* LC Spack Support (#1204)

* Add current GEOSX compilers to spack.

* Added python interface.

* Format python files with YAPF (#1947)

* spack environment file updates for LC


Co-authored-by: Benjamin Curtice Corbett <corbett5@llnl.gov>
Co-authored-by: Christopher Sherman <sherman27@llnl.gov>
Co-authored-by: William R Tobin <4522899+wrtobin@users.noreply.github.com>

* LC Spack Support (#1204)

* 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 <herve.gross@total.com>

* Python interface (#1068)

* Add current GEOSX compilers to spack.

* Added python interface.

* Removed static variables.

* Python improvements.

* Removed std::string.

Co-authored-by: Randolph R. Settgast <settgast1@llnl.gov>

* Corbett/references and exceptions (#1318)

* 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.

* Changes for Summit. (#1367)

* Spack changes. (#1445)

* Use {fmt} for message formatting (#1568)

* Adding features for Wellbore meshing (#1424)

* 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 <45685596+sytuannguyen@users.noreply.github.com>

* 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 <settgast1@llnl.gov>

* 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 <corbett5@llnl.gov>

* Updating function parCSRtoIJ required by latest hypre version

Co-authored-by: wrtobin <tobin6@llnl.gov>
Co-authored-by: Quan Bui <mquan.bui@gmail.com>
Co-authored-by: Sy-Tuan Nguyen <45685596+sytuannguyen@users.noreply.github.com>
Co-authored-by: Ben Corbett <32752943+corbett5@users.noreply.github.com>
Co-authored-by: Benjamin Curtice Corbett <corbett5@llnl.gov>
Co-authored-by: Nicola Castelletto <castelletto1@llnl.gov>

* Format python files with YAPF (#1947)

Enabling yapf formatting of python files

* Add PT-Scotch as a partitioning method option in VTKMesh (#1996)

* Change `geosx` to `geos` in macros, include guards, namespace... (#2392)

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.

* Initial HIP/ROCM Support (#2453)

* Ensure unit tests are enabled by default. (#2464)

* Add geos-specific option to suppress/enable unit tests, active by default.

* Spack Update (#2028)

* 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

* Update spack commit, remove chai and umpire recipes

* Remove fesapi support from spack

* Remove toss_3 recipe (no more toss_3 systems)

* hypre update

* Remove unneeded dependencies for pygeosx, add recommendation to build python3 using Linux package manager > spack

* Attempt to add openmp variant

* Try adding fPIC to cflag as well...

* Guard the cuda release flags

* Update hypre hash

* Try adding cached_cmake.py logic for determining MPIEXEC

* Testing spacked docker images

* Added uberenv as submodule

* Try rocky

* Changes to get things working with tpl version updates - includes spack recipe changes, spack version update

* Try rocky gcc

* Find mpfr, reduce build size

* Do not build pygeosx for gcc, build silo~shared

* Update raja suite and vtk for github action images

* spack environment file updates for LC

* Try curl with error

* Update .gitignore for spack, update cmake version for blueos

* Remove environment variable sets from rocky linux Dockerfiles

* Attempt to update LC build script for uberenv

* Script arg indexing

* Script clang13-cuda12 naming

* Keep gcc env vars for mpi4py installation

* Try pangea3, separate total environment file into separate pangea and pecan

* Remove leftover merge comment

* change openmpi spec

* Spelling, flag geosx recipe adjustments

* Possible rpaths and LD_LIBRARY_PATH options for pangea-3

* cleanup paths, add symlinks so spack can find link dependencies, bump cmake requirement

* Have spack build part of texinfo dependencies, install bzip2 for tar

* Let spack build ncurses

* Use built gettext

* Add bison and flex to env

* Build scotch using make instead of cmake build system; ~shared/static relevant libraries; adjust essl recipe; fix blas/lapack host-config logic; GEOS_LA_INTERFACE spelling

* Disable error for scotch

* Fix vtk recipe multiple cxx flags; add no avx compiler flags

* Changes to fix rockylinux clang; lock-in clang@17, newer clang@18 fails to configure with CMake; add -fPIC fortran flag to some dependencies

* Update hypre version hash

* Update hyper version hash for LC spack.yaml files

* Try caliper/trilinos/cmake updates + different rockylinux clang workaround

* differentiate cuda versions in rocky

* Disable deprecated warning failures

* Sherlock updates, try define spec in gha yml

* uberenv script comment fix

* cleanup comment

* Try fix for ascii codec decode error

* Try set through env variables

* Stick with actual ascii codec decode fix, add comment

* Remove debug env print

* feat: macOS spack environment.

* add addr2line

* remove hdf5

* Fix Sequoia build: update spack version.

* python3-dev

* python3-dev in remaining docker files.

---------

Co-authored-by: Ben Corbett <32752943+corbett5@users.noreply.github.com>
Co-authored-by: Herve Gross <herve.gross@total.com>
Co-authored-by: Randolph R. Settgast <settgast1@llnl.gov>
Co-authored-by: Sergey Klevtsov <s.klevzoff@gmail.com>
Co-authored-by: wrtobin <tobin6@llnl.gov>
Co-authored-by: Quan Bui <mquan.bui@gmail.com>
Co-authored-by: Sy-Tuan Nguyen <45685596+sytuannguyen@users.noreply.github.com>
Co-authored-by: Benjamin Curtice Corbett <corbett5@llnl.gov>
Co-authored-by: Nicola Castelletto <castelletto1@llnl.gov>
Co-authored-by: Christopher Sherman <sherman27@llnl.gov>
Co-authored-by: Sergey Klevtsov <klevtsov@stanford.edu>
Co-authored-by: TotoGaz <49004943+TotoGaz@users.noreply.github.com>
Co-authored-by: William R Tobin <4522899+wrtobin@users.noreply.github.com>
Co-authored-by: Brian Han <han12@llnl.gov>