Silo 4.12.0-pre1 available for testing

[markcmiller86]

What's Changed

• Add CMake build system by @biagas in Add CMake build system #228
• Remove master/slave by @markcmiller86 in Remove master/slave #250
• silo_f.c: add an interface to free an option set with dbaddcaopt by @cessenat in silo_f.c: add an interface to free an option set with dbaddcaopt #244
• hdf5: Support the API changes in 1.13 by @chuckatkins in hdf5: Support the API changes in 1.13 #260
• Miscellaneous CMake improvements by @henryleberre in Miscellaneous CMake improvements #262
• handle nans in diffs by @markcmiller86 in handle nans in diffs #276
• Install pmpio.h to support Cabana builds by @markstock in Install pmpio.h to support Cabana builds #278
• Include only zfp files when needed, re-ran automake by @brtnfld in Include only zfp files when needed, re-ran automake #263
• Make DBInqVarExists for for directories on PDB driver by @markcmiller86 in Make DBInqVarExists for for directories on PDB driver #293
• macOS: Handle deprecated stat64 - orig AC toolchain by @markcmiller86 in macOS: Handle deprecated stat64 - orig AC toolchain #299
• HDF5 add new fields for H5FD_class_t by @kwryankrattiger in HDF5 add new fields for H5FD_class_t #307
• Close file when deallocing by @markcmiller86 in Close file when deallocing #316
• Fix freeing file scope globals by @markcmiller86 in Merge pull request #306 from LLNL/bug-mcm86-13apr23-free-file-globals #326
• Handle Fortran null arrays by @markcmiller86 in Merge pull request #311 from LLNL/mcm86-21jan22-fix-null-fort-arrays #334
• Fix PJ-wrapper caching in PDB driver effecting python behavior by @markcmiller86 in Merge pull request #341 from LLNL/mcm86-24aug23-fix-pjcache-failure #342
• Document compatability mode by @markcmiller86 in Document compatability mode #349
• cmake: fix the name of the version file by @mathstuf in cmake: fix the name of the version file #357
• Reorg docs for GHPages and RTD by @markcmiller86 in Reorg docs for GHPages and RTD #338
• Backport ull for DBGetIndex by @markcmiller86 in Backport ull for DBGetIndex #362
• Improve material docs by @markcmiller86 in Improve material docs #363
• Update DBPutQuadmesh for embedded surface case by @markcmiller86 in Update DBPutQuadmesh for embedded surface case #364
• cmake: strip any suffix from the version by @mathstuf in cmake: strip any suffix from the version #360
• Msvc detection by @mathstuf in Msvc detection #359
• Fix dir on dbtoc by @markcmiller86 in Fix dir on dbtoc #373
• Add consistency in WIN32 define checks by @biagas in Add consistency in WIN32 define checks #384
• Update python testing on Windows. by @biagas in Update python testing on Windows. #385
• Fix typo in CMake var: SILEX_ENABLE_BROWSER -> SILO_ENABLE_BROWSER by @biagas in Fix typo in CMake var: SILEX_ENABLE_BROWSER -> SILO_ENABLE_BROWSER #387
• Fix namescheme tests by @markcmiller86 in Fix namescheme tests #388
• Update qt to version 6, python to version 3 by @biagas in Update qt to version 6, python to version 3 #391
• Update Qt to version 6 by @biagas in Update Qt to version 6 #393
• Initial CI by @markcmiller86 in Initial CI #390
• Fix segv identified during fuzz testing by @markcmiller86 in Fix segv identified during fuzz testing #402
• Fix string lists returned to python by @markcmiller86 in Fix string lists returned to python #403
• Fix fuzz test case and python strlists by @markcmiller86 in Fix fuzz test case and python strlists #404
• Fix some memory leaks in python by @markcmiller86 in Fix some memory leaks #405
• Merge fix for object macro case statements by @markcmiller86 in Merge fix for object macro case statements #408
• tests: add missing header for difftime by @thesamesam in tests: add missing header for difftime #371
• Adding Quadratic elements to Silo abstract knowledge pool by @cessenat in Adding Quadratic elements to Silo abstract knowledge pool #374
• Adjust extents calc logic for void aliasing in newer intel compilers by @markcmiller86 in Adjust extents calc logic for void aliasing #376
• Fix leaks from HDF5 driver and/or tests by @markcmiller86 in Fix leaks from HDF5 driver and/or tests #407
• Fix several small leaks found with valgrind by @markcmiller86 in Fix several small leaks found with valgrind on CZ #413
• Main merge of pull request Fix several small leaks found with valgrind on CZ #413 by @markcmiller86 in Main merge of pull request #413 #415
• Fix python overwrite issue and improve python write tests by @markcmiller86 in Fix python overwrite issue and improve python write tests #414
• Fix for python 2 or python 3 by @markcmiller86 in Fix for python 2 or python 3 #417
• fix runtime -fsanitize error in PDB by @markcmiller86 in fix runtime -fsanitize error in PDB #419
• Update README.md by @willzywiec in Update README.md #423
• Fix missing matname member of DBmultimatspec by @markcmiller86 in Fix missing matname member of DBmultimatspec #431
• cmake: make install locations configurable by @junghans in cmake: make install locations configurable #424
• cmake: add so version to library by @junghans in cmake: add so version to library #425
• Add new tests; ensure existing tests pass with HDF5-1.14.4-3 by @markcmiller86 in Add new tests; ensure existing tests pass with HDF5-1.14.4-3 #434
• Fix filter ids by @markcmiller86 in Fix filter ids #428
• Handle delimter in constant nameschemes by @markcmiller86 in Handle delimter in constant nameschemes #453
• Fix a problem compiling for PDB only by @markcmiller86 in Fix a problem compiling for PDB only #451
• Rpmbuild by @markcmiller86 in Rpmbuild #452
• Add DBEvalNamescheme feature by @markcmiller86 in Add DBEvalNamescheme feature #450
• Test and document handling of standard elements as degenerate hexahedra by @markcmiller86 in Merge pull request #446 from LLNL/feat-mcm86-16apr25-gen-degen-hex #457
• Make MB name generator a public function by @markcmiller86 in Make MB name generator a public function #460
• Finalize CMake replacement for Autotools by @markcmiller86 in Finalize CMake replacement for Autotools #462

New Contributors

• @andrewcorrigan made their first contribution in defines SIZEOF_OFF64_T as CMAKE_SIZEOF_VOID_P when off64_t is not defined to fix Mac/AppleClang compilation #239
• @cessenat made their first contribution in silo_f.c: add an interface to free an option set with dbaddcaopt #244
• @chuckatkins made their first contribution in hdf5: Support the API changes in 1.13 #260
• @henryleberre made their first contribution in Miscellaneous CMake improvements #262
• @markstock made their first contribution in Added parens to isnan conditional to satisfy standard #277
• @brtnfld made their first contribution in Include only zfp files when needed, re-ran automake #263
• @kwryankrattiger made their first contribution in HDF5 add new fields for H5FD_class_t #307
• @pkestene made their first contribution in Fix building tests with cmake. #323
• @mathstuf made their first contribution in cmake: fix the name of the version file #357
• @thesamesam made their first contribution in tests: add missing header for difftime #371
• @willzywiec made their first contribution in Update README.md #423
• @junghans made their first contribution in cmake: make install locations configurable #424

Full Changelog: 4.11.1...4.12.0-pre1

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This discussion was created from the release 4.12.0-pre1.

[markcmiller86]

FYI...Autotools is in process of being deprecated. It will still be available in the official 4.12.0 release but it will no longer be supported and will eventually be removed.

CMake is now used to configure Silo. Here are some example CMake configuration commands...

From the top-level directory of the untar'd Silo source tree...

mkdir cmake_build
cd cmake_build
cmake \
    # Set the installation point 
    -DCMAKE_INSTALL_PREFIX=`pwd`/my_install \
    # By default, only BSD licensed components are built. This excludes HZIP/FPZIP. Turn this default behavior off.
    -DSILO_BUILD_FOR_BSD_LICENSE:BOOL=OFF \
    # Tell CMake we want to build HDF5 driver. It will look in standard places for HDF5
    -DSILO_ENABLE_HDF5:BOOL=ON \
    # If HDF5 is in some non-standard place, tell CMake where to find it.
    -DSILO_HDF5_DIR:PATH=/mnt/nvme/mark/silo/hdf5-1.14.4/build/my_install \
    # Turn on FPZIP compression (only available to set when BSD is OFF and HDF5 is ON)
    # By default, if BSD is OFF and HDF5 is ON, FPZIP and HZIP are enabled so this line is not necessary.
    -DSILO_ENABLE_FPZIP:BOOL=ON \
    # Tell it to build stuff to run testing (via CTest)
    -DBUILD_TESTING:BOOL=ON \
    # Tell it to build the silock tool 
    -DSILO_ENABLE_SILOCK:BOOL=ON \
    # Set which kind of build. Options are (Debug, Release, RelWithDebInfo)
    -DCMAKE_BUILD_TYPE:STRING=Debug \
    # Tell it to build the python module
    -DSILO_ENABLE_PYTHON_MODULE:BOOL=ON \
    # Tell it to install PDB Lite and Score Lite headers
    -DSILO_ENABLE_INSTALL_LITE_HEADERS=ON
    ..