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* Not every system has perl installed in /usr/bin/, so change the shebangDavid Young2019-12-1912-12/+26
| | | | | | | | | | | | | | | (#!) line to `/usr/bin/env perl` to locate perl on the PATH. Everything after the first pathname in the shebang line is treated as a single argument to the command interpreter (/usr/bin/env "perl -w"), and there is not ordinarily any such program as "perl -w". So if the old shebang line used an option such as `-w`, add a `use warnings;` statement to the script---note that the semantics change slightly. `bin/destdep` uses a trick to pass `-p` to `/usr/bin/env perl`. It couldn't hurt to use the same trick to pass `-w`. With these changes, `sh autogen.sh` runs on NetBSD. It ought to still work on every other system HDF5 supports, too.
* Revert "Merge branch 'hdf5_1_12' of ↵Jerome Soumagne2019-12-0912-28/+14
| | | | | | | https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into hdf5_1_12" This reverts commit 9f9336a5bd541752f472bab4c93da8de89f862cd, reversing changes made to 437a1919e7ba60fe75a33a466d264183a0255319.
* Merged HDFFV-10929_2GB_testing to hdf5_1_12Richard Warren2019-12-0612-14/+28
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* Add new H5R API that abstracts object, region and attribute reference typesJerome Soumagne2019-10-081-1/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Also support references to external files Add new H5T_REF type and type conversion routines Support conversion from H5T_REF_OBJ/DSET_REG to H5T_REF Add H5Treclaim() API to reclaim memory of vlen/reference types Deprecate H5Dvlen_reclaim() Fix H5T_vlen_reclaim() and H5T_reclaim() to use private callback Add H5T_ref_reclaim() Move previous H5R APIs to H5Rdeprec.c Clean up H5Ocopy Separate H5O_copy_expand_ref() to H5Ocopy_ref() Add support for copying new reference types Clean up deprecated routines to go through VOL and same code path Fix return codes in existing trefer.c test Rename trefer.c to trefer_deprec.c trefer.c is for new references Add performance test for trefer Add additional obj_copy_ref test Make use of tokens and blobs to store references Skip blob encoding for object references Start adding new reference examples
* Fix H5VL_blob_get to return size of blobJerome Soumagne2019-10-081-0/+1
| | | | | | | | | | | | | | | | | | | | Fix const in blob API Add H5HG_HEAP_ID_SIZE macro to return native blob size Add maximum size for blobs Fix blob API callbacks to pass VOL file object Add public wrappers for blob VOL API Implement passthrough blob callbacks Update H5Tvlen after callback changes Update trace information for H5VL blob routines Fix public header inclusion in native and passthru headers
* Cleanup whitespace and comments compared to developAllen Byrne2019-10-021-3/+3
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* Added the map (H5M) APIDana Robinson2019-08-131-0/+1
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* Escape { and } in regex as required by sh in updated cori.nersc.gov.Larry Knox2019-08-071-3/+3
| | | | Tested change on jam, jelly, emu, ostrich and osx1011test.
* Squashed commit of the following:Larry Knox2019-07-251-0/+2
| | | | | | | | | | | Merge changes from update_merged_S3_HDFS branch into develop. commit d5034315aea88629929ac0c9c59ebfafd5f21a31 Merge: 9c48823 d3fdcd8 Author: Larry Knox <lrknox@hdfgroup.org> Date: Thu Jul 25 08:24:53 2019 -0500 Merge branch 'develop' into update_merged_S3_HDFS
* Updates to warnhist script, along with a few cleanups, and add some commentsQuincey Koziol2019-07-101-7/+18
| | | | to warning cleanups that are a bit obscure.
* Cleaned up code that genericizes warning output, and add "-u" option toQuincey Koziol2019-07-051-269/+65
| | | | | leave unique types in warnings (i.e. don't genericize output). Also fixed the '-S' option to work correctly.
* Add support for GCC9, update warnhist script, and clean up warnings.Quincey Koziol2019-07-032-63/+218
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* Updated configure & CMake compiler flags for GCC 8.x, along with correspondingQuincey Koziol2019-06-281-22/+57
| | | | | changes to warnhist script (and some extra improvements for condensing C++ and Java warnings), and fixed a bunch of warnings.
* Add support for GCC 7.x warnings, update warnhist script to account for them,Quincey Koziol2019-06-211-4/+34
| | | | clean up warnings.
* Added a warning summary script for gcc to binDana Robinson2019-06-171-0/+484
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* Moved h5cc.in and h5redeploy.in from tools/misc to bin directory. TheyLarry Knox2019-06-143-0/+672
| | | | | | | should always be built and installed whether tools are enabled or disabled. Also added Makefile.am to bin to build h5redeploy and to install and uninstall them. h5cc is created from h5cc.in by configure.
* updated -E optionM. Scot Breitenfeld2019-05-102-2/+2
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* remove -M optionM. Scot Breitenfeld2019-05-109-10/+10
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* added -M HPC to ctest commandM. Scot Breitenfeld2019-05-1013-76/+10
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* Adding cross-compilation for theta (ANL) and qsub (COBALT) batch controls.M. Scot Breitenfeld2019-05-091-0/+21
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* Putting ctest command in variable CMD did not work for skipping failingLarry Knox2019-05-062-8/+4
| | | | tests.
* Renamed the autotools check-vol target to check-passthrough-vol.Dana Robinson2019-04-111-11/+14
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* Merge branch 'develop' into c_stdlib_posix_call_cleanupDana Robinson2019-02-1913-13/+224
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| * Remove ' ' (typo).Larry Knox2019-02-171-1/+1
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| * Refactor mpi test namesAllen Byrne2019-02-1110-10/+10
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| * Refactor parallel test namesAllen Byrne2019-02-1110-10/+10
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| * Add LOCAL_BATCH_SCRIPT_ARG variable for submitting account informationLarry Knox2019-02-042-2/+2
| | | | | | | | and other batch command variations with ctest command.
| * Correct H5DIFF to PH5DIFF in *ctestS.sl.in.cmake list of parallel testsLarry Knox2019-02-025-5/+5
| | | | | | | | | | | | reserved for *ctestP.sl.cmake. Revise options to run batch tests and alternative options for cross compile in HPC/*-HDF5options.cmake.
| * Change examples file to zip for CMake zip file.Larry Knox2019-02-011-1/+1
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| * Update bin/release for filename changes and HPC-CMake tar fileLarry Knox2019-02-011-7/+11
| | | | | | | | corrections.
| * Add new files to MANIFEST.Larry Knox2019-02-011-0/+0
| | | | | | | | Update permissions for raybsub to 755.
| * Add more specific batch scripts.Larry Knox2019-01-316-5/+141
| | | | | | | | | | | | Add script raybsub to handle submitting .lsf files on ray with bsub < script.lsf syntax that we couldn't handle with CMake. Add hpc-cmake-tgz option for bin/release.
| * Account info can be submitted as an argument to run the batch scripts.Larry Knox2019-01-282-33/+0
| | | | | | | | Special versions for sandia are not needed.
| * Remove knl configuration from ctestS.sl.in.cmake.Larry Knox2019-01-273-1/+33
| | | | | | | | Add sandia batch files with account info.
| * Add batch files with batch parameters specific to cori and ray.Larry Knox2019-01-268-5/+77
| | | | | | | | Release.txt entry for skipping long double dt_arith tests on ppc64.
* | C and POSIX call cleanupDana Robinson2019-01-111-90/+154
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* Configure build directory in batch scripts.Larry Knox2019-01-056-61/+6
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* Add libhdf5_hl_fortran symlinks for libhdf5hl_fortran files.Larry Knox2018-12-312-2/+2
| | | | | Set ctest*.lsf.in.cmake scripts for sierra. Correct src/CMakelists.txt syntax error.
* Add .lsf batch scripts and insert the build directory into the scriptsLarry Knox2018-12-282-0/+37
| | | | during configuration.
* Add support for "make check-vol", along with a few minor cleanups, etc.Quincey Koziol2018-11-292-0/+7
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* Update API tracing info for VOL functions and regenerate trace macros for VOLQuincey Koziol2018-11-281-0/+2
| | | | API calls.
* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-225-3/+68
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| * Add script and changes to wait for H5Tinit.cLarry Knox2018-11-145-3/+68
| | | | | | | | | | | | | | Add more sample batch scripts, specifically for sbatch, not for knl cross compile. Don't run parallel tests when no parallel test script is configured in HDF5options.cmake.
* | Switch switch remainder of API routines to use VOL callbacks.Quincey Koziol2018-11-101-0/+2
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* | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-061-2/+2
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| * Update HDF5-Examples version to be included in CMake-* tar/zip files.hdftest2018-11-051-2/+2
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* | Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Quincey Koziol2018-11-043-0/+76
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| * Add script to run tests with sbatch when not cross compiling.Larry Knox2018-10-291-0/+28
| | | | | | | | Add new files to MANIFEST.
| * Add files and changes to cross compile with CrayLinuxEnvironment and runLarry Knox2018-10-292-0/+48
| | | | | | | | ctest tests with a batch job on knl compute nodes.
* | Correct error with parsing of "FUNC_ENTER_API_NOINIT"Quincey Koziol2018-10-271-1/+1
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