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* VFD SWMR: Normalization with develop (#1270)Dana Robinson2021-12-081-4/+0
| | | Brings many October-November changes from develop
* VFD SWMR: Sync with develop (#711)Dana Robinson2021-06-011-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings CMake updates from develop * Brings reduction in pedantic casts from develop * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Formatted source * Bring over some VOL registration changes * VOL cleanup * H5VL_request_status_t substitutions * H5F.c cleanup * Minor API tweaks from develop * Moves H5G package init/teardown to H5Gint.c * H5G cleanup * H5M cleanup * H5SM cleanup * H5T cleanup * H5R cleanup * H5Lpublic.h cleanup * H5L cleanup * H5O cleanup * H5A, H5CS, and H5AC cleanup * Moved H5A init/teardown code to H5Aint.c * Moves H5D I/O functions to H5D.c * H5D cleanup * Misc minor cleanup * H5P close cleanup * H5Tpublic.h cleanup * Fixes err_compat test * H5PLpublic.h cleanup * Updates H5Ppublic.h * H5Fpublic.h updates * H5A.c cleanup * Brings over H5Aexists and related changes * Brings CMake shell testing changes from develop * Close callback changes * H5R and H5Tcommit normalization * err_compat test works now * H5O tweaks * Updates VOL registration code * Brings over H5VL_create_object * H5Tconv.c reformatting * H5T.c tweaks * Brings datatype and reference updates from develop * Brings VOL plugin loading changes from develop * Brings event sets from develop * Brings async functions over * Tools changes * Brings over many tools changes from develop * Brings VOL flags from develop * Fixes h5dump double/float tests * Updates h5repack tests * Brings h5diff test changes from develop * Last h5dump changes * Brings test changes from develop * Committing clang-format changes * Tidied h5_testing() * Brings chunk iteration code + misc from develop * Updates vds test * Enables external link parallel test * Brings updated property lists from develop * H5G changes from develop * H5MF cleanup * Brings vfd_swmr test back into CMake * Updates threadsafe test * Updates plist test * Brings recent changes from develop * Require a C++11 compiler to build the C++ wrappers (#693) * Committing clang-format changes * Requires a C++11 compiler to build the C++ wrappers 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) * Removes pre-C99 build and header cruft (#700) * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Updates release documents * Brings parallel changes from develop * Adds a VFD/parallel check program for the VFD SWMR shell test * Updates MANIFEST * Disable building VFD SWMR acceptance tests on CMake * Removes err.h from genall5.c * Partial cleanup of H5Cpkg.h * Fixes printf specifiers in H5Cdbg.c * Java and fortran cmake changes (#694) * 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 Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes alternative function enter/leave macro scheme (#678) * Committing clang-format changes * Converted BEGIN_FUNC, etc. macros to FUNC_ENTER * Rips out the BEGIN_FUNC, etc. macros * Removes 'end if', etc. comments from H5HL package * Committing clang-format changes * Fixes an H5EA iterate issue * Fixes an issue in the H5FA iterator code * Further cleanup in bin/trace after macro removal * Iterator changes in H5EA and H5FA Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Split H5L.c internal code to H5Lint.c (#691) * Committing clang-format changes * Splits internal parts of H5L.c to H5Lint.c Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Clean up type size checks in configure.ac (#702) * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Much normalization with develop (#701)Dana Robinson2021-05-281-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * Brings CMake updates from develop * Brings reduction in pedantic casts from develop * Purges UFAIL from the library (#637) * Committing clang-format changes * Purges UFAIL from the library * H5HL_insert change requested in PR Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Removes gratuitous (double)x.yF casts (#632) * Committing clang-format changes * Removes gratuitous (double)x.yF casts * Committing clang-format changes Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Committing clang-format changes * Cleans up a const warning left over from previous constification (#633) * Committing clang-format changes * Adds consts to a few global variables * Cleans up a const warning left over from previous constification Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Formatted source * Bring over some VOL registration changes * VOL cleanup * H5VL_request_status_t substitutions * H5F.c cleanup * Minor API tweaks from develop * Moves H5G package init/teardown to H5Gint.c * H5G cleanup * H5M cleanup * H5SM cleanup * H5T cleanup * H5R cleanup * H5Lpublic.h cleanup * H5L cleanup * H5O cleanup * H5A, H5CS, and H5AC cleanup * Moved H5A init/teardown code to H5Aint.c * Moves H5D I/O functions to H5D.c * H5D cleanup * Misc minor cleanup * H5P close cleanup * H5Tpublic.h cleanup * Fixes err_compat test * H5PLpublic.h cleanup * Updates H5Ppublic.h * H5Fpublic.h updates * H5A.c cleanup * Brings over H5Aexists and related changes * Brings CMake shell testing changes from develop * Close callback changes * H5R and H5Tcommit normalization * err_compat test works now * H5O tweaks * Updates VOL registration code * Brings over H5VL_create_object * H5Tconv.c reformatting * H5T.c tweaks * Brings datatype and reference updates from develop * Brings VOL plugin loading changes from develop * Brings event sets from develop * Brings async functions over * Tools changes * Brings over many tools changes from develop * Brings VOL flags from develop * Fixes h5dump double/float tests * Updates h5repack tests * Brings h5diff test changes from develop * Last h5dump changes * Brings test changes from develop * Committing clang-format changes * Tidied h5_testing() * Brings chunk iteration code + misc from develop * Updates vds test * Enables external link parallel test * Brings updated property lists from develop * H5G changes from develop * H5MF cleanup * Brings vfd_swmr test back into CMake * Updates threadsafe test * Updates plist test * Brings recent changes from develop Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Many small changes from develop. Should allows running VFD SWMRDana Robinson2021-05-031-7/+11
| | | | tests from CMake.
* Update top-level COPYING file and remove COPYING files from subdirectories ↵Dana Robinson2021-05-031-13/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (#561) * Modify temporary rpath for testing in java example scripts. * Update URL in source file Copyright headers for web copy of COPYING (license) file. * Add release_docs/code-conventions.md file. * Add script to test h5py. * Fix script error. * Add file h5pytest.yml. * Test declaration of counter variables in for loops. * Committing clang-format changes * Committing clang-format changes * Added [] to line 126 of H5LTanalyze.l. Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly. * Revert "Added [] to line 126 of H5LTanalyze.l." This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266. * Revert extra commits to match canonical develop. * Update top-level COPYING file and remove COPYING files from subdirectories. * Remove subdirectory COPYING files from MANIFEST. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Brings many CMake changes from developDana Robinson2021-04-081-5/+64
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* Normalized high-level library with developDana Robinson2021-04-0510-86/+87
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* Updates license url and history docsDana Robinson2021-03-2526-28/+28
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* Formats the source and updates the gcc warning pragmasDana Robinson2021-03-257-2265/+1870
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* HDFFV-11116 Add option for install location of Fortran MOD filesAllen Byrne2020-07-091-1/+20
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* Merge pull request #2610 in HDFFV/hdf5 from ↵David Young2020-06-161-2/+2
|\ | | | | | | | | | | | | ~DYOUNG/werror:hdffv-11060-examples-destdir to develop * commit '4cebd8aa6c965fe2e5dde6dbff36b2be3ca58bf1': Make examples installation respect DESTDIR. Fixes HDFFV-11060.
| * Make examples installation respect DESTDIR. FixesDavid Young2020-05-261-2/+2
| | | | | | | | HDFFV-11060.
* | Removed trailing space from Fortran files.Dana Robinson2020-05-268-252/+252
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* Trim trailing whitespaceQuincey Koziol2020-04-208-72/+72
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* Remove overzealous additionsAllen Byrne2020-04-052-3/+1
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* Flag construction must be after compiler detectionAllen Byrne2020-04-053-59/+27
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* TRILAB-192 add c++ and fortran warnings build systems one fileAllen Byrne2020-04-053-43/+24
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* TRILAB-142 Change minimum CMake version to 3.12Allen Byrne2020-02-214-4/+4
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* HDFFV-11012 - add correct fortran include path propertiesAllen Byrne2020-02-041-2/+2
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* HDFFV-11001 fix if blockAllen Byrne2020-01-151-3/+2
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* HDFFV-11001 need to qualify all by parallel or serial typesAllen Byrne2020-01-152-2/+2
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* HDFFV-11001 Add fine control over testingAllen Byrne2020-01-153-4/+7
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* Let us override the examples directory using --with-examplesdir=DIR.David Young2019-10-032-3/+3
| | | | | | | | | This is handy for NetBSD where HDF5 examples are installed by convention in $prefix/share/examples/hdf5/ rather than in ${prefix}/share/hdf5_examples/, which is the HDF5 default. Place hdf5_examples/ under ${datarootdir} which on most systems will be ${prefix}/share/, anyway.
* Under the examples directories, always find the installed HDF5David Young2019-10-031-1/+1
| | | | | | | | | | executables and scripts using @prefix@ instead of a relative path, because the number of ../ in the relative path will be different on NetBSD than on other systems. Examples on NetBSD are installed at ${prefix}/share/examples/hdf5/ instead of at ${prefix}/share/hdf5_examples/, by convention. It may be the same on other BSDs, I'm not sure.
* Merge pull request #1826 in HDFFV/hdf5 from ↵Dana Robinson2019-08-013-4/+3
|\ | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:develop_minor_pr to develop * commit '4227b8948d7091205b4f8dc1271d7dcae01bb0fb': Reverts the removal of config/conclude_fc.am while keeping the changes to config/gnu-fflags. Fixed a couple of typos.
| * Reverts the removal of config/conclude_fc.am while keepingDana Robinson2019-08-013-4/+3
| | | | | | | | the changes to config/gnu-fflags.
* | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2019-07-293-3/+4
|\ \ | |/ | | | | | | | | | | | | * commit 'd169391529f253a9903b8e6cacf38c59ceefab07': Parallel Fortran tests now use the MPI module instead of including mpif.h. First stab at gfortran versions. Tested on gfortran 7-9 so far. Moved the -std=f2008 option to gfortran 9 for now. Updated gfortran options. * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
| * Merge pull request #1808 in HDFFV/hdf5 from ↵Dana Robinson2019-07-293-3/+4
| |\ | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:gnu-flags-work to develop * commit '7d291d059da6287f769951c4854c566da0b93ce8': Parallel Fortran tests now use the MPI module instead of including mpif.h. First stab at gfortran versions. Tested on gfortran 7-9 so far. Moved the -std=f2008 option to gfortran 9 for now. Updated gfortran options. * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
| | * Updated gfortran options.Dana Robinson2019-07-173-3/+4
| | | | | | | | | | | | | | | | | | | | | | | | * Removed conclude_fc.am, which was causing verbose builds. Need to investigate more, though. * Added gfortran 9 warnings and flags. This will need to be separated into other version blocks based on when the options first appeared. * The standard is now explicitly set at 2008.
* | | HDFFV-10529 Update CMake tests to use test fixturesAllen Byrne2019-07-232-13/+18
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* | HDFFV-10845 use of TARGETFILE disables auto emulatorAllen Byrne2019-07-172-2/+4
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* | HDFFV-10845 add_custom_command requires emulatorAllen Byrne2019-07-171-2/+2
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* HDFFV-10581 fix locations for static pdb filesAllen Byrne2019-07-081-2/+2
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* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-213-4/+4
| | | | clean up warnings.
* HDFFV-10805 Add option to only build shared targetsAllen Byrne2019-06-184-187/+166
| | | | | HDFFV-10805 Add ONLY_SHARED_LIBS option and prefer shared over static HDFFV-10803 Update FindSZIP.cmake find module Remove unneeded modules and update java modules
* Add options to enable or disable building tools and tests. The defaultLarry Knox2019-06-061-1/+7
| | | | is enabled for each.
* HDFFV-10738 Wrong INTENT for H5LTread_dataset_double_fM. Scot Breitenfeld2019-03-254-31/+31
| | | | | | Fixed. Also fixed INTENT issues for H5DS, H5IM and H5TB when reading or getting.
* HDFFV-10703 Update CMake commands to latest standardAllen Byrne2019-02-152-4/+4
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* Remove install-exec-hook from hl/fortran/Makefile.am.Larry Knox2019-01-072-14/+4
| | | | Add check for existing links in hl/fortran/src/Makefile.am.
* Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Larry Knox2019-01-051-0/+14
|\ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '0e34f0feaaeb6d2286f87f695f25fae45c070a42': (26 commits) HDFFV-10664 update reference file HDFFV-10664 update reference files HDFFV-10664 add missing function and check for restriction Remove "bad" statements at end of TEST_ERROR. Formerly arguments to FAIL_PUTS_ERROR Add RELEASE.txt entry for HDFFV-10596. Add semicolon at end of TEST_ERROR() invocation for consistency. Uninstall should remove the libhdf5_hl_fortran links. Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran in Makefile.am to match cmake install and the name pattern for other hl lib files. Change FAIL_PUTS_ERROR to TEST_ERROR. Cleaned up the parallel flush test and set t_pflush1 to always fail. Also set CMake to handle this. Update calls: H5Dcreate to H5Dcreate2, H5Acreate to H5Acreate2. Removed a comment. Fix comment Align H5Lcreate_ud behavior with documentation for NULL udata pointer Update toolchain comment Use c99 standard cmake variable Add PGI toolchain Correction based on code review. HDFFV-10664 add check for state before set call HDFFV-10546 refactor variable name ...
| * Uninstall should remove the libhdf5_hl_fortran links.Larry Knox2019-01-041-0/+1
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| * Add symlinks named libhdf5_hl_fortran* to libhdf5hl_fortran inLarry Knox2019-01-041-0/+13
| | | | | | | | | | | | | | Makefile.am to match cmake install and the name pattern for other hl lib files. Add missing ';' to test/dsets.c line 13075.
* | Add libhdf5_hl_fortran symlinks for libhdf5hl_fortran files.Larry Knox2018-12-311-0/+12
|/ | | | | Set ctest*.lsf.in.cmake scripts for sierra. Correct src/CMakelists.txt syntax error.
* HDFFV-10537: Remove installation of Fortran test mod filesM. Scot Breitenfeld2018-11-091-12/+0
| | | | Removed from autools install, cmake does not have this issue.
* Change prefix in example scripts to relative path to bin. This was doneLarry Knox2018-08-231-1/+1
| | | | | for 1.8, and works wherever installed without the need to replace the original prefix.
* Add mpi include folders for fortran C objectsAllen Byrne2018-06-061-2/+2
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* Remove link flag from compile commandAllen Byrne2018-05-222-2/+0
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* Add missing module_dir propertyAllen Byrne2018-05-092-0/+2
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* Correct command usageAllen Byrne2018-05-073-5/+5
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* Remove APPENDAllen Byrne2018-05-033-6/+6
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