags Don't add gcc flags for intel compiler even though its version display includes "gcc". intel-flags Extend intel version to include icc-12*.
* [svn-r19566] Maintenance: Added -O3 to be used with the C Intel v 11 ↵Elena Pourmal2010-10-081-7/+7
| | | | | | | | | compilers; set default to -O for all unknown versions of the C Intel compilers. Modified apple config file to display Intel compiler information. Updated RELEASE.txt notes accordingly. Platfroms tested: jam, amani and dubna (Mac 64-bit) with Intel C, Fortran and C++ compilers.
* [svn-r19312] Description:Quincey Koziol2010-08-261-1/+1
| | | | | | | | | Bump optimization down for Intel 10.* compilers, due to apparent bad cod e generation. Tested on: Linux/64 2.6 (cobalt) w/debug & production & Intel 11.1 compilers (h5committest not appropriate)
* [svn-r13939] Problem: High level of optimazation causes test failures when ↵Elena Pourmal2007-07-051-0/+3
| | | | | | | | | | library is built with Intel 10.0 compiler. Solution: Use -O1 optimization flag with Intel 10.0 Platforms tested: abe and kagiso with Intel 10.0 and Intel 9.1 compilers; no committest is needed since this is a compiler specific change.
* [svn-r13312] Updated copyright notice.Albert Cheng2007-02-141-2/+3
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* [svn-r12579] Description:Elena Pourmal2006-08-151-1/+5
| | | | | | | | | | | -O3 flag causes compilation problems on most of the platforms with Intel compiler. The problem exists in all vesrions of icc compiler up to the newest 9.1 Solution: Use less agressive default setting O2 to avoid headache Platforms tested: Linux 2.6 ia64 at UCAR (hal), cobalt (NCSA)
* [svn-r12301] Purpose:James Laird2006-04-251-2/+2
| | | | | | | | | | | | | | H5_CFLAGS change Description: Converted a few platforms to use H5_CFLAGS to "test the waters" Solution: Modified a few config/* files to use H5_CFLAGS for non-essential flags. Platforms tested: mir, heping
* [svn-r11614] Frank Baker2005-10-281-1/+1
| | | | | | | Description: Correct typo in copyright notice. Platforms tested: Ran hdf5/bin/chkcopyright without errors.
* [svn-r11592] Frank Baker2005-10-211-0/+13
| | | | | | | | Description: Add source code copyright notice; comment symbols vary by type of file. Platforms tested: No changes that should cause any problems. Nonetheless, the tree will be checked out fresh and tests run immediately post-commit.
* [svn-r9691] Description:Albert Cheng2004-12-181-3/+3
| | | | | | | | | | mpich 1.2.6 does not like the tweaking of using -O2 flag. Comment out the Tweaking since it caused problems to mpich1.2.6. Need to investigate the reasons and effects to tweak. Platforms tested: Tested in heping using mpich 1.2.6 and in eirene uisng mpich 1.2.6.
* [svn-r9631] Purpose:Albert Cheng2004-12-071-2/+3
| | | | | | | | | | | | | | Improvement Description: Added strip option to PROD_CFLAGS to remove symbols for smaller production file size. Solution: Platforms tested: Misc. update:
* [svn-r9629] Purpose:Albert Cheng2004-12-071-3/+3
| | | | | | | | | | | | | | Bug fix. Description: Last commit would impose $arch even if user has provided his own $CFLAGS. Fixed it. Removed the wording of gnu-flags inherited from the copy. Platforms tested: Tested in tg-ncsa. Misc. update:
* [svn-r9625] Purpose:Quincey Koziol2004-12-071-7/+1
| | | | | | | | | | Code cleanup Description: Clean/fix up compiler flags to be more consistent after recent changes. Platforms tested: None - eyeballed - very minor
* [svn-r9623] Purpose:Albert Cheng2004-12-061-2/+3
| | | | | | | | | | | | Bug fix. Description: Restored correct setting of compilers (-Wall etc for debug flags only, c99 by default,...) that were wiped out by the commits before. Platforms tested: Tested in TG-NCSA, both production and development mode. (Still need to figure out the proper flag to use for Profile.)
* [svn-r9619] Purpose:Albert Cheng2004-12-061-9/+12
| | | | | | | | | | Bug fix. Description: v8.0 -O3 infinite loops when compiling test/tselect.c. Use -O2. Platforms tested: Only tested in TG-NCSA, use both default and --disable-production options.
* [svn-r9611] Purpose:Quincey Koziol2004-12-031-1/+1
| | | | | | | | | | | | | Bug fix Description: Correct typo in ia64 configure script. Update intel compiler detection to handle Itanium versions of compilers Platforms tested: Teragrid machine (tg-login) w/icc 7.1 & 8.x Linux 2.4 (verbena) w/icc
* [svn-r9515] Purpose: Bug fixRaymond Lu2004-11-081-0/+13
| | | | | | | | Description: For Intel 8.1 compiler, C99 standard has to be enabled to define macro ULLONG_MAX in its own header file limits.h. Solution: Add flag -std=c99 to Intel compiler if the version is 8.1. Platforms tested: Tested v1.6 because this is a very simple change.
* [svn-r9491] Purpose:Quincey Koziol2004-10-311-1/+1
| | | | | | | | | | | Bug fix Description: "Teach" the configure scripts about Intel 7.1 compilers, which don't have _quite_ the same compiler flags Platforms tested: Linux 2.4 (eirene)
* [svn-r9407] Purpose:Quincey Koziol2004-10-121-5/+0
| | | | | | | | | | | | | | | | | | | | Code cleanup/bug fix Description: Remove the undocumented "$NOFP" shell variable which would allow production builds without removing the stack frame. This was cascading between C and FORTRAN builds and causing problems. Solution: Hard-code removing the stack frame for now. Users would have needed to read the configure scripts anyway, so there's not really much benefit to the extra knob. Users who need this functionality (production builds with stack frames) are debugging probably, so they will need to modify the script and build their own version of the library now. Platforms tested: Linux 2.4 (verbena) Too minor to require h5committest
* [svn-r9385] *** empty log message ***Quincey Koziol2004-10-091-0/+86
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