[WIP] Spack docker containers #261
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* Spack work. * Working with existing LLNL host configs. * SuiteSparse on Lassen progress. * Trilinos working on Lassen. * HYPRE finally working. * Trilinos MKL TPL * Fixed CHAI version. * Initial commit MacOS spack support * Travis host configs. * Expanded VTK libraries. Co-authored-by: Herve Gross <[email protected]>
* Add current GEOSX compilers to spack. * Added python interface. * Removed static variables. * Python improvements. * Removed std::string. Co-authored-by: Randolph R. Settgast <[email protected]>
* Changes to Group and Wrapper to favor references. * Added exceptions to harden the Python interface. * Added a Spack and Uberenv guide. * Changed getConstitutiveRelation and getConstitutiveManager. * Changed getMeshBodies, getMeshBody and getMeshLevel. * Changed getDomainPartition * Changed getRegion and getSubRegion. * Prevent MPI_Init from being called twice, (occurs with pygeosx). * Changed getConstitutiveModel(s). * Removing unnecessary uses of getGroupPointer. * Changed Group::getParent and Wrapper constructor. * Removed function input paths from restart.
* added option to specify inner radius of cartesian mapping * fix error in silo output * modifications to wellbore parallel mesh gen + addNeighbor changes to allow ranks to be mutual periodic neighbors (doubly-neighbored) * add hard coded coordinatese in the radial direction * bugfix for integer overflow with hypre int * fixes for mgr on gpu * - Add additional instrumentation for using MGR (make restrictor, compute Auu) - Update hypre linear algebra interface to the latest hypre/mgr - Update MGR recipes for GPU * modified LAIHelperFunctions::separateComponentFilter to batch insert rows. Introduced MatrixBase::separateComponentFilter as a specialized filter, implemented HypreMatrix::separateComponentFilter. * some cleanup for HypreMatrix::separateComponentFilter Co-authored-by: Sy-Tuan Nguyen <[email protected]> * implement single read variant of HypreMatrix::separateComponentFilter * Use full matrix instead of SDC approximation for mechanics in hydrofrac solver. Fix bug in setting options for mechanics block solver. * Changes to run on Summit. (#1546) Co-authored-by: Randolph R. Settgast <[email protected]> * fix bug from summit update * fix bug in SinglePhasePoromechanicsSolver::implicitStepComplete * resolve host-device ghost index array inconsistency * added annulus option to cylinder geometry. added error check for aperature table * Changes for new compilers on summit/lassen (#1611) * Updated hypre. * Force uberenv to use python3. * Added CUDA 11.0.3 on Summit. * Added GCC 9.1.0 to Summit * Added GCC 9.1.0 to Summit * Changes to work with GCC 9.1.0 on Summit. Co-authored-by: Benjamin Curtice Corbett <[email protected]> * Updating function parCSRtoIJ required by latest hypre version Co-authored-by: wrtobin <[email protected]> Co-authored-by: Quan Bui <[email protected]> Co-authored-by: Sy-Tuan Nguyen <[email protected]> Co-authored-by: Ben Corbett <[email protected]> Co-authored-by: Benjamin Curtice Corbett <[email protected]> Co-authored-by: Nicola Castelletto <[email protected]>
Enabling yapf formatting of python files
This patch aims at shrinking `GEOSX` into `GEOS`. - The `geosx` namespace is renamed `geos`. - All the `GEOSX_ASSERT`, `GEOSX_LOG`, … are renamed `GEOS_…` - All the include guards are modified. - All the paths to the old `http://gihub.com/GEOSX/GEOSX` are renamed appropriately - Mention to `GEOSX` in the text of the documentation is changed to `GEOS` Meanwhile, `GEOSX` is kept for the following cases - The executable is still named `geosx`, the examples in the doc still reflect the current naming. - All the tools named after `geosx` kept their `geosx` (_e.g._ `pygeox`, `geosx_xml_tools`) - All the `cmake` configuration flags (_e.g._ `GEOSX_TPL_DIR`, `GEOSX_USE_CUDA`) are unchanged. - The `host-config` files are not changed. - The variables names, classes or files containing `GEOSX` are not modified.
* Add geos-specific option to suppress/enable unit tests, active by default.
* Add mesa to packages.yaml, vtk issues * modify, add fmt recipe * remove cxx flags from blueos (consistent with RADIUSS and Axom) * Add specific uncrustify version, remove optimization flags from toss3 * Move spack configs and package recipes to separate folders; delete uberenv directory * Add uberenv as a submodule. Add uberenv config file * Bump conduit, add libtools external package * Bill's Conduit/HDF5 changes + switcharoo, try building latest pugixml * Add vtk patches + Try replace hypre-cuda with +hypre+cuda and caliper variant changes * Add camp dependency for RAJA path * make suite-sparse mandatory (spack is not always adding it to spec otherwise) * Change clang@upstream for blueos to clang@9 so clingo doesn't yell * gmpr fix * Use more accurate caliper version and correct readline version * Cleanup vtk script, vtk now builds on lassen * Update to spack 0.18.0 * Update hypre/silo/hdf5/conduit and use older trilinos recipe * Can build all blueos libraries - compilation errors - use netlib-lapack instead of essl * first pass at spack environments * Add spack.yaml for lassen; modify spack.yaml install_tree path to blueos_3_ppc64le_ib_p9_package * Generalize HDF5 and pugixml configuration so both thirdPartyLibs and spack builds work * Update umpire/raja/chai/hypre - only quartz re-tested so far * blueos config - set CUDA 11 as default * Cuda 11 explicit spec * Update CMake version; add gcc-toolchain flag for quartz * Update caliper, adiak, trilinos, cmake requirement, camp version in spack recipe * Update adiak namespace * Add cxx flags (std:: errors), disable hwloc dependency (runtime MPI error) for trilinos recipe * Guard adiak or adiak::adiak target * Add FESAPI spack recipe * pugixml and fmt changes for toss 3 quartz * Update CUDA to 11.2.2, update hypre, add -fPIC flag for hypre~shared, add missing libcublasLt path * use intel-oneapi-mkl instead of intel-mkl; use magic mvapich2; use mpi fortran in superlu-dist; disable fesapi default; update hypre; update cmake * Update CMake to 3.26.3; CMake fortran/CXX error with 3.23.1 * Missing fmt dependency * Upgrade to uberenv spack environments - update uberenv submodule, move to spack.yaml config files, comment out unused recipe patches * Move pygeosx dependencies to a separate spack recipe; update to latest spack release; use older hdf5 recipe; small trilinos change due to spack cmakepackage reorg; add spack environment files for pygeosx; adjust spec check for HYPRE cuda/hip enabled; add project json file for uberenv to build pygeosx; delete old python spec files * Mandate CMake >=3.23 * Spack environment file for toss 3 (rzgenie) * Remove cp unused * Omit uberenv from submodule check * Lock blt version to bypass raja/chai/camp blt::stub error * Make python required dependency; make pygeosx variant toggle * Generate separate host-config for LvArray * Update hypre and umpire versions, Remove some package recipes using git version specifiers where possible
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… cmake requirement
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This PR attempts to build dependencies using uberenv, spack.