add lshape example

mergin with gslib and other changes to streamline eval
adding python and DRLfiner for multi agent local(MAL)
2021-07-13 13:17:58 -07:00 · 2021-06-17 11:52:38 -07:00 · 2021-06-11 13:36:47 -07:00 · 2021-06-11 11:29:38 -07:00 · 2021-04-22 18:02:36 -07:00 · 2021-04-22 12:18:52 -07:00
795 changed files with 24931 additions and 83039 deletions
@@ -1,32 +0,0 @@
-codecov:
-  require_ci_to_pass: yes
-
-coverage:
-  precision: 2
-  round: nearest
-  range: "0...100"
-  status:
-    patch:
-      default:
-        target: auto
-        threshold: 0%
-        base: auto
-        branches:
-          - master
-        if_ci_failed: error
-        informational: true
-        only_pulls: true
-    project:
-      default:
-        target: auto   # compares coverage to the previous base commit
-        threshold: 1%  # allows variations around the target
-        base: auto
-        branches:
-          - master
-        if_ci_failed: error
-        only_pulls: true
-
-github_checks:
-  annotations: false
-
-comment: false
@@ -1,208 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# In this CI section, we build different variants of mfem and run test on them.
-name: builds-and-tests
-
-# Github actions can use the default "GITHUB_TOKEN". By default, this token
-# is set to have permissive access. However, this is not a good practice
-# security-wise. Here we use an external action, so we restrict the
-# permission to the minimum required.
-# When the 'permissions' is set, all the scopes not mentioned are set to the
-# most restrictive setting. So the following is enough.
-permissions:
-  actions: write
-
-on:
-  push:
-    branches:
-      - master
-      - next
-  pull_request:
-
-env:
-  HYPRE_ARCHIVE: v2.19.0.tar.gz
-  HYPRE_TOP_DIR: hypre-2.19.0
-  METIS_ARCHIVE: metis-4.0.3.tar.gz
-  METIS_TOP_DIR: metis-4.0.3
-  MFEM_TOP_DIR: mfem
-
-# Note for future improvements:
-#
-# We cannot reuse cached dependencies and have to build them for each target
-# although they could be shared sometimes. That's because Github cache Action
-# has no read-only mode. But there is a PR ready for this
-# (https://github.com/actions/cache/pull/489)
-
-jobs:
-  builds-and-tests:
-    strategy:
-      matrix:
-        os: [ubuntu-18.04, macos-10.15]
-        target: [dbg, opt]
-        mpi: [seq, par]
-        build-system: [make]
-        hypre-target: [int32]
-        # 'include' allows us to:
-        # - Add a variable to all jobs without creating a new matrix dimension.
-        #   Codecov is defined that way.
-        # - Add a new combination.
-        #   'build-system: cmake' and 'hypre-target: int64'
-        #
-        # note: we will gather coverage info for any non-debug run except the
-        # CMake build.
-        include:
-          - target: dbg
-            codecov: NO
-          - target: opt
-            codecov: YES
-          - os: ubuntu-18.04
-            target: opt
-            codecov: NO
-            mpi: par
-            build-system: cmake
-            hypre-target: int32
-          - os: ubuntu-18.04
-            target: opt
-            codecov: NO
-            mpi: par
-            build-system: make
-            hypre-target: int64
-    name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}
-
-    runs-on: ${{ matrix.os }}
-
-    steps:
-    # This external action allows to interrupt a workflow already running on
-    # the same branch to save resource
-    - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.9.0
-      with:
-        access_token: ${{ github.token }}
-
-    # Checkout MFEM in "mfem" subdirectory. Final path:
-    # /home/runner/work/mfem/mfem/mfem
-    # Note: Done now to access "install-hypre" and "install-metis" actions.
-    - name: checkout mfem
-      uses: actions/checkout@v2
-      with:
-        path: ${{ env.MFEM_TOP_DIR }}
-        # Fetch the complete history for codecov to access commits ID
-        fetch-depth: 0
-
-    # Only get MPI if defined for the job.
-    # TODO: It would be nice to have only one step, e.g. with a dedicated
-    # action, but I (@adrienbernede) don't see how at the moment.
-    - name: get MPI (Linux)
-      if: matrix.mpi == 'par' && matrix.os == 'ubuntu-18.04'
-      run: |
-        sudo apt-get install mpich libmpich-dev
-        export MAKE_CXX_FLAG="MPICXX=mpic++"
-
-    - name: get lcov (Linux)
-      if: matrix.codecov == 'YES' && matrix.os == 'ubuntu-18.04'
-      run: |
-        sudo apt-get install lcov
-
-    - name: Set up Homebrew
-      if: ( matrix.mpi == 'par' || matrix.codecov == 'YES' ) && matrix.os == 'macos-10.15'
-      uses: Homebrew/actions/setup-homebrew@c4aafe8c4620bf08883dd4679c374f11e73329d3
-
-    - name: get MPI (MacOS)
-      if: matrix.mpi == 'par' && matrix.os == 'macos-10.15'
-      run: |
-        export HOMEBREW_NO_INSTALL_CLEANUP=1
-        brew install openmpi
-        export MAKE_CXX_FLAG="MPICXX=mpic++"
-
-    - name: get MPI (MacOS)
-      if: matrix.codecov == 'YES' && matrix.os == 'macos-10.15'
-      run: |
-        export HOMEBREW_NO_INSTALL_CLEANUP=1
-        brew install lcov
-
-    # Get Hypre through cache, or build it.
-    # Install will only run on cache miss.
-    - name: cache hypre
-      id: hypre-cache
-      if: matrix.mpi == 'par'
-      uses: actions/cache@v2
-      with:
-        path: ${{ env.HYPRE_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-${{ matrix.hypre-target }}-v2.0
-
-    - name: get hypre
-      if: matrix.mpi == 'par' && steps.hypre-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-hypre@v2.0
-      with:
-        archive: ${{ env.HYPRE_ARCHIVE }}
-        dir: ${{ env.HYPRE_TOP_DIR }}
-        target: ${{ matrix.hypre-target }}
-
-    # Get Metis through cache, or build it.
-    # Install will only run on cache miss.
-    - name: cache metis
-      id: metis-cache
-      if: matrix.mpi == 'par'
-      uses: actions/cache@v2
-      with:
-        path: ${{ env.METIS_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.0
-
-    - name: install metis
-      if: matrix.mpi == 'par' && steps.metis-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-metis@v2.0
-      with:
-        archive: ${{ env.METIS_ARCHIVE }}
-        dir: ${{ env.METIS_TOP_DIR }}
-
-    # MFEM build and test
-    - name: build
-      uses: mfem/github-actions/build-mfem@v2.0
-      with:
-        os: ${{ matrix.os }}
-        target: ${{ matrix.target }}
-        codecov: ${{ matrix.codecov }}
-        mpi: ${{ matrix.mpi }}
-        build-system: ${{ matrix.build-system }}
-        hypre-dir: ${{ env.HYPRE_TOP_DIR }}
-        metis-dir: ${{ env.METIS_TOP_DIR }}
-        mfem-dir: ${{ env.MFEM_TOP_DIR }}
-
-    # Run checks (and only checks) on debug targets
-    - name: checks
-      if: matrix.build-system == 'make' && matrix.target == 'dbg'
-      run: |
-        cd ${{ env.MFEM_TOP_DIR }}  && make check
-
-    - name: unit tests
-      if: matrix.build-system == 'make' && matrix.target == 'opt'
-      run: |
-        cd ${{ env.MFEM_TOP_DIR }} && make unittest
-
-    - name: tests
-      if: matrix.build-system == 'make' && matrix.target == 'opt'
-      run: |
-        cd ${{ env.MFEM_TOP_DIR }} && make test
-
-    - name: cmake unit tests
-      if: matrix.build-system == 'cmake'
-      run: |
-        cd ${{ env.MFEM_TOP_DIR }}/build/tests/unit && ctest --output-on-failure
-
-    # Code coverage (process and upload reports)
-    - name: codecov
-      if: matrix.codecov == 'YES'
-      uses: mfem/github-actions/upload-coverage@v2.0
-      with:
-        name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}
-        project_dir: ${{ env.MFEM_TOP_DIR }}
-        directories: "fem general linalg mesh"
@@ -1,100 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-name: build-analysis
-
-permissions:
-  actions: write
-
-on:
-  push:
-    branches:
-      - master
-      - next
-  pull_request:
-
-env:
-  HYPRE_ARCHIVE: v2.19.0.tar.gz
-  HYPRE_TOP_DIR: hypre-2.19.0
-  METIS_ARCHIVE: metis-4.0.3.tar.gz
-  METIS_TOP_DIR: metis-4.0.3
-  COVERAGE_ENV: mfem-coverage
-
-jobs:
-  gitignore:
-    runs-on: ubuntu-18.04
-
-    steps:
-    - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.9.0
-      with:
-        access_token: ${{ github.token }}
-
-    - name: checkout MFEM
-      uses: actions/checkout@v2
-      with:
-        path: mfem
-
-    - name: Get MPI (Linux)
-      run: |
-        sudo apt-get install mpich libmpich-dev
-        export MAKE_CXX_FLAG="MPICXX=mpic++"
-
-    - name: Cache Hypre Install
-      id: hypre-cache
-      uses: actions/cache@v2
-      with:
-        path: ${{ env.HYPRE_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-v2.0
-
-    - name: Get Hypre
-      if: steps.hypre-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-hypre@v2.0
-      with:
-        archive: ${{ env.HYPRE_ARCHIVE }}
-        dir: ${{ env.HYPRE_TOP_DIR }}
-        target: int32
-
-    - name: Cache Metis Install
-      id: metis-cache
-      uses: actions/cache@v2
-      with:
-        path: ${{ env.METIS_TOP_DIR }}
-        key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.0
-
-    - name: Install Metis
-      if: steps.metis-cache.outputs.cache-hit != 'true'
-      uses: mfem/github-actions/build-metis@v2.0
-      with:
-        archive: ${{ env.METIS_ARCHIVE }}
-        dir: ${{ env.METIS_TOP_DIR }}
-
-    # MFEM build and test
-    - name: build-mfem
-      uses: mfem/github-actions/build-mfem@v2.0
-      with:
-        os: ${{ runner.os }}
-        target: optim
-        codecov: NO
-        mpi: parallel
-        build-system: make
-        hypre-dir: ${{ env.HYPRE_TOP_DIR }}
-        metis-dir: ${{ env.METIS_TOP_DIR }}
-        mfem-dir: mfem
-
-    - name: test (no clean)
-      run: |
-        cd mfem && make test-noclean
-
-    - name: gitignore
-      run: |
-        cd mfem/tests/scripts
-        ./runtest gitignore
@@ -1,110 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-name: repo-check
-
-permissions:
-  actions: write
-
-on:
-  push:
-
-jobs:
-  file-headers-check:
-    runs-on: ubuntu-18.04
-
-    steps:
-    - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.9.0
-      with:
-        access_token: ${{ github.token }}
-    - name: checkout mfem
-      uses: actions/checkout@v2
-
-    - name: copyright check
-      id: copyright
-      run: |
-        ./config/githooks/pre-push --copyright
-
-      continue-on-error: true
-
-    - name: license check
-      id: license
-      run: |
-        ./config/githooks/pre-push --license
-      continue-on-error: true
-
-    - name: release check
-      id: release
-      run: |
-        ./config/githooks/pre-push --release
-      continue-on-error: true
-
-    - name: wrap-up
-      if: steps.copyright.outcome != 'success' || steps.license.outcome != 'success' || steps.release.outcome != 'success'
-      run: |
-        if [[ "${{ steps.copyright.outcome }}" != "success" ]]; then
-          echo "copyright check failed, unroll log for details"
-        fi
-        if [[ "${{ steps.license.outcome }}" != "success" ]]; then
-          echo "license check failed, unroll log for details"
-        fi
-        if [[ "${{ steps.release.outcome }}" != "success" ]]; then
-          echo "release check failed, unroll log for details"
-        fi
-        exit 1
-
-  code-style:
-    runs-on: ubuntu-16.04 # needed for astyle 2.05.1
-
-    steps:
-    - name: checkout mfem
-      uses: actions/checkout@v2
-
-    - name: get astyle
-      run: |
-        sudo apt-get install astyle=2.05.1-0ubuntu1
-
-    - name: style check
-      run: |
-        ./config/githooks/pre-push --style
-
-  documentation:
-    runs-on: ubuntu-18.04
-
-    steps:
-    - name: checkout mfem
-      uses: actions/checkout@v2
-
-    - name: get doxygen and graphviz
-      run: |
-        sudo apt-get install doxygen graphviz
-
-    - name: build documentation
-      run: |
-        cd tests/scripts
-        ./runtest documentation
-
-  branch-history:
-    if: github.ref != 'refs/heads/next' && github.ref != 'refs/heads/master'
-    runs-on: ubuntu-18.04
-
-    steps:
-    - name: checkout mfem
-      uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-
-    - name: branch-history
-      run: |
-        git fetch origin master:master
-        git checkout -b gh-actions-branch-history
-        ./config/githooks/pre-push --history
@@ -26,7 +26,6 @@ CMakeFiles/
 config/_config.hpp
 config/config.mk
 config/sample-runs-build.log
-config/user.mk
 doc/CodeDocumentation.conf
 doc/CodeDocumentation.html
 doc/CodeDocumentation
@@ -45,8 +44,8 @@ doc/warnings.log

 # Example and miniapp binaries and outputs

-examples/ex[0-9]
-examples/ex[0-9]p
+examples/ex[1-9]
+examples/ex[1-9]p
 examples/ex1[04-9]
 examples/ex1[0-9]p
 examples/ex2[0-9]
@@ -67,7 +66,6 @@ examples/sol_u.*
 examples/sol_p.*
 examples/sol_r.*
 examples/sol_i.*
-examples/ex6p-checkpoint.*
 examples/ex9.mesh
 examples/ex9-mesh.*
 examples/ex9-init.*
@@ -103,9 +101,6 @@ examples/Example23*
 examples/ex25.mesh
 examples/ex25-*.gf
 examples/ex25p-*.*
-examples/ex28_*
-examples/ex28p_*
-examples/flux.*

 examples/amgx/ex1
 examples/amgx/ex1p
@@ -218,11 +213,6 @@ miniapps/meshing/optimized*
 miniapps/meshing/perturbed*
 miniapps/meshing/polar-nc.mesh

-miniapps/mtop/parheat
-miniapps/mtop/ParHeat*
-miniapps/mtop/seqheat
-miniapps/mtop/SeqHeat*
-
 miniapps/navier/navier_mms
 miniapps/navier/navier_kovasznay
 miniapps/navier/navier_kovasznay_vs
@@ -247,13 +237,6 @@ miniapps/performance/refined.mesh
 miniapps/performance/mesh.*
 miniapps/performance/sol.*

-miniapps/shifted/distance
-miniapps/shifted/ParaViewDistance
-miniapps/shifted/diffusion
-miniapps/shifted/diffusion.mesh
-miniapps/shifted/diffusion.gf
-miniapps/shifted/ParaViewDiffusion
-
 miniapps/tools/display-basis
 miniapps/tools/load-dc
 miniapps/tools/convert-dc
@@ -281,23 +264,13 @@ miniapps/toys/lissajous.mesh
 miniapps/toys/lissajous.gf
 miniapps/toys/mondrian.mesh

-miniapps/solvers/block-solvers
-miniapps/solvers/lor_solvers
-miniapps/solvers/plor_solvers
-miniapps/solvers/ParaView
-miniapps/solvers/mesh.*
-miniapps/solvers/sol.*
-
 # Unit test binary and outputs
 tests/unit/output_meshes
 tests/unit/unit_tests
 tests/unit/punit_tests
 tests/unit/sedov_tests_*
 tests/unit/psedov_tests_*
-tests/unit/tmop_pa_tests_*
-tests/unit/ptmop_pa_tests_*
 tests/unit/ceed_tests
-tests/unit/debug_device_tests

 # Test script output
 tests/scripts/*.err
@@ -311,7 +284,3 @@ tests/par-mesh-format/ex1p

 # VPATH builds
 build-*/*
-
-# PETSc automated build
-petsc-build/*
-pkg.gitcommit
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -23,6 +23,10 @@
 # also means that the BUILD_ROOT directory will never be cleaned.
 # TODO: add a clean-up mechanism
 #
+# BUILD_PATH:
+# In BUILD_ROOT, we want to separate builds depending on the machine used,
+# typically because we build on a set of dependencies per machine.
+#
 # REBASELINE:
 # Defines the default choice for updating the saved baseline results. By default
 # the baseline can only be updated from the master branch. This variable offers
@@ -40,67 +44,49 @@
 # Directory used to place artifacts.

 variables:
-  BUILD_ROOT: ${CI_BUILDS_DIR}/MFEM/${CI_PROJECT_NAME}_${CI_COMMIT_REF_SLUG}_${CI_PIPELINE_ID}
-  AUTOTEST_ROOT: ${CI_BUILDS_DIR}/MFEM
+  BUILD_ROOT: ${CI_BUILDS_DIR}/${CI_PROJECT_NAME}_${CI_COMMIT_REF_SLUG}_${CI_PIPELINE_ID}
+  BUILD_PATH: ${CI_BUILDS_DIR}/${CI_PROJECT_NAME}_${CI_COMMIT_REF_SLUG}_${CI_PIPELINE_ID}/${PLAT}/${TOOLCHAIN}
  REBASELINE: "NO"
-  AUTOTEST: "NO"
-  ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
+  MFEM_ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
  TPLS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tpls.git
  TESTS_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/tests.git
-  AUTOTEST_REPO: ssh://git@mybitbucket.llnl.gov:7999/mfem/autotest.git
-  MFEM_DATA_REPO: https://github.com/mfem/data.git
  ARTIFACTS_DIR: artifacts
-  SLURM_OVERLAP: 1

-# The pipeline is divided into stages. Usually, jobs in a given stage wait for
-# the preceding stages to complete before to start. However, we sometimes use
-# the "needs" keyword and express the DAG of jobs for more efficiency.
-# - We use setup and setup_baseline phases to download content outside of mfem
-#   directory.
-# - Allocate/Release is where quartz resources are allocated/released once for all.
-# - Build and Test is where we build and MFEM for multiple toolchains.
+# The pipeline is divided into stages. Usually, these are also synchronization
+# points, however, we use "needs" keyword to express the DAG of jobs for more
+# efficiency.
+# - We use setup phase to download content outside of mfem directory.
+# - Allocate is where quartz resources are allocated once for all.
+# - Libs is where dependencies are built.
+# - Build is where we build MFEM for multiple toolchains.
+# - Test is where we perform a first set of tests on MFEM build.
 # - Baseline_checks gathers baseline-type test suites execution
 # - Baseline_publish, only available on master, allows to update baseline
 #   results
+# - Deallocate releases quartz resources
 stages:
  - setup
-  - q_allocate_resources
-  - q_build_and_test
-  - q_release_resources
-  - l_build_and_test
-  - c_build_and_test
-  - setup_baseline
+  - allocate
+  - libs
+  - build
+  - test
+  - deallocate
+  - lassen_build
+  - lassen_test
  - baseline_check
-  - baseline_to_autotest
  - baseline_publish

-# setup clones the mfem/data repo in ${BUILD_ROOT}. The build_and_test script
-# then symlinks the repo to the parent directory of the MFEM source directory.
-# Unit tests that depend on the mfem/data repo will then detect that this
-# directory is present and be enabled.
+# The setup job in setup stage don't rely on MFEM git repo. It prepares a
+# pipeline-wide working directory downloading/updating external repos.
+# TODO: updating tests and tpls is not necessary anymore since pipelines are
+# now using unique directories so repo are never shared with another pipeline.
+# This is not memory efficient (we keep a lot of data), hence this reminder.
+# Setup
 setup:
  tags:
    - shell
    - quartz
  stage: setup
-  variables:
-    GIT_STRATEGY: none
-  script:
-    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
-    - if [ ! -d data ]; then git clone ${MFEM_DATA_REPO}; fi
-
-# The setup_baseline job in setup stage_baseline doesn't rely on MFEM git repo.
-# It prepares a pipeline-wide working directory downloading/updating external
-# repos. TODO: updating tests and tpls is not necessary anymore since pipelines
-# are now using unique directories so repo are never shared with another
-# pipeline. This is not memory efficient (we keep a lot of data), hence this
-# reminder.
-# Note: This job can start immediately.
-setup_baseline:
-  tags:
-    - shell
-    - quartz
-  stage: setup_baseline
  variables:
    GIT_STRATEGY: none
  script:
@@ -109,46 +95,114 @@ setup_baseline:
    - if [ ! -d "tests" ]; then git clone ${TESTS_REPO}; fi
    - cd tpls && git pull && cd ..
    - cd tests && git pull && cd ..
-    - cd ${AUTOTEST_ROOT}
-    - if [ ! -d "autotest" ]; then git clone ${AUTOTEST_REPO}; fi
-    - cd autotest && git pull && cd ..
-  needs: []

-.build_toss_3_x86_64_ib_script:
-  script:
-    - export THREADS=12
-    - echo ${ALLOC_NAME}
-    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
-    - echo ${JOBID}
-    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 30 -N 1 tests/gitlab/build_and_test
+# Share configurations (templates) for toolchain configuration.
+# Note: Any job using this template shouldn't redefine "before_script" key.
+.with_gcc_6_1_0:
+  variables:
+    TOOLCHAIN: gcc_6_1_0
+    CXX: g++
+    CC: gcc
+  before_script:
+    - module load gcc/6.1.0

-.build_toss_3_x86_64_ib_corona_script:
-  script:
-    - srun -p mi60 -t 15 -N 1 tests/gitlab/build_and_test
+# On lassen
+.with_gcc_8_3_1:
+  variables:
+    TOOLCHAIN: gcc_8_3_1
+    CXX: g++
+    CC: gcc
+  before_script:
+    - module load gcc/8.3.1

-# Lassen uses a different job scheduler (spectrum lsf) that does not allow
-# pre-allocation the same way slurm does.  We use pdebug queue on lassen to
-# speed-up the allocation.  However this would not be scalable to multiple
-# builds.
-.build_blueos_3_ppc64le_ib_script:
+.with_gcc_4_9_3:
+  variables:
+    TOOLCHAIN: gcc_4_9_3
+    CXX: g++
+    CC: gcc
+  before_script:
+    - module load gcc/4.9.3
+
+.if_srun_alloc_for_make: &if_srun_alloc_for_make |
+  if [[ "${MPIEXEC}" == "srun" ]]
+  then
+    export JOB_ID=$(squeue -h --name=${MFEM_ALLOC_NAME} --format=%A)
+    [[ -n "JOB_ID" ]] && export JOB_ID="--jobid=${JOB_ID}"
+    RESOURCES="--extra-node-info=1:${MAKE_PAR}:1 --cpus-per-task=${MAKE_PAR} --ntasks=1"
+    # Allocation prefix:
+    export EXEC_PREFIX="srun ${JOB_ID} ${RESOURCES}"
+  fi
+
+# Build of dependencies and mfem:
+# if on quartz, uses a part of preallocated resources
+# Note: Those jobs don't rely on MFEM repository, hence the use of
+# "GIT_STRATEGY: none" preventing its clone.
+.build_hypre:
+  variables:
+    EXEC_PREFIX: ""
+    GIT_STRATEGY: none
+  stage: libs
  script:
-    - lalloc 1 -W 30 -q pdebug tests/gitlab/build_and_test
+    - cd ${BUILD_ROOT}/tpls
+    - mkdir -p ${BUILD_PATH}
+    - make clean
+    - *if_srun_alloc_for_make
+    - ${EXEC_PREFIX} make -j ${MAKE_PAR} hypre PREFIX=${BUILD_PATH}/hypre/src/ BUILD_DIR=${BUILD_PATH} LOG_DIR=${BUILD_PATH}
+
+.build_metis:
+  variables:
+    EXEC_PREFIX: ""
+    GIT_STRATEGY: none
+  stage: libs
+  script:
+    - cd ${BUILD_ROOT}/tpls
+    - mkdir -p ${BUILD_PATH}
+    - *if_srun_alloc_for_make
+    - ${EXEC_PREFIX} make -j ${MAKE_PAR} ${METIS} PREFIX=${BUILD_PATH}/ BUILD_DIR=${BUILD_PATH} LOG_DIR=${BUILD_PATH} CC=${CC} CXX=${CXX}
+
+# Building MFEM
+.build_mfem:
+  variables:
+    EXEC_PREFIX: ""
+  stage: build
+  script:
+    - mkdir -p ${BUILD_PATH}
+    - cp -r ${CI_PROJECT_DIR} ${BUILD_PATH}/${CI_PROJECT_NAME}_${MFEM_USE_MPI}_${MFEM_DEBUG}
+    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_${MFEM_USE_MPI}_${MFEM_DEBUG}
+    - *if_srun_alloc_for_make
+    - make config CXX=${CXX} MPICXX=mpicxx MFEM_USE_MPI=${MFEM_USE_MPI} MFEM_DEBUG=${MFEM_DEBUG} MFEM_MPIEXEC="${EXEC_PREFIX}" MFEM_MPIEXEC_NP=${MPIEXEC_NP}
+    - ${EXEC_PREFIX} make -j ${MAKE_PAR} all
+
+# TODO: Could this phase use a parallel run?
+.sanitycheck_mfem:
+  stage: test
+  variables:
+    GIT_STRATEGY: none
+  script:
+    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_${MFEM_USE_MPI}_${MFEM_DEBUG}
+    - make test

 # Shared script for baseline and sample-run-baseline, the value of BASELINE_TEST
 # differentiates between the two tests.
 .baseline_script: &baseline_script |
  # locals
+  _glob_out=${BASELINE_TEST}.out
  _glob_err=${BASELINE_TEST}.err
  _base_diff=${BASELINE_TEST}-${SYS_TYPE}.diff
  _base_patch=${BASELINE_TEST}-${SYS_TYPE}.patch
  _base_out=${BASELINE_TEST}-${SYS_TYPE}.out
+
+  _out=${BASELINE_TEST}-${SYS_TYPE}.out
+  _ref=../${BASELINE_TEST}-${SYS_TYPE}.saved
+  _out_txt=${BASELINE_TEST}.txt
+  _diff=${BASELINE_TEST}-diff.txt
  # prepare
  cd ${BUILD_ROOT}
  ln -snf ${CI_PROJECT_DIR} mfem
  cd tests
  mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
  # run
-  srun --nodes=1 -p pdebug ../runtest ../../mfem "${BASELINE_TEST} ${ADDITIONAL_DIR}"
+  salloc --nodes=1 -p pdebug ../runtest ../../mfem "${BASELINE_TEST} ${ADDITIONAL_DIR}"
  # post
  mkdir ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}
  if [[ -s ${_glob_err} ]]
@@ -156,7 +210,7 @@ setup_baseline:
    echo "ERROR during ${BASELINE_TEST} execution";
    echo "Here is the ${_glob_err} file content";
    cat ${_glob_err}
-    cp ${_glob_err} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_glob_err}
+    cp ${_glob_err} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_glob_err}.txt
    exit 1;
  elif [[ ! -f ${_base_patch} && ! -f ${_base_out} ]]
  then
@@ -166,20 +220,18 @@ setup_baseline:
  elif [[ -f ${_base_patch} ]]
  then
    echo "${BASELINE_TEST}: Differences found, patch generated"
-    cp ${_base_patch} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_patch}
+    cp ${_base_patch} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_patch}.txt
  elif [[ -f ${_base_out} ]]
  then
    echo "${BASELINE_TEST}: Differences found, replacement file generated"
-    cp ${_base_out} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_out}
+    cp ${_base_out} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_out}.txt
  fi
  # _base_diff won't even exist if there is no difference.
  if [[ -f ${_base_diff} ]]
  then
    echo "${BASELINE_TEST}: Relevant differences (filtered diff) ..."
    cat ${_base_diff}
-    cp ${_base_diff} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_diff}
-    # We create a .err file, because that's how we signal that there was a diff.
-    cp ${_base_diff} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/gitlab-${BASELINE_TEST}-${SYS_TYPE}.err
+    cp ${_base_diff} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_diff}.txt
  fi
  if [[ ! -s ${_base_diff} ]]
  then
@@ -218,7 +270,7 @@ setup_baseline:
      - ${ARTIFACTS_DIR}
  allow_failure: true

-# This job can only be manually triggered on a pipeline for master branch, or if
+# This job can only be manually triggers on a pipeline for master branch, or if
 # the pipeline was triggered with REBASELINE="YES"
 .rebaseline_mfem:
  stage: baseline_publish
@@ -231,18 +283,19 @@ setup_baseline:
    - export DIFF_FILE=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}.diff
    - cd ${BUILD_ROOT}/tests
    - |
-      if [[ ! -f "${DIFF_FILE}" ]]
+      if [[ ! -f "${DIFF_FILE}.txt" ]]
      then
          echo "Nothing to be done: no relevant change in baseline"
          exit 0
-      elif [[ -f "${PATCH_FILE}" ]]
+      elif [[ -f "${PATCH_FILE}.txt" ]]
      then
+          mv ${PATCH_FILE}.txt ${PATCH_FILE}
          patch "./baseline-${SYS_TYPE}.saved" < "${PATCH_FILE}"
-      elif [[ -f "${FULL_FILE}t" ]]
+      elif [[ -f "${FULL_FILE}.txt" ]]
      then
-          cp "${FULL_FILE}" "./baseline-${SYS_TYPE}.saved"
+          cp "${FULL_FILE}.txt" "./baseline-${SYS_TYPE}.saved"
      else
-          echo "File missing: expected ${PATCH_FILE} or ${FULL_FILE}"
+          echo "File missing: expected ${PATCH_FILE}.txt or ${FULL_FILE}.txt"
          exit 1
      fi
    - git add baseline-${SYS_TYPE}.saved
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -15,20 +15,43 @@
  tags:
    - shell
    - lassen
-  rules:
-    - if: '$CI_COMMIT_BRANCH =~ /_lnone/ || $ON_LASSEN == "OFF"' #run except if ...
-      when: never
-    - when: on_success
-
-# Spack helped builds
-# Generic lassen build job, extending build script
-# Note: Lassen jobs can start as soon as the setup job is complete.
-.build_and_test_on_lassen:
-  extends: [.build_blueos_3_ppc64le_ib_script, .on_lassen]
-  stage: l_build_and_test
-  needs: [setup]
-
-opt_mpi_cuda_xl_16_1_1_8:
  variables:
-    SPEC: "%xl@16.1.1.8 +mpi +cuda cuda_arch=70"
-  extends: .build_and_test_on_lassen
+    PLAT: lassen
+
+# Build MFEM
+build_mfem_ser_lassen:
+  extends: [.with_gcc_8_3_1, .on_lassen]
+  needs: [setup]
+  stage: lassen_build
+  script:
+    - mkdir -p ${BUILD_PATH}
+    - cp -r ${CI_PROJECT_DIR} ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser
+    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser
+    - lalloc 1 -W 5 -q pdebug make -j cuda CUDA_ARCH=sm_70
+
+build_mfem_debug_ser_lassen:
+  extends: [.with_gcc_8_3_1, .on_lassen]
+  needs: [setup]
+  stage: lassen_build
+  script:
+    - mkdir -p ${BUILD_PATH}
+    - cp -r ${CI_PROJECT_DIR} ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser_debug
+    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser_debug
+    - lalloc 1 -W 5 -q pdebug make -j cuda MFEM_DEBUG="YES" CPPFLAGS=-O2 CUDA_ARCH=sm_70
+
+# Sanity check
+sanitycheck_mfem_ser_lassen:
+  extends: [.with_gcc_8_3_1, .on_lassen]
+  stage: lassen_test
+  needs: [build_mfem_ser_lassen]
+  script:
+    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser
+    - lalloc 1 -W 15 -q pdebug make -j test
+
+sanitycheck_mfem_debug_ser_lassen:
+  extends: [.with_gcc_8_3_1, .on_lassen]
+  stage: lassen_test
+  needs: [build_mfem_debug_ser_lassen]
+  script:
+    - cd ${BUILD_PATH}/${CI_PROJECT_NAME}_lassen_ser_debug
+    - lalloc 1 -W 30 -q pdebug make -j test
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -15,170 +15,131 @@
  tags:
    - shell
    - quartz
-  rules:
-    # Don't run quartz jobs if...
-    - if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_QUARTZ == "OFF"'
-      when: never
-    # Don't run autotest update if...
-    - if: '$CI_JOB_NAME =~ /update_autotest/ && $AUTOTEST != "YES"'
-      when: never
-    # Don't run autotest update if...
-    - if: '$CI_JOB_NAME =~ /q_report/ && $AUTOTEST != "YES"'
-      when: never
-    # Report success on success status
-    - if: '$CI_JOB_NAME =~ /q_report_success/ && $AUTOTEST == "YES"'
-      when: on_success
-    # Report failure on failure status
-    - if: '$CI_JOB_NAME =~ /q_report_failure/ && $AUTOTEST == "YES"'
-      when: on_failure
-    # Always release resources
-    - if: '$CI_JOB_NAME =~ /release_resources/'
-      when: always
-    # Default is to run if previous stage succeeded
-    - when: on_success
-
-# This is a yaml anchor, it can be used to avoid duplication like here.
-# The code below will simply be pasted wherever the anchor is placed.
-.safe_create_rundir: &safe_create_rundir |
-  if ! mkdir ${rundir}; then
-    n=1
-    while ! mkdir ${rundir}_${n}
-    do
-      n=$((n+1))
-    done
-    rundir=${rundir}_${n}
-  fi
+  variables:
+    PLAT: quartz
+    MPIEXEC: srun
+    MPIEXEC_NP: "-n"
+    MAKE_PAR: 6
+    BASELINE_PAR: 18

 # Allocate
-q_allocate_resources:
+allocate_quartz:
  variables:
    GIT_STRATEGY: none
  extends: .on_quartz
-  stage: q_allocate_resources
+  stage: allocate
  script:
-    - salloc --exclusive --nodes=1 --partition=pdebug --time=30 --no-shell --job-name=${ALLOC_NAME}
+    - |
+      if [[ "${MPIEXEC}" == "srun" ]]
+      then
+      salloc --nodes=1 --extra-node-info=2:18:1 --partition=pdebug --time=30 --no-shell --job-name=${MFEM_ALLOC_NAME}
+      fi
  timeout: 6h

 # Release
-q_release_resources:
+deallocate_quartz:
  variables:
    GIT_STRATEGY: none
  extends: .on_quartz
-  stage: q_release_resources
+  stage: deallocate
  script:
-    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
-    - ([[ -n "${JOBID}" ]] && scancel ${JOBID})
+    - |
+      if [[ "${MPIEXEC}" == "srun" ]]
+      then
+      export JOB_ID=$(squeue -h --name=${MFEM_ALLOC_NAME} --format=%A)
+      ([[ -n "${JOB_ID}" ]] && scancel ${JOB_ID})
+      fi
+  when: always

-# Release
-q_report_success:
+# Build external libraries (tpls)
+build_hypre_gcc_6_1_0_quartz:
+  extends: [.build_hypre, .with_gcc_6_1_0, .on_quartz]
+
+build_parmetis_gcc_6_1_0_quartz:
+  extends: [.build_metis, .with_gcc_6_1_0, .on_quartz]
  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  stage: q_release_resources
-  script:
-    - echo "Can only run if all the quartz jobs passed"
-    - cd ${AUTOTEST_ROOT}/autotest && git pull
-    - rundir="gitlab/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
-    - *safe_create_rundir
-    - echo "The Quartz jobs were successful" > ${rundir}/gitlab.out
-    - echo "See the pipeline here -> $CI_PIPELINE_URL" >> ${rundir}/gitlab.err
-    - git add ${rundir}
-    - git commit -am "Gitlab CI log for baseline on quartz with intel ($(date +%Y-%m-%d))"
-    - git push origin master
+    METIS: parmetis

-q_report_failure:
+build_metis4_gcc_6_1_0_quartz:
+  extends: [.build_metis, .with_gcc_6_1_0, .on_quartz]
  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  stage: q_release_resources
-  script:
-    - echo "Runs if there was at least one failure on quartz"
-    - cd ${AUTOTEST_ROOT}/autotest && git pull
-    - rundir="gitlab/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
-    - *safe_create_rundir
-    - echo "There was an error while running CI on Quartz" > ${rundir}/gitlab.err
-    - echo "See the pipeline here -> $CI_PIPELINE_URL" >> ${rundir}/gitlab.err
-    - cp ${rundir}/gitlab.err ${rundir}/autotest-email.html
-    - git add ${rundir}
-    - git commit -am "Gitlab CI log for baseline on quartz with intel ($(date +%Y-%m-%d))"
-    - git push origin master
+    METIS: metis4

-# Spack helped builds
-# Generic quartz build job, extending build script
-.build_and_test_on_quartz:
-  extends: [.build_toss_3_x86_64_ib_script, .on_quartz]
-  stage: q_build_and_test
+build_metis5_gcc_6_1_0_quartz:
+  extends: [.build_metis, .with_gcc_6_1_0, .on_quartz]
+  variables:
+    METIS: metis5
+  allow_failure: true

 # Build MFEM
-debug_ser_gcc_4_9_3:
+build_mfem_debug_ser_gcc_4_9_3_quartz:
+  extends: [.build_mfem, .with_gcc_4_9_3, .on_quartz]
  variables:
-    SPEC: "%gcc@4.9.3 +debug~mpi"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "YES"
+    MFEM_USE_MPI: "NO"

-debug_ser_gcc_6_1_0:
+build_mfem_debug_ser_gcc_6_1_0_quartz:
+  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
  variables:
-    SPEC: "%gcc@6.1.0 +debug~mpi"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "YES"
+    MFEM_USE_MPI: "NO"

-debug_par_gcc_6_1_0:
+build_mfem_debug_par_gcc_6_1_0_quartz:
+  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
  variables:
-    SPEC: "%gcc@6.1.0 +debug+mpi"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "YES"
+    MFEM_USE_MPI: "YES"
+  needs: [build_hypre_gcc_6_1_0_quartz, build_parmetis_gcc_6_1_0_quartz]

-opt_ser_gcc_6_1_0:
+build_mfem_opt_ser_gcc_6_1_0_quartz:
+  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
  variables:
-    SPEC: "%gcc@6.1.0 ~mpi"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "NO"
+    MFEM_USE_MPI: "NO"

-opt_par_gcc_6_1_0:
+build_mfem_opt_par_gcc_6_1_0_quartz:
+  extends: [.build_mfem, .with_gcc_6_1_0, .on_quartz]
  variables:
-    SPEC: "%gcc@6.1.0"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "NO"
+    MFEM_USE_MPI: "YES"
+  needs: [build_hypre_gcc_6_1_0_quartz, build_parmetis_gcc_6_1_0_quartz]

-opt_par_gcc_6_1_0_sundials:
+### Tests
+
+# Sanity check
+sanitycheck_mfem_debug_ser_gcc_4_9_3_quartz:
+  extends: [.sanitycheck_mfem, .with_gcc_4_9_3, .on_quartz]
  variables:
-    SPEC: "%gcc@6.1.0 +sundials"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "YES"
+    MFEM_USE_MPI: "NO"
+  needs: [build_mfem_debug_ser_gcc_4_9_3_quartz, allocate_quartz]

-opt_par_gcc_6_1_0_petsc:
+sanitycheck_mfem_debug_ser_gcc_6_1_0_quartz:
+  extends: [.sanitycheck_mfem, .with_gcc_6_1_0, .on_quartz]
  variables:
-    SPEC: "%gcc@6.1.0 +petsc ^petsc+mumps"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "YES"
+    MFEM_USE_MPI: "NO"
+  needs: [build_mfem_debug_ser_gcc_6_1_0_quartz, allocate_quartz]

-opt_par_gcc_6_1_0_pumi:
+sanitycheck_opt_ser_mfem_gcc_6_1_0_quartz:
+  extends: [.sanitycheck_mfem, .with_gcc_6_1_0, .on_quartz]
  variables:
-    SPEC: "%gcc@6.1.0 +pumi"
-  extends: .build_and_test_on_quartz
+    MFEM_DEBUG: "NO"
+    MFEM_USE_MPI: "NO"
+  needs: [build_mfem_opt_ser_gcc_6_1_0_quartz, allocate_quartz]

-# Baseline jobs form an independent set of jobs. We use `needs:[]` to specify
-# that "setup-baseline" can start immediately. Then, we have to use needs for
-# each one of the baseline jobs, otherwise they will wait for the rest of the
-# pipeline.
+sanitycheck_opt_par_mfem_gcc_6_1_0_quartz:
+  extends: [.sanitycheck_mfem, .with_gcc_6_1_0, .on_quartz]
+  variables:
+    MFEM_DEBUG: "NO"
+    MFEM_USE_MPI: "YES"
+  needs: [build_mfem_opt_par_gcc_6_1_0_quartz, allocate_quartz]

+# Baseline
 baselinecheck_mfem_intel_quartz:
  extends: [.baselinecheck_mfem, .on_quartz]
-  needs: [setup_baseline]
-
-update_autotest:
-  extends: [.on_quartz]
-  needs: [baselinecheck_mfem_intel_quartz]
-  stage: baseline_to_autotest
-  script:
-    - cd ${AUTOTEST_ROOT}/autotest && git pull
-    - rundir="quartz/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
-    - *safe_create_rundir
-    - cp ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/* ${rundir}
-    # We create an autotest-email.html file, because that's how we signal that there was a diff (temporary).
-    - |
-      if [[ -f ${rundir}/*.err ]]
-      then
-        echo "See the pipeline here -> $CI_PIPELINE_URL" >> ${rundir}/*.err
-        cp ${rundir}/*.err ${rundir}/autotest-email.html
-      fi
-    - git add ${rundir}
-    - git commit -am "Gitlab CI log for baseline on quartz with intel ($(date +%Y-%m-%d))"
-    - git push origin master
+  needs: [allocate_quartz]

 baselinepublish_mfem_quartz:
-  extends: [.on_quartz, .rebaseline_mfem]
+  extends: [.rebaseline_mfem, .on_quartz]
  needs: [baselinecheck_mfem_intel_quartz]
@@ -0,0 +1,469 @@
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
+# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+# LICENSE and NOTICE for details. LLNL-CODE-806117.
+#
+# This file is part of the MFEM library. For more information and source code
+# availability visit https://mfem.org.
+#
+# MFEM is free software; you can redistribute it and/or modify it under the
+# terms of the BSD-3 license. We welcome feedback and contributions, see file
+# CONTRIBUTING.md for details.
+
+language: cpp
+
+os: linux
+dist: bionic
+
+stages:
+  - checks
+  - tests
+  - optional
+
+env:
+  global:
+    - HYPRE_ARCHIVE=v2.19.0.tar.gz
+      HYPRE_URL=https://github.com/hypre-space/hypre/archive/$HYPRE_ARCHIVE
+      HYPRE_TOP_DIR=hypre-2.19.0
+
+jobs:
+  include:
+
+    # ========================
+    #         Checks
+    # ========================
+    # - code-style
+    # - documentation
+    # - gitignore
+
+    - stage: checks
+      os: linux
+      dist: xenial
+      name: "code-style"
+      addons:
+        apt:
+          packages:
+            - astyle=2.05.1-0ubuntu1
+      script:
+        - cd ${TRAVIS_BUILD_DIR}
+        - cd tests/scripts
+        - ./runtest code-style
+
+    - stage: checks
+      os: linux
+      name: "documentation"
+      addons:
+        apt:
+          packages:
+            - doxygen
+            - graphviz
+      script:
+        - cd ${TRAVIS_BUILD_DIR}
+        - cd tests/scripts
+        - ./runtest documentation
+
+    - stage: checks
+      os: linux
+      name: "gitignore"
+      addons:
+        apt:
+          packages:
+            - mpich
+            - libmpich-dev
+      env: MPI=YES
+      before_script:
+        - cd ${TRAVIS_BUILD_DIR}
+        - mpicxx -v
+        - make config MFEM_USE_MPI=YES MFEM_MPI_NP=2
+        - make all -j3
+        - make test-noclean
+      script:
+        - cd tests/scripts
+        - ./runtest gitignore
+      cache:
+        ccache: true
+        directories:
+          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
+          - $TRAVIS_BUILD_DIR/../metis-4.0
+      before_cache:
+        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
+          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
+          rm -f Lib/*.{c,o}
+
+    # ========================
+    #  Optional Checks/Tests
+    # ========================
+    # - branch-history
+
+    - stage: optional
+      name: "branch-history"
+      if: branch != next
+      # need full git history for the binary/big files check
+      git:
+        depth: false
+      script:
+        - cd ${TRAVIS_BUILD_DIR}
+        # update master
+        - git fetch origin master:master
+        # checkout a branch (otherwise Travis works in detached head)
+        - git checkout -b travis_tests
+        - cd tests/scripts
+        - ./runtest branch-history
+
+    # ========================
+    #       Linux tests
+    # ========================
+    # - serial + debug
+    # - serial
+    # - parallel + debug
+    # - parallel
+
+    - stage: tests
+      os: linux
+      compiler: gcc
+      name: "Linux: Serial + Debug"
+      env: DEBUG=YES
+           MPI=NO
+           CODECOV=NO
+           MFEM_TEST_TARGET=check
+      cache:
+        ccache: true
+
+    - os: linux
+      compiler: gcc
+      name: "Linux: Serial"
+      env: DEBUG=NO
+           MPI=NO
+           CODECOV=NO
+           MFEM_TEST_TARGET=test
+      cache:
+        ccache: true
+
+    - os: linux
+      compiler: gcc
+      name: "Linux: Parallel + Debug"
+      addons:
+        apt:
+          # sources:
+            # - ubuntu-toolchain-r-test
+          packages:
+            # GCC 4.9
+            # - g++-4.9
+            # MPICH
+            - mpich
+            - libmpich-dev
+            # OpenMPI
+            # - openmpi-bin
+            # - libopenmpi-dev
+      env: DEBUG=YES
+           MPI=YES
+           CODECOV=NO
+           MFEM_TEST_TARGET=check
+           NPROCS=2
+      cache:
+        ccache: true
+        directories:
+          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
+          - $TRAVIS_BUILD_DIR/../metis-4.0
+      before_cache:
+        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
+          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
+          rm -f Lib/*.{c,o}
+
+    - os: linux
+      compiler: gcc
+      name: "Linux: Parallel"
+      addons:
+        apt:
+          # sources:
+            # - ubuntu-toolchain-r-test
+          packages:
+            # GCC 4.9
+            # - g++-4.9
+            # MPICH
+            - mpich
+            - libmpich-dev
+            # OpenMPI
+            # - openmpi-bin
+            # - libopenmpi-dev
+      env: DEBUG=NO
+           MPI=YES
+           CODECOV=YES
+           MFEM_TEST_TARGET=test
+           NPROCS=2
+      cache:
+        ccache: true
+        directories:
+          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
+          - $TRAVIS_BUILD_DIR/../metis-4.0
+      before_cache:
+        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
+          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
+          rm -f Lib/*.{c,o}
+
+    - os: linux
+      compiler: gcc
+      name: "Linux: Parallel (cmake)"
+      addons:
+        apt:
+          packages:
+            - mpich
+            - libmpich-dev
+      env: MPI=YES
+           NPROCS=2
+      script:
+        - cd ${TRAVIS_BUILD_DIR}
+        - mkdir ${TRAVIS_BUILD_DIR}/build
+        - cd ${TRAVIS_BUILD_DIR}/build
+        - cmake ..
+             -DMFEM_USE_MPI=ON
+             -DHYPRE_DIR=${TRAVIS_BUILD_DIR}/../$HYPRE_TOP_DIR/src/hypre
+             -DMFEM_MPI_NP=$NPROCS
+        - make -j3 mfem examples
+        - cd ${TRAVIS_BUILD_DIR}/build/tests/unit
+        - make -j3
+        - ctest --output-on-failure
+      cache:
+        ccache: true
+        directories:
+          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
+          - $TRAVIS_BUILD_DIR/../metis-4.0
+      before_cache:
+        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
+          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
+          rm -f Lib/*.{c,o}
+
+    # ========================
+    #      Mac OS X tests
+    # ========================
+    # - serial + debug
+    # - serial
+    # - parallel + debug
+    # - parallel
+
+    - os: osx
+      osx_image: xcode11.2
+      compiler: clang
+      name: "Mac: Serial + Debug"
+      addons:
+        homebrew:
+          packages:
+            - ccache
+      env: DEBUG=YES
+           MPI=NO
+           CODECOV=NO
+           MFEM_TEST_TARGET=check
+      cache:
+        ccache: true
+
+    - os: osx
+      osx_image: xcode11.2
+      compiler: clang
+      name: "Mac: Serial"
+      addons:
+        homebrew:
+          packages:
+            - ccache
+      env: DEBUG=NO
+           MPI=NO
+           CODECOV=NO
+           MFEM_TEST_TARGET=test
+      cache:
+        ccache: true
+
+    - os: osx
+      osx_image: xcode11.2
+      compiler: clang
+      name: "Mac: Parallel + Debug"
+      addons:
+        homebrew:
+          packages:
+            - ccache
+      env: DEBUG=YES
+           MPI=YES
+           CODECOV=NO
+           MFEM_TEST_TARGET=check
+           NPROCS=4
+           TMPDIR=/tmp
+      cache:
+        ccache: true
+        directories:
+          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
+          - $TRAVIS_BUILD_DIR/../metis-4.0
+          - $HOME/local-cached
+      before_cache:
+        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
+          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
+          rm -f Lib/*.{c,o}
+
+    - os: osx
+      osx_image: xcode11.2
+      compiler: clang
+      name: "Mac: Parallel"
+      addons:
+        homebrew:
+          packages:
+            - ccache
+      env: DEBUG=NO
+           MPI=YES
+           CODECOV=YES
+           MFEM_TEST_TARGET=test
+           NPROCS=4
+           TMPDIR=/tmp
+      cache:
+        ccache: true
+        directories:
+          - $TRAVIS_BUILD_DIR/../$HYPRE_TOP_DIR/src/hypre
+          - $TRAVIS_BUILD_DIR/../metis-4.0
+          - $HOME/local-cached
+      before_cache:
+        - cd $TRAVIS_BUILD_DIR/../metis-4.0;
+          mv libmetis.a Lib ..; rm -rf * ; mv ../libmetis.a ../Lib .;
+          rm -f Lib/*.{c,o}
+
+before_install:
+   # No addon for brew yet, have to install OSX packages this way.
+   # - if [ $TRAVIS_OS_NAME == "osx" ] && [ $MPI == "YES" ]; then
+   #      brew install open-mpi;
+   #   fi
+
+   # Disable ccache while building dependencies that are cached:
+   - echo "before \$PATH = $PATH";
+     export PATH=${PATH//\/usr\/lib\/ccache:/};
+     echo "after  \$PATH = $PATH"
+
+   # On Mac OS X, build and cache OpenMPI 2.1.6:
+   - if [ $TRAVIS_OS_NAME == "osx" ] && [ $MPI == "YES" ]; then
+        if [ ! -e $HOME/local-cached/bin/mpicc ]; then
+           mkdir -p $HOME/builds && cd $HOME/builds &&
+           wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.6.tar.bz2 &&
+           tar jxf openmpi-2.1.6.tar.bz2 &&
+           mkdir openmpi-build && cd openmpi-build &&
+           ../openmpi-2.1.6/configure --prefix=$HOME/local-cached &&
+           make -j3 all && make install;
+        fi;
+        PATH=$HOME/local-cached/bin:$PATH;
+        cd $TRAVIS_BUILD_DIR;
+     fi
+
+   # Update environment to find g++ 4.9 installation first.
+   # - if [ $TRAVIS_OS_NAME == "linux" ]; then
+   #      mkdir -p latest-gcc-symlinks;
+   #      ln -s /usr/bin/g++-4.9 latest-gcc-symlinks/g++;
+   #      ln -s /usr/bin/gcc-4.9 latest-gcc-symlinks/gcc;
+   #      ln -s /usr/bin/gcov-4.9 latest-gcc-symlinks/gcov;
+   #      export PATH=$PWD/latest-gcc-symlinks:$PATH;
+   #   fi
+
+   # Install tool to upload code coverage reports to coveralls.io
+   - if [ "$CODECOV" == "YES" ]; then
+        export PYTHONUSERBASE=$HOME/local;
+        pip install --user cpp-coveralls;
+        pip install --user pyyaml;
+        PATH=$HOME/local/bin:$PATH;
+     fi
+
+install:
+   # Set MPI compilers, print compiler version
+   - if [ $MPI == "YES" ]; then
+        if [ "$TRAVIS_OS_NAME" == "linux" ]; then
+           export MPICH_CC="$CC";
+           export MPICH_CXX="$CXX";
+        else
+           export OMPI_CC="$CC";
+           export OMPI_CXX="$CXX";
+           mpic++ --showme:version;
+        fi;
+        mpic++ -v;
+     else
+        $CXX -v;
+     fi
+
+   # Back out of the mfem directory to install the libraries
+   - cd ..
+
+   # hypre
+   - if [ $MPI == "YES" ]; then
+        if [ ! -e $HYPRE_TOP_DIR/src/hypre/lib/libHYPRE.a ]; then
+           wget $HYPRE_URL;
+           rm -rf $HYPRE_TOP_DIR;
+           tar xvzf $HYPRE_ARCHIVE;
+           cd $HYPRE_TOP_DIR/src;
+           ./configure --disable-fortran CC=mpicc CXX=mpic++;
+           make -j3;
+           cd ../..;
+        else
+            echo "Reusing cached $HYPRE_TOP_DIR/";
+        fi;
+        ln -s $HYPRE_TOP_DIR hypre;
+     else
+        echo "Serial build, not using hypre";
+     fi
+
+   # METIS, use a mirror because the original source server is not always up.
+   # Original url:
+   #    http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz
+   - if [ $MPI == "YES" ]; then
+        if [ ! -e metis-4.0/libmetis.a ]; then
+           wget https://mfem.github.io/tpls/metis-4.0.3.tar.gz;
+           tar xvzf metis-4.0.3.tar.gz;
+           make -j3 -C metis-4.0.3/Lib CC="$CC" OPTFLAGS="-O2";
+           rm -rf metis-4.0;
+           mv metis-4.0.3 metis-4.0;
+        else
+           echo "Reusing cached metis-4.0/";
+        fi;
+     fi
+
+   # Re-enable ccache on linux; enable ccache on mac os:
+   - if [ $TRAVIS_OS_NAME == "linux" ]; then
+        export PATH="/usr/lib/ccache:$PATH";
+     else
+        if [ $TRAVIS_OS_NAME == "osx" ]; then
+           export PATH="/usr/local/opt/ccache/libexec:$PATH";
+        fi;
+     fi
+
+   - printf "which \$CC  = "; which $CC;
+     printf "which \$CXX = "; which $CXX
+
+script:
+   # Compiler
+   - if [ $MPI == "YES" ]; then
+        export MYCXX=mpic++;
+        export MAKE_CXX_FLAG=MPICXX=$MYCXX;
+     else
+        export MYCXX="$CXX";
+        export MAKE_CXX_FLAG=CXX=$MYCXX;
+     fi
+
+   # Print the compiler version
+   - $MYCXX -v
+
+   # Set some variables
+   - cd $TRAVIS_BUILD_DIR;
+     CPPFLAGS="";
+     SKIP_TEST_DIRS="";
+     if [ "$CODECOV" == "YES" ]; then
+        CPPFLAGS="--coverage -g";
+     fi;
+     if [ "$TRAVIS_OS_NAME" != "linux" ] || [ "$DEBUG" == "YES" ]; then
+        CPPFLAGS+=" -pedantic -Wall -Werror";
+     fi
+
+   # Configure the library
+   - make config MFEM_USE_MPI=$MPI MFEM_DEBUG=$DEBUG $MAKE_CXX_FLAG
+        MFEM_MPI_NP=$NPROCS CPPFLAGS="$CPPFLAGS"
+   # Show the configuration
+   - make info
+   # Build the library
+   - make -j3
+   # Build the examples and the miniapps
+   - make -j3 all
+   # Run tests
+   - make $MFEM_TEST_TARGET SKIP_TEST_DIRS="$SKIP_TEST_DIRS"
+
+after_success:
+   - if [ "$CODECOV" == "YES" ]; then
+        coveralls --include fem --include general --include linalg --include
+           mesh --exclude /usr --gcov-options '\-lp' --root $TRAVIS_BUILD_DIR;
+     fi
@@ -8,109 +8,11 @@
                               https://mfem.org


-Version 4.3.1 (development)
+Version 4.2.1 (development)
 ===========================
- Added support for hr-adaptivity using TMOP-based error estimator.

- Adding lowest order Nedelec and Raviart-Thomas basis functions on wedge
-  shaped elements.
-
- Added initial support for meshes with pyramidal elements, including several
-  pyramidal meshes in the data/ directory and support for the lowest order H1,
-  Nedelec, Raviart-Thomas, and L2 basis functions on pyramids.
-
- Updated the hypre interface according to changes in hypre-2.22.1. The ADS
-  solver is now fully working on GPUs.
-
- Tetrahedral meshes no longer need to be reordered to support high order
-  Nedelec basis functions. This will allow future support for Nedelec basis
-  functions on wedges and pyramids which are not amenable to reordering. The
-  ReorientTetMesh method of the Mesh and ParMesh classes has been deprecated.
-
-
-Version 4.3, released on July 29, 2021
-======================================
-
-Discretization improvements
---------------------------
- Variable order spaces, p- and hp-refinement. This is the initial (serial)
-  support for variable-order FiniteElementCollection and FiniteElementSpace.
-  The new method FiniteElementSpace::SetElementOrder can be called to set an
-  arbitrary order for each mesh element. The conforming interpolation matrix
-  will now automatically constrain p- and hp- interfaces, enabling general
-  hp-refinement in both 2D and 3D, on uniform or mixed NC meshes. Support for
-  parallel variable-order spaces will follow shortly.
-
- Extended the support for field transfer between high-order and low-order
-  refined finite element spaces to include: dual fields and H1 fields (both
-  primary and dual). These are illustrated in the lor-transfer miniapp.
-
- Improved libCEED integration, including support for VectorCoefficient,
-  ConvectionIntegrator, and VectorConvectionNLFIntegrator with libCEED backends.
-
- Extending support for L2 basis functions using MapTypes VALUE and INTEGRAL in
-  linear interpolators and GridFunction "GetValue" methods.
-
- Changed the interface for the error estimator and implemented the Kelly error
-  indicator for scalar-valued problems, supported in serial and parallel builds.
-
- Added support for the "BR2" discontinuous Galerkin discretization for
-  diffusion via DGDiffusionBR2Integrator (see Example 14/14p).
-
- Added convective and skew-symmetric integrators for the nonlinear term in the
-  Navier-Stokes equations.
-
- Added new classes DenseSymmetricMatrix and SymmetricMatrixCoefficient for
-  efficient evaluation of symmetric matrix coefficients. This replaces the now
-  deprecated EvalSymmetric in MatrixCoefficient. Added DiagonalMatrixCoefficient
-  for clarity, which is a typedef of VectorCoefficient.
-
- Added support for nonscalar coefficient with VectorDiffusionIntegrator.
-
-Linear and nonlinear solvers
----------------------------
- Added support for AMG preconditioners on GPUs based on the hypre library
-  (version 2.22.0 or later). These include BoomerAMG, AMS and ADS and most
-  MFEM examples that use hypre have been ported to support this functionality.
-  The GPU preconditioners require that both hypre and MFEM are built with CUDA
-  support. Hypre builds with CUDA and unified memory are also supported and
-  can be used with `-d cuda:uvm` as a command-line option.
-
- Added support for AMG preconditioners for non-symmetric systems (e.g.
-  advection-dominated problems) using hypre's approximate ideal restriction
-  (AIR) AMG. Requires hypre version 2.14.0 or newer. Usage is illustrated in
-  example 9/9p.
-
- Added new functionality for constructing low-order refined discretizations and
-  solvers, see the LORDiscretization and LORSolver classes. A new basis type for
-  H(curl) and H(div) spaces is introduced to give spectral equivalence. This
-  functionality is illustrated in the LOR solvers miniapp in miniapps/solvers.
-
- Generalized the Multigrid class to support non-geometric multigrid. Previous
-  functionality, based on FiniteElementSpaceHierarchy, is now available in the
-  derived class GeometricMultigrid.
-
- Introduced solver interface for linear problems with constraints, a few
-  concrete solvers that implement the interface, and a demonstration of their
-  use in Example 28(p), which solves an elasticity problem with zero normal
-  displacement (but allowed tangential displacement) on two boundaries.
-
- Added high-order matrix-free auxiliary Maxwell solver for H(curl) problems,
-  as described in Barker and Kolev 2020 (https://doi.org/10.1002/nla.2348). See
-  Example 3p and linalg/auxiliary.?pp.
-
- Improved interface for using the Ginkgo library, including: support for matrix-
-  free operators in Ginkgo solvers, new wrappers for Ginkgo preconditioners, HIP
-  support, and reduction of unnecessary data copies.
-
- Added initial support for hypre's mixed integer (mixedint) capability, which
-  uses different data types for local and global indices in order to save memory
-  in large problems. This capability requires that hypre was configured with the
-  --enable-mixedint option. Note that this option is currently tested only in
-  ex1p, ex3p, and ex4p, and may not work in more general settings.
-
- Added AlgebraicCeedSolver that does matrix-free algebraic p-multigrid for
-  diffusion problems with the Ceed backend.
+- Added matrix-free GPU-enabled implementations of GradientInterpolator and
+  IdentityInterpolator.

 - Added interface to MUMPS direct solver. Its usage is demonstrated in ex25p.
  See http://mumps.enseeiht.fr/ for more details. Supported versions >= 5.1.1.
@@ -118,198 +20,64 @@ Linear and nonlinear solvers
 - Added three ESDIRK time integrators: implicit trapezoid rule, L-stable
  ESDIRK-32, and A-stable ESDIRK-33.

- Implemented a variable step-size IMEX (VSSIMEX) method for the Navier miniapp.
+- Added a "scaled Jacobian" visualization option in the Mesh Explorer miniapp to
+  help identify elements with poor mesh quality.

- Implemented an adaptive linear solver tolerance option for NewtonSolver based
-  on the algorithm of Eisenstat and Walker.
+- Added support for the "BR2" discontinuous Galerkin discretization for
+  diffusion via DGDiffusionBR2Integrator (see Example 14/14p).

-Meshing improvements
--------------------
- Added support for reading high-order Lagrange meshes in VTK format. Arbitrary-
-  orders and all element types are supported. See the VTK blog for more info:
-  https://blog.kitware.com/wp-content/uploads/2018/09/Source_Issue_43.pdf.
+- Generalized the Multigrid class to support non-geometric multigrid. The
+  previous functionality, based on FiniteElementSpaceHierarchy, is now available
+  in the derived class GeometricMultigrid.

- Introduced a new non-conforming mesh format that fixes known inconsistencies
-  of legacy "MFEM mesh v1.1" NC format and works consistently in both serial and
-  parallel. ParMesh::ParPrint can now print non-conforming AMR meshes that can
-  be used to restart a parallel AMR computation. Example 6p has been extended to
-  demonstrate restarting from a previously saved checkpoint. Note that parallel
-  NC data files are compatible with serial code, e.g., can be viewed with serial
-  GLVis. Loading of legacy NC mesh files is still supported.
-
- Added FMS support (https://github.com/CEED/FMS) to mfem. FMS can represent
-  unstructured high-order meshes with general high-order finite element fields
-  on them. When enabled, mfem can convert data collections to/from FMS data
-  collections in memory. In addition, an FMS data collection class was added so
-  the convert-dc miniapp can read and generate data files in FMS format.
-
- Added new mesh quality metrics and improved the untangling capabilities of the
-  TMOP-based mesh optimization algorithms.
-
- The TMOP mesh optimization algorithms were extended to GPU:
-  * QualityMetric 1, 2, 7, 77 are available in 2D, 302, 303, 315, 321 in 3D
-  * Both AnalyticAdaptTC and DiscreteAdaptTC TargetConstructor are available
-  * Kernels for normalization and limiting have been added
-  * The AdvectorCG now also supports AssemblyLevel::PARTIAL
-
- Added support for creating refined meshes for all element types (e.g. by
-  splitting high-order elements into low-order refined elements), including
-  mixed meshes. The LOR Transfer miniapp (miniapps/tools/lor-transfer.cpp) now
-  supports meshes with any element geometry.
-
- Meshes consisting of any type of elements (including mixed meshes) can be
-  converted to all-simplex meshes using Mesh::MakeSimplicial.
-
- Several of the mesh constructors (creating Cartesian meshes, refined (LOR)
-  meshes, simplex meshes, etc.) are now available as "named constructors", e.g.
-  Mesh::MakeCartesian2D or Mesh::MakeRefined. The legacy constructors are marked
-  as deprecated.
-
- Added support for creating periodic meshes with Mesh::MakePeriodic. The
-  requisite periodic vertex mappings can be created with
-  Mesh::CreatePeriodicVertexMapping.
-
- Added support for 1D non-conforming meshes (which can be useful for parallel
-  load balancing and derefinement).
-
- Added sample meshes in the `data` subdirectory showing the reference elements
-  of the six currently supported element types; ref-segment.mesh,
-  ref-triangle.mesh, ref-square.mesh, ref-tetrahedron.mesh, ref-cube.mesh, and
-  ref-prism.mesh.
-
-High-performance computing
--------------------------
- Added initial support for GPU-accelerated versions of PETSc that works with
-  MFEM_USE_CUDA if PETSc has been configured with CUDA support. Examples 1 and 9
-  in the examples/petsc directory have been modified to work with --device cuda.
-  Examples with GAMG (ex1p) and SLEPc (ex11p) are also provided.
-
- Added support for explicit vectorization in the high-performance templated
-  code for Fujitsu's A64FX ARM microprocessor architecture.
-
- Added support for different modes of QuadratureInterpolator on GPU.
-  The layout (QVectorLayout::byNODES|byVDIM) and the tensor products modes can
-  be enabled before calling the Mult, Values, Derivatives, PhysDerivatives and
-  Determinants methods.
-
- Added method Device::SetMemoryTypes that can be used to change the default
-  host and device MemoryTypes before Device setup.
-
- In class MemoryManager, added methods GetDualMemoryType and SetDualMemoryType;
-  dual MemoryTypes are used to determine the second MemoryType (host or device)
-  when only one MemoryType is specified in methods of class Memory.
-
- Added Memory constructor for setting both the host and device MemoryTypes.
-
- Switched the default behavior of device memory allocations so that they are
-  deferred until the device pointer is needed.
-
- Added a second Umpire device MemoryType, DEVICE_UMPIRE_2, with corresponding
-  allocator that can be set with the method SetUmpireDevice2AllocatorName.
-
- Added HOST_PINNED MemoryType and a pinned host allocator for CUDA and HIP.
-
- Added matrix-free GPU-enabled implementations of GradientInterpolator and
-  IdentityInterpolator.
-
-New and updated examples and miniapps
-------------------------------------
- Added a new, very simple example (ex0 and parallel version ex0p). This example
-  solves a simple Poisson problem using H1 elements (the same problem as ex1),
-  but is intended to be extremely simple and approachable for new users.
-
- Added new miniapps demonstrating: 1) the use of GSLIB for overlapping grids,
-  see gslib/schwarz_ex1, and 2) coupling different physics in different domains,
-  see navier/cht. Note that gslib v1.0.7 is require (see INSTALL for details).
-
- Added a new miniapp for computing (signed) distance functions to a point
-  source or zero level set. See miniapps/shifted/distance.cpp.
-
- Added a high-order extension of the shifted boundary method to solve PDEs on
-  non body-fitted meshes. This is illustrated in the new Shifted Diffusion
-  miniapp, see miniapps/shifted/diffusion.cpp.
-
- Added new miniapp directory mtop/ with optimization-oriented block parametric
-  non-linear form and abstract integrators. Two new miniapps, ParHeat and
-  SeqHeat, demonstrate parallel and sequential implementation of gradients
-  evaluation for linear diffusion with discrete density.
-
- Added a new miniapp block-solvers that compares the performance of various
-  solvers for mixed finite element discretization of the second order scalar
-  elliptic equations. Currently available solvers in the miniapp include a
-  block-diagonal preconditioner that is based on approximate Schur complement
-  (implemented in ex5p), and a newly implemented solver DivFreeSolver, which
-  exploits a multilevel decomposition of the Raviart-Thomas space and its
-  divergence-free subspace. See the miniapps/solvers directory for more details.
-
- Introduced new options for the mesh-explorer miniapp to visualize the actual
-  element attributes in parallel meshes while retaining the visualization of the
-  domain decomposition.
-
- Added partial assembly and device support to Example 25/25p, with diagonal
-  preconditioning.
+- Upgraded the Catch unit test framework from version 2.13.0 to version 2.13.2.

 - Implemented a filter method for the Navier miniapp to stabilize highly
  turbulent flows in direct numerical simulation.

-Improved testing
----------------
- Transitioned from Travis to GitHub Action for testing/CI on GitHub.
+- Added HIP support to the CMake build system.

- Use Spack (and Uberenv) to automate TPL building in LLNL GitLab tests.
-
- Extended `make test` to include GPU tests when MFEM is built with CUDA or HIP
-  support.
-
- Added a set of suggested git hooks for developers in config/githooks.
-
- Added support for Caliper: a library to integrate performance profiling
-  capabilities into applications. See examples/caliper for more details.
-
- Added a new command line boolean option (`--all`) to the unit tests to launch
-  *all* non-regression tests.
-
- Upgraded the Catch unit test framework from version 2.13.0 to version 2.13.2.
-
-Miscellaneous
-------------
- The following integrations have updated minimum version requirements:
-  * CUDA >= 10.1.168
-  * Ginkgo >= 1.4.0
-  * GSLIB >= 1.0.7
-  * HIOP >= 0.4
-  * HYPRE >= 2.20.0 for mixedint support
-  * HYPRE >= 2.22.0 for CUDA support
-  * libCEED >= 0.8
-  * PETSc >= 3.15.0 for CUDA support
-  * RAJA >= 0.13.0
-  see INSTALL for more details.
-
- Added a "scaled Jacobian" visualization option in the Mesh Explorer miniapp to
-  help identify elements with poor mesh quality.
+- Added support for reading high-order Lagrange meshes in VTK format. Arbitrary-
+  orders and all element types are supported. See the VTK blog for more info:
+  https://blog.kitware.com/wp-content/uploads/2018/09/Source_Issue_43.pdf.

 - Added support for reading VTK meshes in XML format.

- Added makefile rule to generate TAGS table for vi or Emacs users.
+- Added partial assembly and device support to Example 25/25p, with diagonal
+  preconditioning.

- Added HIP support to the CMake build system.
+- Implemented a variable step-size IMEX (VSSIMEX) method for the Navier miniapp.

- Various other simplifications, extensions, and bugfixes in the code.
+- Added new mesh quality metrics and improved the untangling capabilities of the
+  TMOP-based mesh optimization algorithms.

-API changes
-----------
- Added an abstract interface `mfem::FaceRestriction` for `H1FaceRestriction`
-  and `L2FaceRestriction`.
-  In order to conform with the semantic of `MultTranspose` in `mfem::Operator`,
-  `mfem::FaceRestriction::MultTranspose` now sets instead of adding values, and
-  `mfem::FaceRestriction::AddMultTranspose` should replace previous calls to
-  `mfem::FaceRestriction::MultTranspose`.
+- Changed the interface for the error estimator.
+
+- Implemented the parallel Kelly error indicator for scalar-valued problems.
+
+- Added new classes DenseSymmetricMatrix and SymmetricMatrixCoefficient for
+  efficient evaluation of symmetric matrix coefficients. This replaces the now
+  deprecated EvalSymmetric in MatrixCoefficient. Added DiagonalMatrixCoefficient
+  for clarity, which is a typedef of VectorCoefficient.
+
+- Added support for AMG preconditioners for non-symmetric systems (e.g.
+  advection-dominated problems) using hypre's approximate ideal restriction
+  (AIR) AMG. Requires hypre version 2.14.0 or newer. Usage is illustrated in
+  example 9/9p.
+
+- Implemented an adaptive linear solver tolerance option for NewtonSolver based
+  on the algorithm of Eisenstat and Walker.
+
+- Added support for nonscalar coefficient with VectorDiffusionIntegrator.
+
+- Extending support for L2 basis functions using MapTypes VALUE and INTEGRAL in
+  linear interpolators and GridFunction "GetValue" methods.


 Version 4.2, released on October 30, 2020
 =========================================

-High-performance computing
+High-Performance Computing
 --------------------------
 - Added support for explicit vectorization in the high-performance templated
  code, which can now take advantage of specific classes on the following
@@ -501,7 +269,7 @@ New and updated examples and miniapps
    L2, with partial assembly support in Example 24/24p.
  * Weak Dirichlet boundary conditions (Nitsche) to the NURBS miniapp.

-Data management and visualization
+Data management and Visualization
 ---------------------------------
 - Added support for ADIOS2 for parallel I/O with ParaView visualization. See
  Examples 5, 9, 12, 16. The classes adios2stream and ADIOS2DataCollection
@@ -1177,7 +945,7 @@ New and updated examples and miniapps

 - Added a new meshing miniapp, Shaper, that can be used to resolve complicated
  material interfaces by mesh refinement, e.g. as a tool for initial mesh
-  generation from prescribed "material()" function. Both conforming and
+  generation from prescribed "material()" function.  Both conforming and
  non-conforming (isotropic and anisotropic) refinements are supported.

 - Added a new meshing miniapp, Mesh Optimizer, that demonstrates the use of TMOP
@@ -1189,7 +957,7 @@ Discretization improvements
 ---------------------------
 - Added a FindPoints method of the Mesh and ParMesh classes that returns the
  elements that contain a given set of points, together with the coordinates of
-  the points in the reference space of the corresponding element. In parallel,
+  the points in the reference space of the corresponding element.  In parallel,
  if a point is shared by multiple processors, only one of them will mark that
  point as found. Note that the current implementation of this method is not
  optimal and/or 100% reliable. See the mesh-explorer miniapp for an example.
@@ -1516,7 +1284,7 @@ New and improved linear solvers
  which is a sparse direct solver for distributed memory architectures. As such
  it can only be enabled along with MFEM_USE_MPI. When MFEM is configured with
  MFEM_USE_SUPERLU, one also needs to alter the version of METIS, since SuperLU
-  requires ParMETIS (which comes packaged with a serial version of METIS). See
+  requires ParMETIS (which comes packaged with a serial version of METIS).  See
  http://crd-legacy.lbl.gov/~xiaoye/SuperLU for SuperLU_DIST details.

 - Added a wrapper for the KLU solver in SuiteSparse see
@@ -1927,7 +1695,7 @@ New and updated examples
  (ADS) in hypre.

 - Modified Example 1 to use isoparametric discretization (use the FE space from
-  the mesh) including NURBS meshes and spaces. Updated Example 2 to support
+  the mesh) including NURBS meshes and spaces.  Updated Example 2 to support
  arbitrary order spaces. Updated all examples to work with NURBS meshes and
  spaces, as well as to not use projection onto discontinuous polynomial spaces
  for visualization (this is now handled directly in GLVis when necessary).
@@ -2019,7 +1787,7 @@ Version 1.1, released on Sep 13, 2010
 New MFEM format for general meshes
 ----------------------------------
 - New MFEM mesh v1.0 format with uniform structure for any dimension and support
-  for curved meshes including in 3D. Class Mesh will recognize and read the new
+  for curved meshes including in 3D.  Class Mesh will recognize and read the new
  format (in addition to all previously used formats) and Mesh::Print uses the
  new format by default. The old print function was renamed to Mesh::PrintXG.

@@ -1,66 +0,0 @@
-cff-version: 1.2.0
-message: "If you use MFEM, please cite it as follows."
-authors:
- family-names: "MFEM Team"
-title: "MFEM: Modular Finite Element Methods [Software]"
-doi: 10.11578/dc.20171025.1248
-url: "https://mfem.org"
-preferred-citation:
-  type: article
-  authors:
-  - family-names: "Anderson"
-    given-names: "Robert"
-    orcid: "https://orcid.org/0000-0002-3508-9944"
-  - family-names: "Andrej"
-    given-names: "Julian"
-    orcid: "https://orcid.org/0000-0001-7661-4840"
-  - family-names: "Barker"
-    given-names: "Andrew"
-    orcid: "https://orcid.org/0000-0003-3572-911X"
-  - family-names: "Bramwell"
-    given-names: "Jamie"
-  - family-names: "Camier"
-    given-names: "Jean-Sylvain"
-    orcid: "https://orcid.org/0000-0003-2421-1999"
-  - family-names: "Cerveny"
-    given-names: "Jakub"
-    orcid: "https://orcid.org/0000-0003-4231-2531"
-  - family-names: "Dobrev"
-    given-names: "Veselin"
-    orcid: "https://orcid.org/0000-0003-1793-5622"
-  - family-names: "Dudouit"
-    given-names: "Yohann"
-    orcid: "https://orcid.org/0000-0001-5831-561X"
-  - family-names: "Fisher"
-    given-names: "Aaron"
-  - family-names: "Kolev"
-    given-names: "Tzanio"
-    orcid: "https://orcid.org/0000-0002-2810-3090"
-  - family-names: "Pazner"
-    given-names: "Will"
-    orcid: "https://orcid.org/0000-0003-4885-2934"
-  - family-names: "Stowell"
-    given-names: "Mark"
-    orcid: "https://orcid.org/0000-0002-5389-7435"
-  - family-names: "Tomov"
-    given-names: "Vladimir"
-    orcid: "https://orcid.org/0000-0002-1846-6816"
-  - family-names: "Akkerman"
-    given-names: "Ido"
-    orcid: "https://orcid.org/0000-0002-5937-0300"
-  - family-names: "Dahm"
-    given-names: "Johann"
-    orcid: "https://orcid.org/0000-0001-9657-3564"
-  - family-names: "Medina"
-    given-names: "David"
-  - family-names: "Zampini"
-    given-names: "Stefano"
-    orcid: "https://orcid.org/0000-0002-0435-0433"
-  doi: "10.1016/j.camwa.2020.06.009"
-  journal: "Computers \\& Mathematics with Applications"
-  month: 1
-  start: 42 # First page number
-  end: 74 # Last page number
-  title: "MFEM: A Modular Finite Element Methods Library"
-  volume: 81
-  year: 2021
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -16,9 +16,6 @@ set(USER_CONFIG "${CMAKE_CURRENT_SOURCE_DIR}/config/user.cmake" CACHE PATH

 # Require C++11 and disable compiler-specific extensions
 set(CMAKE_CXX_STANDARD 11)
-if (MFEM_USE_GINKGO)
-  set(CMAKE_CXX_STANDARD 14)
-endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)

@@ -54,7 +51,7 @@ project(mfem NONE)
 # Current version of MFEM, see also `makefile`.
 #   mfem_VERSION = (string)
 #   MFEM_VERSION = (int)   [automatically derived from mfem_VERSION]
-set(${PROJECT_NAME}_VERSION 4.3.1)
+set(${PROJECT_NAME}_VERSION 4.2.1)

 # Prohibit in-source build
 if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
@@ -102,9 +99,6 @@ if (MFEM_USE_CUDA)
   endif()
   enable_language(CUDA)
   set(CMAKE_CUDA_STANDARD 11)
-   if (MFEM_USE_GINKGO)
-     set(CMAKE_CUDA_STANDARD 14)
-   endif()
   set(CMAKE_CUDA_STANDARD_REQUIRED ON)
   set(CMAKE_CUDA_EXTENSIONS OFF)
   set(CUDA_FLAGS "--expt-extended-lambda")
@@ -175,20 +169,10 @@ else()
  set(MFEM_DEBUG OFF)
 endif()

-if (WIN32)
-	add_definitions(-D_USE_MATH_DEFINES)
-endif()
-
 # MPI -> hypre; PETSc (optional)
 if (MFEM_USE_MPI)
  find_package(MPI REQUIRED)
  set(MPI_CXX_INCLUDE_DIRS ${MPI_CXX_INCLUDE_PATH})
-  if (MFEM_MPIEXEC)
-    set(MPIEXEC ${MFEM_MPIEXEC})
-  endif()
-  if (MFEM_MPIEXEC_NP)
-    set(MPIEXEC_NUMPROC_FLAG ${MFEM_MPIEXEC_NP})
-  endif()
  # Parallel MFEM depends on hypre
  find_package(HYPRE REQUIRED)
  set(MFEM_HYPRE_VERSION ${HYPRE_VERSION})
@@ -250,7 +234,6 @@ if (MFEM_USE_OPENMP OR MFEM_USE_LEGACY_OPENMP)
    message(FATAL_ERROR " *** MFEM_USE_LEGACY_OPENMP requires MFEM_THREAD_SAFE=ON.")
  endif()
  find_package(OpenMP REQUIRED)
-  set(OPENMP_LIBRARIES ${OpenMP_CXX_LIBRARIES})
 endif()

 # SuiteSparse (before SUNDIALS which may depend on KLU)
@@ -335,10 +318,6 @@ if (MFEM_USE_CONDUIT)
    find_package(Conduit REQUIRED conduit relay blueprint )
 endif()

-if (MFEM_USE_FMS)
-    find_package(FMS REQUIRED fms )
-endif()
-
 # Axom/Sidre
 if (MFEM_USE_SIDRE)
  find_package(Axom REQUIRED Axom)
@@ -381,20 +360,12 @@ if (MFEM_USE_UMPIRE)
   find_package(UMPIRE REQUIRED)
 endif()

-# Caliper
-if (MFEM_USE_CALIPER)
-  find_package(Caliper REQUIRED)
-endif()
-
 # AMD HIP
 if (MFEM_USE_HIP)
  find_package(HIP REQUIRED)
  if (HIP_ARCH)
    message(STATUS "Using HIP architecture: ${HIP_ARCH}")
    list(APPEND HIP_HIPCC_FLAGS "--amdgpu-target=${HIP_ARCH}")
-    if (MFEM_USE_GINKGO)
-      list(APPEND HIP_HIPCC_FLAGS "-std=c++14")
-    endif()
  endif()
 endif()

@@ -432,11 +403,10 @@ endif()
 #    With newer versions of SuiteSparse which include METIS header using 64-bit
 #    integers, the METIS header (with 32-bit indices, as used by mfem) needs to
 #    be before SuiteSparse.
-set(MFEM_TPLS MPI_CXX OPENMP HYPRE BLAS LAPACK SuperLUDist METIS SuiteSparse SUNDIALS PETSC
-    SLEPC MESQUITE MUMPS STRUMPACK AXOM FMS CONDUIT Ginkgo GNUTLS GSLIB NETCDF
+set(MFEM_TPLS MPI_CXX OPENMP BLAS LAPACK METIS HYPRE SuiteSparse SUNDIALS PETSC
+    SLEPC MESQUITE SuperLUDist MUMPS STRUMPACK AXOM CONDUIT Ginkgo GNUTLS GSLIB NETCDF
    MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE ADIOS2
-    CUSPARSE MKL_CPARDISO AMGX CALIPER)
-
+    CUSPARSE MKL_CPARDISO AMGX)
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
 set(TPL_INCLUDE_DIRS "")
@@ -455,9 +425,6 @@ include_directories(${TPL_INCLUDE_DIRS})
 if (OPENMP_FOUND)
  message(STATUS "MFEM: using package OpenMP")
  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-  if (MFEM_USE_CUDA)
-    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcompiler=${OpenMP_CXX_FLAGS}")
-  endif()
 endif()

 message(STATUS "MFEM build type: CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
@@ -542,8 +509,6 @@ if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
  endforeach()
 endif()

-set(MFEM_CUSTOM_TARGET_PREFIX CACHE STRING "")
-
 #-------------------------------------------------------------------------------
 # Examples, miniapps, and testing
 #-------------------------------------------------------------------------------
@@ -594,17 +559,16 @@ if (NOT ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}"))
 endif()

 # Add 'check' target - quick test
-set(MFEM_CHECK_TARGET_NAME ${MFEM_CUSTOM_TARGET_PREFIX}check)
 if (NOT MFEM_USE_MPI)
-  add_custom_target(${MFEM_CHECK_TARGET_NAME}
+  add_custom_target(check
    ${CMAKE_CTEST_COMMAND} -R \"^ex1_ser\" -C ${CMAKE_CFG_INTDIR}
    USES_TERMINAL)
-  add_dependencies(${MFEM_CHECK_TARGET_NAME} ex1)
+  add_dependencies(check ex1)
 else()
-  add_custom_target(${MFEM_CHECK_TARGET_NAME}
+  add_custom_target(check
    ${CMAKE_CTEST_COMMAND} -R \"^ex1p\" -C ${CMAKE_CFG_INTDIR}
    USES_TERMINAL)
-  add_dependencies(${MFEM_CHECK_TARGET_NAME} ex1p)
+  add_dependencies(check ex1p)
 endif()

 #-------------------------------------------------------------------------------
@@ -658,7 +622,7 @@ endif()
 if (MFEM_USE_CEED)
  install(DIRECTORY ${MFEM_SOURCE_DIRS}
    DESTINATION ${INSTALL_INCLUDE_DIR}/mfem
-    FILES_MATCHING PATTERN "fem/ceed/*.h")
+    FILES_MATCHING PATTERN "fem/libceed/*.h")
 endif()

 # Install ${HEADERS}
@@ -4,9 +4,7 @@

 <p align="center">
 <a href="https://github.com/mfem/mfem/blob/master/LICENSE"><img alt="License" src="https://img.shields.io/badge/License-BSD-brightgreen.svg"></a>
-<a href="https://github.com/mfem/mfem/actions?query=workflow%3Arepo-check+branch%3Amaster"><img alt="Repo check" src="https://github.com/mfem/mfem/actions/workflows/repo-check.yml/badge.svg?branch=master"></a>
-<a href="https://github.com/mfem/mfem/actions?query=workflow%3Abuild-analysis+branch%3Amaster"><img alt="Build Analysis" src="https://github.com/mfem/mfem/actions/workflows/mfem-analysis.yml/badge.svg?branch=master"></a>
-<a href="https://github.com/mfem/mfem/actions?query=workflow%3Abuilds-and-tests+branch%3Amaster"><img alt="Builds and Tests" src="https://github.com/mfem/mfem/actions/workflows/builds-and-tests.yml/badge.svg?branch=master"></a>
+<a href="https://travis-ci.org/mfem/mfem"><img alt="Build Status" src="https://travis-ci.org/mfem/mfem.svg?branch=master"></a>
 <a href="https://ci.appveyor.com/project/mfem/mfem"><img alt="Build Status" src="https://ci.appveyor.com/api/projects/status/19non9sqm6msi2wy?svg=true"></a>
 <a href="https://mfem.github.io/doxygen/html/index.html"><img alt="Doxygen" src="https://img.shields.io/badge/code-documented-brightgreen.svg"></a>
 </p>
@@ -65,8 +63,6 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
  development branches off `mfem:master`.
 - Please follow the [developer guidelines](#developer-guidelines), in particular
  with regards to documentation and code styling.
- Please do not commit large/binary files to the central repository (use a fork
-  instead).
 - Pull requests  should be issued toward `mfem:master`. Make sure
  to check the items off the [Pull Request Checklist](#pull-request-checklist).
 - When your contribution is fully working and ready to be reviewed, add
@@ -75,7 +71,6 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
  reviewers to evaluate the changes.
 - The reviewers have 3 weeks to evaluate the PR and work with the author to
  fix issues and implement improvements.
- During review there should be no force pushes/rewriting history in the branch.
 - After approval, MFEM developers merge the PR manually in the [mfem:next branch](#masternext-workflow).
 - After a week of testing in `mfem:next`, the original PR is merged in `mfem:master`.
 - We use [milestones](https://github.com/mfem/mfem/milestones) to coordinate the
@@ -96,13 +91,12 @@ The MFEM source code has the following structure:
 ```
  .
  ├── config
-  │   ├── cmake
-  │   └── githooks
+  │   └── cmake
+  │       └── ...
  ├── data
  ├── doc
  ├── examples
  │   ├── amgx
-  │   ├── caliper
  │   ├── ginkgo
  │   ├── hiop
  │   ├── petsc
@@ -110,9 +104,7 @@ The MFEM source code has the following structure:
  │   ├── sundials
  |   └── superlu
  ├── fem
-  │   ├── ceed
-  │   ├── qinterp
-  │   └── tmop
+  │   └── libceed
  ├── general
  ├── linalg
  │   └── simd
@@ -123,21 +115,17 @@ The MFEM source code has the following structure:
  │   ├── electromagnetics
  │   ├── gslib
  │   ├── meshing
-  │   ├── mtop
  │   ├── navier
  │   ├── nurbs
  │   ├── performance
-  │   ├── shifted
-  │   ├── solvers
  │   ├── tools
  │   └── toys
  └── tests
      ├── convergence
-      ├── gitlab
-      ├── mem_manager
      ├── par-mesh-format
      ├── scripts
      └── unit
+          └── ...
 ```

 #### Main directories and classes
@@ -368,10 +356,6 @@ Before you can start, you need a GitHub account, here are a few suggestions:
  two reviewers to evaluate the changes. The reviewers have 3 weeks to evaluate
  the PR and work with the author to implement improvements and fix issues.

- Once the `ready-for-review` label has been applied and reviewers have been
-  assigned, the PR is considered under review. To help with the review process
-  there should be no force pushes/rewriting history in the branch.
-
 - After approval, the PR is [tested](#masternext-workflow) for a week with
  other approved PRs in the `mfem:next` branch.

@@ -379,20 +363,16 @@ Before you can start, you need a GitHub account, here are a few suggestions:
  `mfem:next`, see the [README](tests/scripts/README) file in that directory
  for more details.

- Track the GitHub Actions and Appveyor [continuous integration](#automated-testing)
+- Track the Travis CI and Appveyor [continuous integration](#automated-testing)
  builds at the end of the PR. These should generally run clean, so address any
  errors as soon as possible. Please ask if you are unsure how to do that.

- Note that some tests, such as the `branch-history` check in GitHub Actions
-  are safeguards that are allowed to fail in certain cases.
+- Note that some tests, such as the `branch-history` check in Travis are
+  safeguards that are allowed to fail in certain cases.

 - Other tests, such as the `code-style`, `documentation` and `gitignore`
-  checks in GitHub Actions enforce MFEM-specific rules which are explained in
-  the error messages and the `tests/scripts` directory.
-
- Also note that the tests `branch-history` and `repos-checks` found in GitHub
-  Actions can be triggered automatically before each push using git hooks. See
-  the [git hooks README](config/githooks/README.md) for a detailed explanation.
+  checks in Travis enforce MFEM-specific rules which are explained in the
+  error messages and the `tests/scripts` directory.

 - If triggered, track the status of the LLNL GitLab tests. If failing, ask
  one of the _LLNL developers_ for details.
@@ -412,7 +392,7 @@ Before a PR can be merged, it should satisfy the following:
    - [ ] Does `make` or `cmake` have a new target?
    - [ ] Did the requirements or the installation process change? *(rare)*
 - [ ] Update continuous integration server configurations if necessary (e.g. with new version requirements for each of MFEM's dependencies)
-    - [ ] `.github`
+    - [ ] `.travis.yml`
    - [ ] `.appveyor.yml`
 - [ ] Update `.gitignore`:
    - [ ] Check if `make distclean; git status` shows any files that were generated from the source by the project (not an IDE) but we don't want to track in the repository.
@@ -442,7 +422,6 @@ Before a PR can be merged, it should satisfy the following:
      - [ ] Add/update the `CMakeLists.txt` file in the new miniapp directory.
      - [ ] Consider adding a new test for the new miniapp.
   - [ ] List the new miniapp in `doc/CodeDocumentation.dox`
-   - [ ] If new miniapps directory (e.g.`miniapps/nurbs`), add it to `MINIAPP_SUBDIRS` in the `makefile`.
   - [ ] If new miniapps directory (e.g.`miniapps/nurbs`), list it in `doc/CodeDocumentation.conf.in`
   - [ ] Companion pull request for documentation in [mfem/web](https://github.com/mfem/web) repo:
     - [ ] Update or add miniapp-specific documentation, see e.g. the `src/meshing.md` and `src/electromagnetics.md` files.
@@ -529,7 +508,7 @@ MFEM uses a `master`/`next`-branch workflow as described below:
    - [ ] `doc/CodeDocumentation.conf.in`
 - [ ] Check that version requirements for each of MFEM's dependencies are documented in `INSTALL` and up-to-date
 - [ ] Check that continuous integration server configurations reflect the dependency version requirements of the new release
-    - [ ] `.github`
+    - [ ] `.travis.yml`
    - [ ] `.appveyor.yml`
 - [ ] Update the `CHANGELOG` to organize all release contributions
 - [ ] Review the whole source code once over
@@ -582,25 +561,19 @@ MFEM uses a `master`/`next`-branch workflow as described below:
  Computing systems. Gitlab pipeline status is reported in the corresponding
  GitHub pull request.

- In Gitlab pipelines, TPLs (dependencies) are built using Spack, driven by Uberenv.
-
- No change to the MFEM repo can be made on this instance.
+- No change can be made on this instance.

 ## Automated Testing

 MFEM has several levels of automated testing running on GitHub, as well as on
 local Mac and Linux workstations, and Livermore Computing clusters at LLNL.

-In addition, developers can set local git hooks to run some quick checks on
-commit or push, see the [README](config/githooks/README.md) in the `config/githooks`
-directory.
-
 ### Linux and Mac smoke tests
-We use GitHub Actions to drive the default tests on the `master` and `next`
-branches. See the `.github/workflows` files and the logs at
-[https://github.com/mfem/mfem/actions](https://github.com/mfem/mfem/actions).
+We use Travis CI to drive the default tests on the `master` and `next`
+branches. See the `.travis` file and the logs at
+[https://travis-ci.org/mfem/mfem](https://travis-ci.org/mfem/mfem).

-Testing using GitHub Actions should be kept lightweight, as there is a time
+Testing using Travis CI should be kept lightweight, as there is a 50 minute time
 constraint on jobs. Two virtual machines are configured - Mac (OS X) and Linux.

 - Tests on the `master` branch are triggered whenever a PR is issued on this branch.
@@ -58,7 +58,6 @@ following package managers:

 - Spack, https://github.com/spack/spack
 - OpenHPC, http://openhpc.community
- Conda-forge, https://conda-forge.org (pre-built binaries linked with OpenMPI/MPICH, hypre, and METIS)
 - Homebrew/Science, https://github.com/Homebrew/homebrew-science (deprecated)

 We also recommend downloading and building the MFEM-based GLVis visualization
@@ -351,9 +350,10 @@ MFEM_USE_SUPERLU5 = YES/NO

 MFEM_USE_MUMPS = YES/NO
   Enable MFEM functionality based on the MUMPS library. Currently, this
-   option adds the class MUMPSSolver (a parallel sparse direct solver).
-   When enabled, this option uses the MUMPS_* library options, see below.
-
+   option adds the class MUMPSSolver (a parallel sparse direct solver). 
+   When enabled, this option uses the MUMPS_* library options, see
+   below.
+   
 MFEM_USE_STRUMPACK = YES/NO
   Enable MFEM functionality based on the STRUMPACK sparse direct solver and
   preconditioner through the STRUMPACKSolver and STRUMPACKRowLocMatrix
@@ -460,8 +460,8 @@ MFEM_USE_UMPIRE = YES/NO
   memory devices like NUMA and GPUs.

 MFEM_USE_HIOP = YES/NO
-   Enable the usage of HiOp (https://github.com/LLNL/hiop) in MFEM. HiOp is an
-   HPC solver for nonlinear optimization problems.
+  Enable the usage of HiOp (https://github.com/LLNL/hiop) in MFEM. HiOp is an
+  HPC solver for nonlinear optimization problems.

 MFEM_USE_CUDA = YES/NO
   Enables support for CUDA devices in MFEM. CUDA is a parallel computing
@@ -474,7 +474,7 @@ MFEM_USE_HIP = YES/NO
   Enables support for AMD devices in MFEM. HIP is a heterogeneous-compute
   interface for portability developed by AMD that can target both AMD and
   NVIDIA GPUs. The variable HIP_ARCH is used to specify the AMD GPU processor
-   used during compilation (by default, HIP_ARCH=gfx900). When enabled, this
+   used during compilation (by default, HIP_ARCH=gfx900).  When enabled, this
   option uses the HIP_* build options, see below.

 MFEM_USE_RAJA = YES/NO
@@ -508,21 +508,6 @@ MFEM_USE_MKL_CPARDISO = YES/NO
   MFEM_USE_LAPACK=YES, verify that the MKL LAPACK libraries are used. The
   OpenMP capabilities are disabled at link time.

-MFEM_USE_CALIPER = YES/NO
-   Enables the interface to Caliper. Caliper is a library to integrate
-   performance profiling capabilities into applications. To use Caliper,
-   developers mark code regions of interest using either Caliper's annotation
-   API or their equivalent in MFEM. Applications can then enable performance
-   profiling at runtime with Caliper's configuration API. Alternatively, one
-   can configure Caliper through environment variables or config files.
-
-MFEM_USE_FMS = YES/NO
-   Enables support for the FMS library which consists of the DataCollection
-   sub-class mfem::FMSDataCollection for I/O in FMS formats, see the header file
-   fem/fmsdatacollection.hpp. In addition, this option enables in-memory
-   convetion routines between FMS's FmsDataCollection structure and MFEM's
-   DataCollection class, see the header file fem/fmsconvert.hpp.
-
 MFEM_BUILD_TAG = (any value)
   An optional tag to characterize the build. Exported to config/config.mk.
   Can be used to identify the MFEM build from other makefiles.
@@ -544,12 +529,9 @@ directory and use the string @MFEM_DIR@, e.g. HYPRE_OPT = -I@MFEM_DIR@/../hypre.
 The specific libraries and their options are:

 - HYPRE, required for the parallel build, i.e. when MFEM_USE_MPI = YES.
-  See also the "Specific options for hypre" section at the end of this file.
  URL: https://github.com/hypre-space/hypre and https://www.llnl.gov/casc/hypre
  Options: HYPRE_OPT, HYPRE_LIB.
-  Versions: HYPRE >= 2.10.0b  (HYPRE built without CUDA)
-            HYPRE >= 2.20.0   (HYPRE built with '--enable-mixedint')
-            HYPRE >= 2.22.1   (HYPRE built with CUDA)
+  Versions: HYPRE >= 2.10.0b.

 - METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
  MFEM_USE_METIS_5 = YES (default is to use METIS 4).
@@ -619,11 +601,10 @@ The specific libraries and their options are:
  Versions: STRUMPACK >= 3.0.0.

 - Ginkgo (optional), used when MFEM_USE_GINKGO = YES. Note that Ginkgo needs a
-  C++ compiler that supports the C++-14 standard. For additional requirements
-  and dependencies of specific modules, see the Ginkgo webpage below.
+  C++ compiler that supports the C++-11 standard. For additional requirements
+  and dependencies of specific modules see the Ginkgo webpage below.
  URL: https://ginkgo-project.github.io
-  Options: GINKGO_OPT, GINKGO_LIB, GINKGO_DIR, GINKGO_BUILD_TYPE (Release or Debug).
-  Versions: Ginkgo >= 1.4.0.
+  Options: GINKGO_OPT (Not used), GINKGO_LIB.

 - AmgX (optional), used when MFEM_USE_AMGX = YES.
  URL: https://github.com/NVIDIA/AMGX
@@ -655,8 +636,7 @@ The specific libraries and their options are:
                --with-shared-libraries=0
  URL: https://www.mcs.anl.gov/petsc
  Options: PETSC_OPT, PETSC_LIB.
-  Versions: PETSc >= 3.8.0   (PETSc build without CUDA)
-            PETSc >= 3.15.0  (PETSc built with CUDA)
+  Versions: PETSc >= 3.8.0.

 - SLEPc (optional), used when MFEM_USE_SLEPC = YES. SLEPc depends on PETSc and
  uses some of the PETSc options when compiled.
@@ -692,17 +672,17 @@ The specific libraries and their options are:
 - HiOp (optional), used when MFEM_USE_HIOP = YES.
  URL: https://github.com/LLNL/hiop
  Options: HIOP_OPT, HIOP_LIB.
-  Versions: HIOP >= 0.4.
+  Versions: HIOP >= 0.1.

 - GSLIB (optional), used when MFEM_USE_GSLIB = YES. The gslib library must be
-  built prior to the MFEM build, as follows: download gslib-1.0.7, untar it at
-  the same level as MFEM and create a symbolic link: "ln -s gslib-1.0.7 gslib".
+  built prior to the MFEM build, as follows: download gslib-1.0.5, untar it at
+  the same level as MFEM and create a symbolic link: "ln -s gslib-1.0.5 gslib".
  Build gslib in parallel or in serial based on the desired MFEM build: "make
  clean; make CC=mpicc" or "make clean; make CC=gcc MPI=0". Build MFEM with
  MFEM_USE_GSLIB=YES.
-  URL: https://github.com/gslib/gslib/archive/v1.0.7.tar.gz
+  URL: https://github.com/gslib/gslib/archive/v1.0.5.tar.gz
  Options: GSLIB_OPT, GSLIB_LIB.
-  Versions: GSLIB >= 1.0.7.
+  Versions: GSLIB >= 1.0.5.

 - MKL CPardiso (optional), used when MFEM_USE_MKL_CPARDISO = YES.
  URL: https://software.intel.com/content/www/us/en/develop/tools/math-kernel-library.html
@@ -712,7 +692,7 @@ The specific libraries and their options are:
 - CUDA (optional), used when MFEM_USE_CUDA = YES.
  URL: https://developer.nvidia.com/cuda-toolkit
  Options: CUDA_CXX, CUDA_ARCH, CUDA_OPT, CUDA_LIB.
-  Versions: CUDA >= 10.1.168.
+  Versions: CUDA >= 9.1, older versions may work too.

 - HIP (optional), used when MFEM_USE_HIP = YES.
  URL: https://rocm.github.io/ROCmInstall.html
@@ -727,7 +707,7 @@ The specific libraries and their options are:
  URL: https://github.com/CEED/libCEED
       https://ceed.exascaleproject.org/libceed
  Options: CEED_DIR, CEED_OPT, CEED_LIB.
-  Versions: libCEED >= 0.8.
+  Versions: libCEED >= 0.7.

 - RAJA (optional), used when MFEM_USE_RAJA = YES.
  Beginning with MFEM v4.3, only RAJA v0.13.0+ is supported.
@@ -735,13 +715,7 @@ The specific libraries and their options are:
  Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
  Versions: RAJA >= 0.13.0.

- Caliper (optional), used when MFEM_USE_CALIPER = YES.
-  URL: https://github.com/LLNL/Caliper
-  Options: CALIPER_DIR
-  Versions: CALIPER >= 2.5.0, older versions may work too.
-
 - Umpire, used when MFEM_USE_UMPIRE = YES.
-  Umpire requires camp when the Umpire version is >= 3.0.0.
  URL: https://github.com/LLNL/Umpire
  Options: UMPIRE_DIR, UMPIRE_OPT, UMPIRE_LIB.
  Versions: Umpire >= 2.0.0.
@@ -761,11 +735,6 @@ The specific libraries and their options are:
  URL: https://zlib.net
  Options: ZLIB_OPT, ZLIB_LIB.

- FMS (optional), used when MFEM_USE_FMS = YES.
-  URL: https://github.com/CEED/FMS
-  Options: FMS_OPT, FMS_LIB.
-  Versions: FMS >= 0.2.
-
 Building with CMake
 ===================
 The MFEM build system consists of two steps: configuration and compilation.
@@ -896,8 +865,6 @@ MFEM_USE_CEED
 MFEM_USE_RAJA
 MFEM_USE_UMPIRE
 MFEM_USE_SIDRE
-MFEM_USE_CALIPER
-MFEM_USE_FMS

 The following options are CMake specific:

@@ -951,8 +918,6 @@ The CMake build system adds auto-detection for the following packages/libraries:
 - RAJA
 - UMPIRE
 - AXOM - Used when MFEM_USE_SIDRE is enabled
- - CALIPER
- - FMS

 The following built-in CMake packages are also used:

@@ -970,7 +935,7 @@ config/config.hpp.in:

   cp config/config.hpp.in config/_config.hpp

-The file config/_config.hpp can then be edited to enable desired options. The
+The file config/_config.hpp can then be edited to enable desired options.  The
 MFEM library is simply a combination of all object files obtained by compiling
 the .cpp source files in the source directories: general, linalg, mesh, and fem.

@@ -978,7 +943,7 @@ the .cpp source files in the source directories: general, linalg, mesh, and fem.
 Specifying an MPI job launcher
 ==============================
 By default, MFEM will use 'mpirun -np #' to launch any of its parallel tests or
-miniapps, where # is the number of MPI tasks. An alternate MPI launcher can be
+miniapps, where # is the number of MPI tasks.  An alternate MPI launcher can be
 provided by setting the MFEM_MPIEXEC and MFEM_MPIEXEC_NP config variables.

 MFEM will expect the launcher command, plus the command line option to allow it
@@ -988,19 +953,3 @@ MFEM_MPIEXEC    = mpirun # default
 MFEM_MPIEXEC_NP = -np    # default
 MFEM_MPIEXEC    = srun   # example for platforms using SLURM
 MFEM_MPIEXEC_NP = -n     # example for platforms using SLURM
-
-
-Specific options for hypre
-==========================
-The hypre library has multiple options to define local and global index storage
-sizes. By default, all indices are stored as an architecture aware integer. For
-most platforms, this will be 32-bit. This limits the maximum number of global
-degrees of freedom in a vector or matrix to about 2 billion. In order to solve
-larger problems, there are two options:
-
-1. Building hypre with '--enable-bigint' defines the local and global indices to
-   be 64-bit. This is convenient, but requires more memory than necessary.
-
-2. Building hypre with '--enable-mixedint' defines the local indiced to be
-   32-bit, while using a 64-bit storage for global indices. This option is
-   currently tested only in ex1p, and may not work in more general settings.
@@ -1,6 +1,6 @@
 BSD 3-Clause License

-Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC
+Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC
 All rights reserved.

 Redistribution and use in source and binary forms, with or without
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -256,10 +256,6 @@ IF (DEFINED TPL_ENABLE_SIDRE)
  SET(MFEM_USE_SIDRE ${TPL_ENABLE_SIDRE} CACHE BOOL "Enable Axom/Sidre usage" FORCE)
 ENDIF()

-IF (DEFINED TPL_ENABLE_FMS)
-  SET(MFEM_USE_FMS ${TPL_ENABLE_FMS} CACHE BOOL "Enable FMS usage" FORCE)
-ENDIF()
-
 IF (DEFINED TPL_ENABLE_CONDUIT)
  SET(MFEM_USE_CONDUIT ${TPL_ENABLE_CONDUIT} CACHE BOOL "Enable Conduit usage" FORCE)
 ENDIF()
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -44,7 +44,6 @@ set(MFEM_USE_PETSC @MFEM_USE_PETSC@)
 set(MFEM_USE_SLEPC @MFEM_USE_SLEPC@)
 set(MFEM_USE_MPFR @MFEM_USE_MPFR@)
 set(MFEM_USE_SIDRE @MFEM_USE_SIDRE@)
-set(MFEM_USE_FMS @MFEM_USE_FMS@)
 set(MFEM_USE_CONDUIT @MFEM_USE_CONDUIT@)
 set(MFEM_USE_PUMI @MFEM_USE_PUMI@)
 set(MFEM_USE_CUDA @MFEM_USE_CUDA@)
@@ -54,7 +53,6 @@ set(MFEM_USE_CEED @MFEM_USE_CEED@)
 set(MFEM_USE_UMPIRE @MFEM_USE_UMPIRE@)
 set(MFEM_USE_SIMD @MFEM_USE_SIMD@)
 set(MFEM_USE_ADIOS2 @MFEM_USE_ADIOS2@)
-set(MFEM_USE_CALIPER @MFEM_USE_CALIPER@)

 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")
@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 // at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 // LICENSE and NOTICE for details. LLNL-CODE-806117.
 //
@@ -119,9 +119,6 @@
 // Enable the use of SIMD in the high performance templated classes
 #cmakedefine MFEM_USE_SIMD

-// Enable MFEM functionality based on the FMS library
-#cmakedefine MFEM_USE_FMS
-
 // Enable MFEM functionality based on Conduit
 #cmakedefine MFEM_USE_CONDUIT

@@ -154,9 +151,6 @@
 // Enable MFEM functionality based on the ADIOS2 library
 #cmakedefine MFEM_USE_ADIOS2

-// Enable MFEM functionality based on the Caliper library
-#cmakedefine MFEM_USE_CALIPER
-
 // Which library functions to use in class StopWatch for measuring time.
 // For a list of the available options, see INSTALL.
 // If not defined, an option is selected automatically.
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -15,10 +15,6 @@
 #   - AMGX_INCLUDE_DIRS

 include(MfemCmakeUtilities)
-set(AMGX_REQUIRED_LIBRARIES cusparse cusolver cublas cublasLt nvToolsExt)
+set(AMGX_REQUIRED_LIBRARIES cusparse cusolver cublas nvToolsExt)
 mfem_find_package(AMGX AMGX AMGX_DIR "include" "amgx_c.h" "lib" "amgx"
  "Paths to headers required by AMGX." "Libraries required by AMGX.")
-# Make sure the library location is locked down
-foreach(lib ${AMGX_REQUIRED_LIBRARIES})
-  list(APPEND AMGX_LIBRARIES ${CUDA_TOOLKIT_ROOT_DIR}/lib64/lib${lib}${CMAKE_SHARED_LIBRARY_SUFFIX})
-endforeach()
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,22 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Defines the following variables:
-#   - CALIPER_FOUND
-#   - CALIPER_LIBRARIES
-#   - CALIPER_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(Caliper CALIPER CALIPER_DIR
-       	"include" "caliper/cali.h"
-       	"lib" "caliper"
-  	"Paths to headers required by Caliper."
-       	"Libraries required by Caliper.")
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,20 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Defines the following variables:
-#   - FMS_FOUND
-#   - FMS_LIBRARIES
-#   - FMS_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(FMS FMS FMS_DIR
-  "include" fms.h "lib" fms
-  "Paths to headers required by FMS." "Libraries required by FMS.")
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -15,20 +15,5 @@
 #   - NETCDF_INCLUDE_DIRS

 include(MfemCmakeUtilities)
-
-# FindHDF5.cmake uses HDF5_ROOT, so we "translate" from the MFEM convention
-set(HDF5_ROOT ${HDF5_DIR} CACHE PATH "")
-# We need to guard against the case where HDF5 was already found but without
-# the HL extensions (in which case mfem_find_package will treat the package
-# as already having been found), so we reset the variable to force FindHDF5.cmake
-# to be called for a second time
-set(HDF5_FOUND OFF)
-enable_language(C) # FindHDF5.cmake uses the C compiler
 mfem_find_package(NetCDF NETCDF NETCDF_DIR "include" netcdf.h "lib" netcdf
  "Paths to headers required by NetCDF." "Libraries required by NetCDF.")
-# The HL extension libraries are in a separate variable and must precede
-# the "regular" hdf5 library, as hdf5_hl depends on hdf5
-# The netcdf library will always be the first element of NETCDF_LIBRARIES
-# and we need to insert after that library but before the hdf5 library, so
-# position 1 is used
-list(INSERT NETCDF_LIBRARIES 1 ${HDF5_C_LIBRARY_hdf5_hl})
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -47,7 +47,6 @@ endfunction()
 macro(mfem_add_executable NAME)
  if (MFEM_USE_HIP)
    hip_add_executable(${NAME} ${ARGN})
-    set_target_properties(${NAME} PROPERTIES LINKER_LANGUAGE CXX)
  else()
    add_executable(${NAME} ${ARGN})
  endif()
@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 // at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 // LICENSE and NOTICE for details. LLNL-CODE-806117.
 //
@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 // at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 // LICENSE and NOTICE for details. LLNL-CODE-806117.
 //
@@ -117,9 +117,6 @@
 // Enable the use of SIMD in the high performance templated classes
 // #define MFEM_USE_SIMD

-// Enable FMS support
-// #define MFEM_USE_FMS
-
 // Enable Conduit support
 // #define MFEM_USE_CONDUIT

@@ -161,9 +158,6 @@
 // Enable functionality based on the libCEED library.
 // #define MFEM_USE_CEED

-// Enable functionality based on the Caliper library.
-// #define MFEM_USE_CALIPER
-
 // Enable functionality based on the Umpire library.
 // #define MFEM_USE_UMPIRE

@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -43,7 +43,6 @@ MFEM_USE_PETSC         = @MFEM_USE_PETSC@
 MFEM_USE_SLEPC         = @MFEM_USE_SLEPC@
 MFEM_USE_MPFR          = @MFEM_USE_MPFR@
 MFEM_USE_SIDRE         = @MFEM_USE_SIDRE@
-MFEM_USE_FMS           = @MFEM_USE_FMS@
 MFEM_USE_CONDUIT       = @MFEM_USE_CONDUIT@
 MFEM_USE_PUMI          = @MFEM_USE_PUMI@
 MFEM_USE_HIOP          = @MFEM_USE_HIOP@
@@ -53,7 +52,6 @@ MFEM_USE_HIP           = @MFEM_USE_HIP@
 MFEM_USE_RAJA          = @MFEM_USE_RAJA@
 MFEM_USE_OCCA          = @MFEM_USE_OCCA@
 MFEM_USE_CEED          = @MFEM_USE_CEED@
-MFEM_USE_CALIPER       = @MFEM_USE_CALIPER@
 MFEM_USE_UMPIRE        = @MFEM_USE_UMPIRE@
 MFEM_USE_SIMD          = @MFEM_USE_SIMD@
 MFEM_USE_ADIOS2        = @MFEM_USE_ADIOS2@
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -45,7 +45,6 @@ option(MFEM_USE_PETSC "Enable PETSc support." OFF)
 option(MFEM_USE_SLEPC "Enable SLEPc support." OFF)
 option(MFEM_USE_MPFR "Enable MPFR usage." OFF)
 option(MFEM_USE_SIDRE "Enable Axom/Sidre usage" OFF)
-option(MFEM_USE_FMS "Enable FMS usage" OFF)
 option(MFEM_USE_CONDUIT "Enable Conduit usage" OFF)
 option(MFEM_USE_PUMI "Enable PUMI" OFF)
 option(MFEM_USE_HIOP "Enable HiOp" OFF)
@@ -56,14 +55,8 @@ option(MFEM_USE_CEED "Enable CEED" OFF)
 option(MFEM_USE_UMPIRE "Enable Umpire" OFF)
 option(MFEM_USE_SIMD "Enable use of SIMD intrinsics" OFF)
 option(MFEM_USE_ADIOS2 "Enable ADIOS2" OFF)
-option(MFEM_USE_CALIPER "Enable Caliper support" OFF)
 option(MFEM_USE_MKL_CPARDISO "Enable MKL CPardiso" OFF)

-# Optional overrides for autodetected MPIEXEC and MPIEXEC_NUMPROC_FLAG
-# set(MFEM_MPIEXEC "mpirun" CACHE STRING "Command for running MPI tests")
-# set(MFEM_MPIEXEC_NP "-np" CACHE STRING
-#     "Flag for setting the number of MPI tasks")
-
 set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")

 # Allow a user to disable testing, examples, and/or miniapps at CONFIGURE TIME
@@ -97,11 +90,6 @@ set(HYPRE_DIR "${MFEM_DIR}/../hypre/src/hypre" CACHE PATH
 # If hypre was compiled to depend on BLAS and LAPACK:
 # set(HYPRE_REQUIRED_PACKAGES "BLAS" "LAPACK" CACHE STRING
 #     "Packages that HYPRE depends on.")
-if (MFEM_USE_CUDA)
-   # This is only necessary when hypre is built with cuda:
-   set(HYPRE_REQUIRED_LIBRARIES "-lcusparse" "-lcurand" CACHE STRING
-       "Libraries that HYPRE depends on.")
-endif()

 set(METIS_DIR "${MFEM_DIR}/../metis-4.0" CACHE PATH "Path to the METIS library.")

@@ -138,10 +126,10 @@ set(MUMPS_DIR "${MFEM_DIR}/../MUMPS_5.2.0" CACHE PATH
    "Path to the MUMPS library.")
 # Packages required by MUMPS, depending on how it was compiled.
 set(MUMPS_REQUIRED_PACKAGES "MPI" "BLAS" "METIS" "ScaLAPACK" CACHE STRING
-    "Additional packages required by MUMPS.")
+    "Additional packages required by MUMPS.")    
 # If the MPI package does not find all required Fortran libraries:
 # set(MUMPS_REQUIRED_LIBRARIES "gfortran" "mpi_mpifh" CACHE STRING
-#     "Additional libraries required by MUMPS.")
+#     "Additional libraries required by MUMPS.")    

 set(STRUMPACK_DIR "${MFEM_DIR}/../STRUMPACK-build" CACHE PATH
    "Path to the STRUMPACK library.")
@@ -180,7 +168,8 @@ set(GNUTLS_DIR "" CACHE PATH "Path to the GnuTLS library.")
 set(GSLIB_DIR "" CACHE PATH "Path to the GSLIB library.")

 set(NETCDF_DIR "" CACHE PATH "Path to the NetCDF library.")
-set(NetCDF_REQUIRED_PACKAGES "HDF5/C/HL" CACHE STRING
+# May need to add "HDF5" as requirement.
+set(NetCDF_REQUIRED_PACKAGES "" CACHE STRING
    "Additional packages required by NetCDF.")

 set(PETSC_DIR "${MFEM_DIR}/../petsc" CACHE PATH
@@ -193,12 +182,6 @@ set(SLEPC_ARCH "arch-linux2-c-debug" CACHE STRING "SLEPC build architecture.")

 set(MPFR_DIR "" CACHE PATH "Path to the MPFR library.")

-set(FMS_DIR "${MFEM_DIR}/../fms" CACHE PATH
-    "Path to the FMS library.")
-# If FMS is built with Conduit:
-# set(FMS_REQUIRED_PACKAGES "Conduit/relay" CACHE STRING
-#     "Additional packages required by FMS.")
-
 set(CONDUIT_DIR "${MFEM_DIR}/../conduit" CACHE PATH
    "Path to the Conduit library.")

@@ -223,7 +206,6 @@ set(OCCA_DIR "${MFEM_DIR}/../occa" CACHE PATH "Path to OCCA")
 set(RAJA_DIR "${MFEM_DIR}/../raja" CACHE PATH "Path to RAJA")
 set(CEED_DIR "${MFEM_DIR}/../libCEED" CACHE PATH "Path to libCEED")
 set(UMPIRE_DIR "${MFEM_DIR}/../umpire" CACHE PATH "Path to Umpire")
-set(CALIPER_DIR "${MFEM_DIR}/../caliper" CACHE PATH "Path to Caliper")

 set(BLAS_INCLUDE_DIRS "" CACHE STRING "Path to BLAS headers.")
 set(BLAS_LIBRARIES "" CACHE STRING "The BLAS library.")
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -18,9 +18,6 @@
 # Some choices below are based on the OS type:
 NOTMAC := $(subst Darwin,,$(shell uname -s))

-ETAGS_BIN = $(shell command -v etags 2> /dev/null)
-EGREP_BIN = $(shell command -v egrep 2> /dev/null)
-
 CXX = g++
 MPICXX = mpicxx

@@ -136,7 +133,6 @@ MFEM_USE_PETSC         = NO
 MFEM_USE_SLEPC         = NO
 MFEM_USE_MPFR          = NO
 MFEM_USE_SIDRE         = NO
-MFEM_USE_FMS           = NO
 MFEM_USE_CONDUIT       = NO
 MFEM_USE_PUMI          = NO
 MFEM_USE_HIOP          = NO
@@ -146,7 +142,6 @@ MFEM_USE_HIP           = NO
 MFEM_USE_RAJA          = NO
 MFEM_USE_OCCA          = NO
 MFEM_USE_CEED          = NO
-MFEM_USE_CALIPER       = NO
 MFEM_USE_UMPIRE        = NO
 MFEM_USE_SIMD          = NO
 MFEM_USE_ADIOS2        = NO
@@ -175,10 +170,6 @@ LIBUNWIND_LIB = $(if $(NOTMAC),-lunwind -ldl,)
 HYPRE_DIR = @MFEM_DIR@/../hypre/src/hypre
 HYPRE_OPT = -I$(HYPRE_DIR)/include
 HYPRE_LIB = -L$(HYPRE_DIR)/lib -lHYPRE
-ifeq (YES,$(MFEM_USE_CUDA))
-   # This is only necessary when hypre is built with cuda:
-   HYPRE_LIB += -lcusparse -lcurand
-endif

 # METIS library configuration
 ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK)$(MFEM_USE_MUMPS),NONONO)
@@ -293,23 +284,9 @@ STRUMPACK_LIB = -L$(STRUMPACK_DIR)/lib -lstrumpack $(MPI_FORTRAN_LIB)\

 # Ginkgo library configuration (currently not needed)
 GINKGO_DIR = @MFEM_DIR@/../ginkgo/install
-GINKGO_BUILD_TYPE=Release
-ifeq ($(MFEM_USE_GINKGO),YES)
-   BASE_FLAGS = -std=c++14
-endif
 GINKGO_OPT = -isystem $(GINKGO_DIR)/include
-GINKGO_LIB_DIR = $(sort $(dir $(wildcard $(GINKGO_DIR)/lib*/libginkgo*.a  $(GINKGO_DIR)/lib*/libginkgo*.so $(GINKGO_DIR)/lib*/libginkgo*.dylib $(GINKGO_DIR)/lib*/libginkgo*.dll)))
-ALL_GINKGO_LIBS_DEBUG = $(notdir $(basename $(wildcard $(GINKGO_DIR)/lib*/libginkgo*d.a  $(GINKGO_DIR)/lib*/libginkgo*d.so $(GINKGO_DIR)/lib*/libginkgo*d.dylib $(GINKGO_DIR)/lib*/libginkgo*d.dll)))
-ALL_GINKGO_LIBS = $(notdir $(basename $(wildcard $(GINKGO_DIR)/lib*/libginkgo*.a  $(GINKGO_DIR)/lib*/libginkgo*.so $(GINKGO_DIR)/lib*/libginkgo*.dylib $(GINKGO_DIR)/lib*/libginkgo*.dll)))
-ALL_GINKGO_LIBS_RELEASE = $(filter-out $(ALL_GINKGO_LIBS_DEBUG),$(ALL_GINKGO_LIBS))
-GINKGO_LINK = $(subst libginkgo,-lginkgo,$(ALL_GINKGO_LIBS_RELEASE))
-ifeq ($(GINKGO_BUILD_TYPE),Debug)
-  ifneq (,$(ALL_GINKGO_LIBS_DEBUG))
-    GINKGO_LINK = $(subst libginkgo,-lginkgo,$(ALL_GINKGO_LIBS_DEBUG))
-  endif
-else
-endif
-GINKGO_LIB = $(XLINKER)-rpath,$(GINKGO_LIB_DIR) -L$(GINKGO_LIB_DIR) $(GINKGO_LINK)
+GINKGO_LIB = $(XLINKER)-rpath,$(GINKGO_DIR)/lib -L$(GINKGO_DIR)/lib -lginkgo\
+ -lginkgo_omp -lginkgo_cuda -lginkgo_reference

 # AmgX library configuration
 AMGX_DIR = @MFEM_DIR@/../amgx
@@ -362,11 +339,6 @@ endif
 MPFR_OPT =
 MPFR_LIB = -lmpfr

-# FMS and required libraries configuration
-FMS_DIR = $(MFEM_DIR)/../fms
-FMS_OPT = -I$(FMS_DIR)/include
-FMS_LIB = -Wl,-rpath,$(FMS_DIR)/lib -L$(FMS_DIR)/lib -lfms
-
 # Conduit and required libraries configuration
 CONDUIT_DIR = @MFEM_DIR@/../conduit
 CONDUIT_OPT = -I$(CONDUIT_DIR)/include/conduit
@@ -424,11 +396,6 @@ OCCA_DIR = @MFEM_DIR@/../occa
 OCCA_OPT = -I$(OCCA_DIR)/include
 OCCA_LIB = $(XLINKER)-rpath,$(OCCA_DIR)/lib -L$(OCCA_DIR)/lib -locca

-# CALIPER library configuration
-CALIPER_DIR = @MFEM_DIR@/../caliper
-CALIPER_OPT = -I$(CALIPER_DIR)/include
-CALIPER_LIB = $(XLINKER)-rpath,$(CALIPER_DIR)/lib64 -L$(CALIPER_DIR)/lib64 -lcaliper
-
 # libCEED library configuration
 CEED_DIR ?= @MFEM_DIR@/../libCEED
 CEED_OPT = -I$(CEED_DIR)/include
@@ -440,14 +407,11 @@ RAJA_OPT = -I$(RAJA_DIR)/include
 ifdef CUB_DIR
   RAJA_OPT += -I$(CUB_DIR)
 endif
-ifdef CAMP_DIR
-   RAJA_OPT += -I$(CAMP_DIR)/include
-endif
 RAJA_LIB = $(XLINKER)-rpath,$(RAJA_DIR)/lib -L$(RAJA_DIR)/lib -lRAJA

 # UMPIRE library configuration
 UMPIRE_DIR = @MFEM_DIR@/../umpire
-UMPIRE_OPT = -I$(UMPIRE_DIR)/include $(if $(CAMP_DIR), -I$(CAMP_DIR)/include)
+UMPIRE_OPT = -I$(UMPIRE_DIR)/include
 UMPIRE_LIB = -L$(UMPIRE_DIR)/lib -lumpire

 # MKL CPardiso library configuration
@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 // at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 // LICENSE and NOTICE for details. LLNL-CODE-806117.
 //
@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 // at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 // LICENSE and NOTICE for details. LLNL-CODE-806117.
 //
@@ -1,41 +0,0 @@
-                    Finite Element Discretization Library
-                                   __
-                       _ __ ___   / _|  ___  _ __ ___
-                      | '_ ` _ \ | |_  / _ \| '_ ` _ \
-                      | | | | | ||  _||  __/| | | | | |
-                      |_| |_| |_||_|   \___||_| |_| |_|
-
-                               https://mfem.org
-
-
-This directory contains recommended git hooks, which are scripts that can be
-used to improve your development experience with MFEM:
-
-### The hooks
-
-* `pre-commit` is a hook that will be applied before each commit and run
-`astyle` on the code. This will ensure that your changes comply with the MFEM
-code styling guidelines.
-
-* `pre-push` is a hook that will be applied before each push to run a quick set
-of tests that verify that your files headers are in compliance, and that you did
-not add any large files to the repo.
-
-### Setup
-
-To setup the git hooks, run `make hooks`, which creates symlinks to the hooks in
-the `.git/hooks` directory. Individual hooks can be enabled by manually creating
-symlinks.
-
-(You may also copy the scripts directly and customize them further, but this way
-you may miss additional updates in the future.)
-
-### Failures
-
-The `branch-history` check can fail in some cases when the history is OK. For
-example, when a large number of files were modified for a legitimate reason, or
-when a picture was added for documentation.
-
-If that is the case, make sure the failure is indeed justified, and rerun the
-push command with the `--no-verify` option. This will skip the hooks, allowing
-you to push those changes.
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-# Apply automated code formatting
-make -C $(git rev-parse --show-toplevel) style
@@ -1,107 +0,0 @@
-#!/bin/bash
-
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-option=${1:-""}
-
-if [[ "${option}" == "--help" ]]; then
-  echo "This script runs checks on the repository."
-  echo "It has 2 modes: with and without an option."
-  echo ""
-  echo "Options are used in GitHub Actions and can be:"
-  echo "  --copyright"
-  echo "  --license"
-  echo "  --release"
-  echo "  --style"
-  echo "  --history"
-  echo ""
-  echo "As a githook, the script is used without options."
-  echo "In that case, it will run all the checks except style."
-  echo ""
-  echo "Use --help to print this help message."
-fi
-
-cd $(git rev-parse --show-toplevel)
-
-# copyright check
-copyright=true
-if [[ "${option}" == "--copyright" || "${option}" == "" ]]; then
-  if git grep -l "^\(#\|//\).*\(\-2020\|\ 2010,\)" > matches.txt; then
-    echo "Please update the following files to Copyright (c) 2010-2021:"
-    cat matches.txt
-    copyright=false
-  fi
-fi
-
-# license check
-license=true
-if [[ "${option}" == "--license" || "${option}" == "" ]]; then
-  if git grep -li "^\(#\|//\).*GNU\ Lesser\ General\ Public\ License" > matches.txt; then
-    echo "Please update the following files to the BSD-3 license:"
-    cat matches.txt
-    license=false
-  fi
-fi
-
-# release check
-release=true
-if [[ "${option}" == "--release" || "${option}" == "" ]]; then
-  if git grep -l "^\(#\|//\).*LLNL\-CODE\-443211" > matches.txt
-  then
-    echo "Please update the following files to LLNL-CODE-806117:"
-    cat matches.txt
-    release=false
-  fi
-fi
-
-# wrap-up
-code=0
-if ! $copyright ; then
-  echo "copyright check failed, unroll log for details"
-  code=1
-fi
-if ! $license ; then
-  echo "license check failed, unroll log for details"
-  code=1
-fi
-if ! $release ; then
-  echo "release check failed, unroll log for details"
-  code=1
-fi
-
-# `code-style` is not just a check, it will actually reformat the code if
-# necessary. This means that if one pushes while the repo is in dirty state
-# (changes not staged), those changes may be mixed with format changes.
-# To activate this, you will need to hard-copy this hook script in the hook
-# directory and uncomment only then. (See README.md)
-#
-## style check
-#if [[ "${option}" == "--style" || "${option}" == "" ]]; then
-if [[ "${option}" == "--style" ]]; then
-  if which astyle && [[ "$(astyle --version)" == "Artistic Style Version 2.05.1" ]]; then
-    cd tests/scripts
-    if ! ./runtest code-style; then code=1; fi
-    cd -
-  else
-    echo "Warning: astyle not found or version is not 2.05.1"
-  fi
-fi
-
-# branch-history
-if [[ "${option}" == "--history" || "${option}" == "" ]]; then
-  git fetch origin master:master
-  cd tests/scripts
-  if ! ./runtest branch-history; then code=1; fi
-  cd -
-fi
-
-exit $code
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,6 +1,6 @@
 #!/bin/bash

-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -42,52 +42,12 @@ groups_serial=(
   "Performance miniapps:"
   "miniapps/performance"
   "ex1.cpp"'
-'"amgx"
-   "AmgX examples:"
-   "examples/amgx"
-   "ex1.cpp"'
-'"caliper"
-   "Caliper examples:"
-   "examples/caliper"
-   "ex1.cpp"'
-'"ginkgo"
-   "Ginkgo examples:"
-   "examples/ginkgo"
-   "ex1.cpp"'
-'"hiop"
-   "HiOp examples:"
-   "examples/hiop"
-   "ex9.cpp"'
-'"pumi"
-   "PUMI examples:"
-   "examples/pumi"
-   "ex1.cpp ex2.cpp"'
 #   ""'
 '"meshing"
   "Meshing miniapps:"
   "miniapps/meshing"
   "mobius-strip.cpp klein-bottle.cpp extruder.cpp toroid.cpp
    mesh-optimizer.cpp minimal-surface.cpp"'
-'"adjoint"
-   "Adjoint miniapps:"
-   "miniapps/adjoint"
-   "cvsRoberts_ASAi_dns.cpp"'
-'"gslib"
-   "GSLIB miniapps:"
-   "miniapps/gslib"
-   "field-diff.cpp field-interp.cpp findpts.cpp schwarz_ex1.cpp "'
-'"nurbs"
-   "NURBS miniapps:"
-   "miniapps/nurbs"
-   "nurbs_ex1.cpp"'
-'"tools"
-   "Tools miniapps:"
-   "miniapps/tools"
-   "convert-dc.cpp display-basis.cpp get-values.cpp load-dc.cpp lor-transfer.cpp"'
-'"toys"
-   "Toys miniapps:"
-   "miniapps/toys"
-   "automata.cpp life.cpp lissajous.cpp mandel.cpp mondrian.cpp rubik.cpp snake.cpp"'
 '"convergence"
   "Convergence tests:"
   "tests/convergence"
@@ -112,26 +72,6 @@ groups_parallel=(
   "Performance miniapps:"
   "miniapps/performance"
   "ex1p.cpp"'
-'"amgx"
-   "AmgX examples:"
-   "examples/amgx"
-   "ex1p.cpp"'
-'"caliper"
-   "Caliper examples:"
-   "examples/caliper"
-   "ex1p.cpp"'
-'"hiop"
-   "HiOp examples:"
-   "examples/hiop"
-   "ex9p.cpp"'
-'"pumi"
-   "PUMI examples:"
-   "examples/pumi"
-   "ex1p.cpp ex6p.cpp"'
-'"superlu"
-   "Superlu examples:"
-   "examples/superlu"
-   "ex1p.cpp"'
 #   ""'
 '"meshing"
   "Meshing miniapps:"
@@ -142,34 +82,6 @@ groups_parallel=(
   "miniapps/electromagnetics"
   "joule.cpp"'
 #   "{volta,tesla,joule}.cpp"' # todo: multiline sample runs
-'"adjoint"
-   "Adjoint miniapps:"
-   "miniapps/adjoint"
-   "adjoint_advection_diffusion.cpp"'
-'"gslib"
-   "GSLIB miniapps:"
-   "miniapps/gslib"
-   "pfindpts.cpp schwarz_ex1p.cpp"'
-'"navier"
-   "Navier miniapps:"
-   "miniapps/navier"
-   "navier_cht.cpp"'
-'"nurbs"
-   "NURBS miniapps:"
-   "miniapps/nurbs"
-   "nurbs_ex1p.cpp nurbs_ex11p.cpp"'
-'"shifted"
-   "Shifted miniapps:"
-   "miniapps/shifted"
-   "distance.cpp"'
-'"solvers"
-   "Solvers miniapps:"
-   "miniapps/solvers"
-   "block-solvers.cpp"'
-'"tools"
-   "Tools miniapps:"
-   "miniapps/tools"
-   "convert-cd.cpp get-values.cpp load-dc.cpp"'
 '"convergence"
   "Convergence tests:"
   "tests/convergence"
@@ -197,30 +109,6 @@ groups_all=(
   "Performance miniapps:"
   "miniapps/performance"
   "ex1{,p}.cpp"'
-'"amgx"
-   "AmgX examples:"
-   "examples/amgx"
-   "ex1.cpp ex1p.cpp"'
-'"caliper"
-   "Caliper examples:"
-   "examples/caliper"
-   "ex1.cpp ex1p.cpp"'
-'"ginkgo"
-   "Ginkgo examples:"
-   "examples/ginkgo"
-   "ex1.cpp"'
-'"hiop"
-   "HiOp examples:"
-   "examples/hiop"
-   "ex9.cpp ex9p.cpp"'
-'"pumi"
-   "PUMI examples:"
-   "examples/pumi"
-   "ex1.cpp ex1p.cpp ex2.cpp ex6p.cpp"'
-'"superlu"
-   "Superlu examples:"
-   "examples/superlu"
-   "ex1p.cpp"'
 '"meshing"
   "Meshing miniapps:"
   "miniapps/meshing"
@@ -231,38 +119,6 @@ groups_all=(
   "miniapps/electromagnetics"
   "joule.cpp"'
 #   "{volta,tesla,joule}.cpp"' # todo: multiline sample runs
-'"adjoint"
-   "Adjoint miniapps:"
-   "miniapps/adjoint"
-   "adjoint_advection_diffusion.cpp cvsRoberts_ASAi_dns.cpp"'
-'"gslib"
-   "GSLIB miniapps:"
-   "miniapps/gslib"
-   "field-diff.cpp field-interp.cpp findpts.cpp schwarz_ex1.cpp pfindpts.cpp schwarz_ex1p.cpp"'
-'"navier"
-   "Navier miniapps:"
-   "miniapps/navier"
-   "navier_cht.cpp"'
-'"nurbs"
-   "NURBS miniapps:"
-   "miniapps/nurbs"
-   "nurbs_ex1.cpp nurbs_ex1p.cpp nurbs_ex11p.cpp"'
-'"shifted"
-   "Shifted miniapps:"
-   "miniapps/shifted"
-   "distance.cpp"'
-'"solvers"
-   "Solvers miniapps:"
-   "miniapps/solvers"
-   "block-solvers.cpp"'
-'"tools"
-   "Tools miniapps:"
-   "miniapps/tools"
-   "convert-dc.cpp display-basis.cpp get-values.cpp load-dc.cpp lor-transfer.cpp"'
-'"toys"
-   "Toys miniapps:"
-   "miniapps/toys"
-   "automata.cpp life.cpp lissajous.cpp mandel.cpp mondrian.cpp rubik.cpp snake.cpp"'
 '"convergence"
   "Convergence tests:"
   "tests/convergence"
@@ -588,8 +444,6 @@ function go_group()
      mkdir -p "${group_output_dir}" || exit 1
   fi
   for src in "$@"; do
-      ex_run_suffix=${run_suffix} && [[ $src =~ ex0p?\.cpp ]] \
-         && ex_run_suffix=""
      cd "${mfem_dir}/${group_dir}" || exit 1
      extract_sample_runs "${src}" || continue
      [ "${#runs[@]}" -eq 0 ] && continue
@@ -609,7 +463,7 @@ function go_group()
      fi
      for run in "${runs[@]}"; do
         if [ "${run}" == "" ]; then continue; fi
-         eval go \"\${run_prefix} \${run} \${ex_run_suffix}\" $output
+         eval go \"\${run_prefix} \${run} \${run_suffix}\" $output
      done
   done
   ${make} clean-exec
@@ -1,4 +1,4 @@
-// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 // at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 // LICENSE and NOTICE for details. LLNL-CODE-806117.
 //
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -39,7 +39,7 @@ set -- $$($(1) $(SHELL) -c "$(2)" 2>&1); while [ "$$#" -gt 3 ]; do shift; done
 endef
 define TIMECMD.NOTGNU
 set -- $$($(1) -l $(SHELL) -c "{ $(2); } > /dev/null 2>&1" 2>&1; echo $$?); \
-set -- "$$1"s "$$(($$7/1024))"kB "$${!#}"
+set -- "$$1"s "$$(($$7/1024))"kB "$${60}"
 endef
 define TIMECMD.BASH
 TIMEFORMAT=$$'%3Rs'; \
@@ -57,27 +57,22 @@ TIMECMD := $(word 1,$(TIMECMD))
 ifneq (,$(filter test%,$(MAKECMDGOALS)))
   MAKEFLAGS += -k
 endif
-# Test runs of the examples/miniapps with parameters - check exit code:
-# 0 means success, 255 means the test was skipped, anything else means error
+# Test runs of the examples/miniapps with parameters - check exit code
 mfem-test = \
   printf "   $(3) [$(2) $(1) ... ]: "; \
   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) $(if $(5),,-no-vis )$(4) \
     > $(1).stderr 2>&1); \
-   err="$$3"; \
-   if [ "$$3" = 0 ]; then $(PRINT_OK); \
-   else if [ "$$3" = 255 ]; then $(PRINT_SKIP); err=0; \
-   else $(PRINT_FAILED); cat $(1).stderr; fi; fi; \
-   rm -f $(1).stderr; exit $$err
+   if [ "$$3" = 0 ]; \
+   then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; fi; \
+   rm -f $(1).stderr; exit $$3

 # Test runs of the examples/miniapps - check exit code and if a file exists
-# See mfem-test for the interpretation of the error code
 mfem-test-file = \
   printf "   $(3) [$(2) $(1) ... ]: "; \
   $(call $(TIMEFUN),$(TIMECMD),$(2) ./$(1) -no-vis > $(1).stderr 2>&1); \
   err="$$3"; \
-   if [ "$$3" = 0 ] && [ -e $(4) ]; then $(PRINT_OK); \
-   else if [ "$$3" = 255 ] && [ -e $(4) ]; then $(PRINT_SKIP); err=0; \
-   else $(PRINT_FAILED); cat $(1).stderr; err=64; fi; fi; \
+   if [ "$$3" = 0 ] && [ -e $(4) ]; \
+   then $(PRINT_OK); else $(PRINT_FAILED); cat $(1).stderr; err=64; fi; \
   rm -f $(1).stderr; exit $$err

 .PHONY: test test-par-YES test-par-NO test-ser test-par test-clean test-print
@@ -85,26 +80,6 @@ mfem-test-file = \
 # What sets of tests to run in serial and parallel
 test-par-YES: $(PAR_$(MFEM_TESTS):=-test-par) $(SEQ_$(MFEM_TESTS):=-test-seq)
 test-par-NO:  $(SEQ_$(MFEM_TESTS):=-test-seq)
-ifeq ($(MFEM_USE_CUDA),YES)
-.PHONY: test-par-YES-cuda test-par-NO-cuda test-ser-cuda test-par-cuda test-cuda
-test-par-YES: test-par-YES-cuda
-test-par-NO:  test-par-NO-cuda
-test-par-YES-cuda: test-par-cuda test-ser-cuda
-test-par-NO-cuda:  test-ser-cuda
-test-ser-cuda: $(SEQ_DEVICE_$(MFEM_TESTS):=-test-seq-cuda)
-test-par-cuda: $(PAR_DEVICE_$(MFEM_TESTS):=-test-par-cuda)
-test-cuda: test-par-$(MFEM_USE_MPI)-cuda clean-exec
-endif
-ifeq ($(MFEM_USE_HIP),YES)
-.PHONY: test-par-YES-hip test-par-NO-hip test-ser-hip test-par-hip test-hip
-test-par-YES: test-par-YES-hip
-test-par-NO:  test-par-NO-hip
-test-par-YES-hip: test-par-hip test-ser-hip
-test-par-NO-hip:  test-ser-hip
-test-ser-hip: $(SEQ_DEVICE_$(MFEM_TESTS):=-test-seq-hip)
-test-par-hip: $(PAR_DEVICE_$(MFEM_TESTS):=-test-par-hip)
-test-hip: test-par-$(MFEM_USE_MPI)-hip clean-exec
-endif
 test-ser:     test-par-NO
 test-par:     test-par-YES
 test:         all test-par-$(MFEM_USE_MPI) clean-exec
@@ -1,258 +1,241 @@
-MFEM NC mesh v1.0
+MFEM mesh v1.1

-# NCMesh supported geometry types:
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
 # SEGMENT     = 1
 # TRIANGLE    = 2
 # SQUARE      = 3
 # TETRAHEDRON = 4
 # CUBE        = 5
-# PRISM       = 6
+#

 dimension
 3

-# rank attr geom ref_type nodes/children
 elements
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-# attr geom nodes
 boundary
 96
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+4 3 54 129 57 23
 4 3 23 57 140 77
 4 3 57 19 80 140
 5 3 19 58 141 80
+5 3 58 24 67 141
+6 3 62 25 75 142
 5 3 141 67 15 79
 6 3 15 62 142 79
-6 3 62 25 75 142
-4 3 77 140 78 14
-6 3 142 75 14 78
 4 3 140 80 6 78
 5 3 80 141 79 6
 6 3 79 142 78 6
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+2 3 31 21 65 172
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+5 3 34 16 64 173
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+2 3 64 172 60 4
+5 3 173 64 4 63
+6 3 4 60 174 63

-# vert_id p1 p2
 vertex_parents
 215
 8 0 1
@@ -471,9 +454,28 @@ vertex_parents
 221 171 178
 222 203 219

-# top-level node coordinates
-coordinates
-8
+coarse_elements
+17
+7 11 12 9 10 6 5 8 7
+7 0 14 13 1 3 4 120 2
+7 27 22 21 28 26 23 24 25
+7 15 18 19 29 16 17 20 122
+7 31 38 37 32 34 35 36 33
+7 30 40 41 44 124 39 42 43
+7 49 50 51 52 56 55 54 53
+7 47 48 45 46 57 126 59 58
+7 113 114 111 112 108 107 110 109
+7 116 115 128 117 119 105 106 118
+7 93 96 95 94 92 97 98 91
+7 103 102 99 130 104 101 100 90
+7 85 84 83 86 88 81 82 87
+7 132 80 77 76 89 79 78 75
+7 63 64 65 66 70 69 68 67
+7 62 134 60 61 72 71 74 73
+7 121 123 125 127 129 131 133 135
+
+vertices
+223
 3
 0 0 0
 1 0 0
@@ -483,5 +485,218 @@ coordinates
 1 0 1
 0 1 1
 1 1 1
-
-mfem_mesh_end
+0.5 0 0
+1 0.5 0
+0.5 1 0
+0 0.5 0
+0.5 0 1
+1 0.5 1
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+0.375 0.375 0.75
+0.375 0.375 0.625
@@ -1,64 +1,56 @@
-MFEM NC mesh v1.0
+MFEM mesh v1.1

-# NCMesh supported geometry types:
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
 # SEGMENT     = 1
 # TRIANGLE    = 2
 # SQUARE      = 3
 # TETRAHEDRON = 4
 # CUBE        = 5
-# PRISM       = 6
+#

 dimension
 2

-# rank attr geom ref_type nodes/children
 elements
-37
-1 1 3 3 1 10 19 28
-1 1 3 3 2 3 4 9
-0 1 3 0 0 9 21 12
-0 1 3 0 9 4 10 21
-1 1 3 3 5 6 7 8
-0 1 3 0 21 22 37 25
-0 1 3 0 22 10 23 37
-0 1 3 0 37 23 8 24
-0 1 3 0 25 37 24 11
-0 1 3 0 12 21 11 7
-1 1 3 3 11 12 13 14
-0 1 3 0 4 13 26 10
-0 1 3 0 13 1 14 26
-0 1 3 0 26 14 5 15
-1 1 3 3 15 16 17 18
-0 1 3 0 10 27 38 23
-0 1 3 0 27 26 28 38
-0 1 3 0 38 28 15 29
-0 1 3 0 23 38 29 8
-1 1 3 3 20 25 26 27
-1 1 3 3 21 22 23 24
-0 1 3 0 8 29 39 33
-0 1 3 0 29 15 31 39
-0 1 3 0 39 31 30 32
-0 1 3 0 33 39 32 18
-0 1 3 0 15 5 16 30
-0 1 3 0 30 16 3 17
-0 1 3 0 18 30 17 6
-1 1 3 3 29 30 35 36
-0 1 3 0 7 11 34 20
-1 1 3 3 31 32 33 34
-0 1 3 0 11 24 40 35
-0 1 3 0 24 8 33 40
-0 1 3 0 40 33 18 36
-0 1 3 0 35 40 36 34
-0 1 3 0 34 18 6 19
-0 1 3 0 20 34 19 2
+28
+1 3 0 9 21 12
+1 3 12 21 11 7
+1 3 21 22 37 25
+1 3 25 37 24 11
+1 3 37 23 8 24
+1 3 22 10 23 37
+1 3 9 4 10 21
+1 3 4 13 26 10
+1 3 13 1 14 26
+1 3 26 14 5 15
+1 3 38 28 15 29
+1 3 27 26 28 38
+1 3 10 27 38 23
+1 3 23 38 29 8
+1 3 8 29 39 33
+1 3 33 39 32 18
+1 3 39 31 30 32
+1 3 29 15 31 39
+1 3 15 5 16 30
+1 3 30 16 3 17
+1 3 18 30 17 6
+1 3 34 18 6 19
+1 3 40 33 18 36
+1 3 24 8 33 40
+1 3 11 24 40 35
+1 3 35 40 36 34
+1 3 7 11 34 20
+1 3 20 34 19 2

-# attr geom nodes
 boundary
 16
 1 1 0 9
 4 1 12 0
-1 1 9 4
 4 1 7 12
+1 1 9 4
 1 1 4 13
 1 1 13 1
 2 1 1 14
@@ -67,12 +59,11 @@ boundary
 2 1 16 3
 3 1 3 17
 3 1 17 6
-4 1 20 7
 3 1 6 19
+4 1 20 7
 3 1 19 2
 4 1 2 20

-# vert_id p1 p2
 vertex_parents
 37
 4 0 1
@@ -113,13 +104,59 @@ vertex_parents
 39 29 32
 40 24 36

-# top-level node coordinates
-coordinates
-4
+coarse_elements
+9
+3 2 5 4 3
+3 0 6 28 1
+3 12 11 10 13
+3 7 8 9 30
+3 14 17 16 15
+3 32 18 19 20
+3 24 23 22 25
+3 26 34 21 27
+3 29 31 33 35
+
+vertices
+41
 2
 0 0
 1 0
 0 1
 1 1
-
-mfem_mesh_end
+0.5 0
+1 0.5
+0.5 1
+0 0.5
+0.5 0.5
+0.25 0
+0.5 0.25
+0.25 0.5
+0 0.25
+0.75 0
+1 0.25
+0.75 0.5
+1 0.75
+0.75 1
+0.5 0.75
+0.25 1
+0 0.75
+0.25 0.25
+0.375 0.25
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+0.25 0.75
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+0.375 0.75
+0.375 0.375
+0.625 0.375
+0.625 0.625
+0.375 0.625
@@ -1,43 +1,51 @@
-MFEM NC mesh v1.0
+MFEM mesh v1.1

-# NCMesh supported geometry types:
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
 # SEGMENT     = 1
 # TRIANGLE    = 2
 # SQUARE      = 3
 # TETRAHEDRON = 4
 # CUBE        = 5
-# PRISM       = 6
+#

 dimension
 2

-# rank attr geom ref_type nodes/children
 elements
-20
-0 1 3 0 1 2 11 10
-0 1 3 0 2 3 12 11
-0 1 3 0 3 4 13 12
-0 2 3 0 4 5 14 13
-0 2 3 0 5 6 15 14
-0 2 3 0 6 7 16 15
-0 2 3 0 7 8 17 16
-1 1 3 3 8 13 14 15
-1 1 3 3 9 10 11 12
-0 1 3 0 0 23 30 26
-0 1 3 0 23 18 24 30
-0 1 3 0 30 24 22 25
-0 1 3 0 26 30 25 21
-0 1 3 0 18 1 19 22
-0 1 3 0 22 19 10 20
-1 1 3 3 16 17 18 19
-0 1 3 0 21 25 31 29
-0 1 3 0 25 22 27 31
-0 1 3 0 31 27 20 28
-0 1 3 0 29 31 28 9
+17
+1 3 0 23 30 26
+1 3 26 30 25 21
+1 3 30 24 22 25
+1 3 23 18 24 30
+1 3 18 1 19 22
+1 3 22 19 10 20
+1 3 31 27 20 28
+1 3 25 22 27 31
+1 3 21 25 31 29
+1 3 29 31 28 9
+1 3 1 2 11 10
+1 3 2 3 12 11
+1 3 3 4 13 12
+2 3 4 5 14 13
+2 3 5 6 15 14
+2 3 6 7 16 15
+2 3 7 8 17 16

-# attr geom nodes
 boundary
 25
+3 1 0 23
+1 1 26 0
+1 1 21 26
+3 1 23 18
+3 1 18 1
+3 1 10 20
+3 1 20 28
+1 1 29 21
+3 1 28 9
+1 1 9 29
 3 1 1 2
 3 1 11 10
 3 1 2 3
@@ -53,18 +61,7 @@ boundary
 3 1 7 8
 2 1 8 17
 3 1 17 16
-3 1 0 23
-1 1 26 0
-3 1 23 18
-1 1 21 26
-3 1 18 1
-3 1 10 20
-1 1 29 21
-3 1 20 28
-3 1 28 9
-1 1 9 29

-# vert_id p1 p2
 vertex_parents
 14
 18 0 1
@@ -82,21 +79,14 @@ vertex_parents
 30 23 25
 31 25 28

-# root element orientation
-root_state
-8
-1
-1
-1
-1
-1
-1
-0
-0
+coarse_elements
+3
+3 0 3 2 1
+3 8 7 6 9
+3 17 4 5 18

-# top-level node coordinates
-coordinates
-18
+vertices
+32
 2
 0 0
 1 0
@@ -116,5 +106,17 @@ coordinates
 6 1
 7 1
 8 1
-
-mfem_mesh_end
+0.5 0
+1 0.5
+0.5 1
+0 0.5
+0.5 0.5
+0.25 0
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+0.25 0.5
+0 0.25
+0.5 0.75
+0.25 1
+0 0.75
+0.25 0.25
+0.25 0.75
@@ -1,9 +0,0 @@
-MFEM INLINE mesh v1.0
-
-type = pyramid
-nx = 4
-ny = 4
-nz = 4
-sx = 1.0
-sy = 1.0
-sz = 1.0
@@ -1,43 +0,0 @@
-MFEM mesh v1.0
-
-#
-# MFEM Geometry Types (see mesh/geom.hpp):
-#
-# POINT       = 0
-# SEGMENT     = 1
-# TRIANGLE    = 2
-# SQUARE      = 3
-# TETRAHEDRON = 4
-# CUBE        = 5
-# PRISM       = 6
-# PYRAMID     = 7
-#
-
-dimension
-3
-
-elements
-2
-1 7 4 3 2 1 0
-1 7 1 2 3 4 5
-
-boundary
-8
-1 2 0 2 1
-2 2 0 3 2
-3 2 0 4 3
-4 2 0 1 4
-5 2 1 2 5
-6 2 2 3 5
-7 2 3 4 5
-8 2 4 1 5
-
-vertices
-6
-3
-0 0 -1
-1 0 0
-0 1 0
-1 0 0
-0 -1 0
-0 0 1
@@ -1,38 +0,0 @@
-// 0 for tetrahedra, 1 for hexahedra
-tet_or_hex = 1;
-
-Point(1) = {0, 0, 0, 1.0};
-Point(2) = {1, 0, 0, 1.0};
-Point(3) = {1, 1, 0, 1.0};
-Point(4) = {0, 1, 0, 1.0};
-
-Characteristic Length {:} = 0.25;
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-
-Periodic Curve {1} = {-3};
-Periodic Curve {2} = {-4};
-
-Curve Loop(1) = {1, 2, 3, 4};
-Plane Surface(1) = {1};
-Transfinite Surface {1};
-
-If (tet_or_hex == 1)
-   Recombine Surface {1};
-   out[] = Extrude {0, 0, 1} { Surface{1}; Layers{4}; Recombine; };
-Else
-   out[] = Extrude {0, 0, 1} { Surface{1}; Layers{4}; }
-EndIf
-
-Physical Volume(1) = {out[1]};
-Physical Surface(1) = {1,out[0],out[2],out[3],out[4],out[5]};
-
-Mesh 3;
-Mesh.MshFileVersion = 2.2;
-
-Periodic Surface {out[0]} = {1} Translate {0, 0, 1};
-Periodic Surface {out[4]} = {out[2]} Translate {0, 1, 0};
-Periodic Surface {out[3]} = {out[5]} Translate {1, 0, 0};
@@ -1,381 +0,0 @@
-$MeshFormat
-2.2 0 8
-$EndMeshFormat
-$Nodes
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-2 1 0 0
-3 1 1 0
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-MFEM mesh v1.0
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-MFEM mesh v1.0
-
-#
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-MFEM mesh v1.0
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-MFEM mesh v1.0
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-MFEM mesh v1.0
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-MFEM mesh v1.0
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-0.097964, 0.195929, -0.097964, 
-0.195928, -0.173234, -0.078922, 
-0.489821, -0.391856, -0.467007, 
-0.397859, -0.746293, -0.904802, 
-0.945206, -0.849559, -1.380330, 
-1.221820, -1.440880, -1.342910, 
-1.100830, -0.923191, -1.049020, 
-1.146990, -0.774515, -0.621542, 
-0.951057, -0.951057, -0.803055, 
-0.635255, -0.951057, -0.951057, 
-0.792548, -0.634038, -0.454301, 
-0.479369, -0.158510, -0.317019, 
-0.149331, 0.178643, 0.295860, 
-0.306275, 0.246225, 0.406610, 
-0.367954, 0.498458, -0.014929, 
-0.084917, -0.094272, -0.000726, 
-0.245374, -0.340755, -0.435351, 
-0.490564, -0.176355, -0.294974, 
-0.148010, -0.328246, 0.136248, 
-0.182883, 0.328957, 0.309903, 
-0.646446, 0.622546, 0.800859, 
-0.801803, 0.643087, 0.654473, 
-0.796963, 0.816799, 0.748189, 
-0.898148, 0.819092, 0.970033, 
-1.049540, 1.162660, 1.115310, 
-1.266700, 0.539960, 0.728396, 
-0.656318, 0.783152, 0.302716, 
-0.403858, 0.219006, 0.309252, 
-0.009667, 0.107161, -0.118211, 
-0.011786, -0.284704, -0.179858, 
-0.411567, -0.296676, -0.570168, 
-0.635348, -0.726784, -0.793211, 
-1.016860, -1.112970, -1.170910, 
-1.281530, -0.737860, -0.851723, 
-0.883732, -0.995070, -0.653153, 
-0.769939, -0.631918, -0.797688, 
-0.616289, -0.806819, -0.638485, 
-0.790356, -0.136399, -0.322769, 
-0.165339, -0.309622]
-DataCollection/Mesh/PartitionInfo/Size: 2
-DataCollection/Mesh/PartitionInfo/Type: FMS_UINT64
-DataCollection/Mesh/PartitionInfo/Values: [0, 1]
-DataCollection/Mesh/NumDomainNames: 1
-DataCollection/Mesh/NumComponents: 1
-DataCollection/Mesh/NumTags: 0
-DataCollection/Mesh/DomainNames/0/Name: Domain
-DataCollection/Mesh/DomainNames/0/NumDomains: 1
-DataCollection/Mesh/DomainNames/0/Domains/0/Dimension: 2
-DataCollection/Mesh/DomainNames/0/Domains/0/NumVertices: 31
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/EntityType: FMS_EDGE
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/NumEntities: 50
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/Size: 100
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/Type: FMS_INT32
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/0/Values: [11, 0, 26, 
-11, 26, 14, 
-14, 0, 27, 
-14, 27, 17, 
-17, 0, 28, 
-17, 28, 20, 
-20, 0, 29, 
-20, 29, 23, 
-23, 0, 30, 
-23, 30, 11, 
-11, 1, 12, 
-1, 26, 12, 
-12, 3, 13, 
-3, 26, 13, 
-13, 2, 14, 
-2, 15, 2, 
-27, 15, 15, 
-5, 16, 5, 
-27, 16, 16, 
-4, 17, 4, 
-18, 4, 28, 
-18, 18, 7, 
-19, 7, 28, 
-19, 19, 6, 
-20, 6, 21, 
-6, 29, 21, 
-21, 9, 22, 
-9, 29, 22, 
-22, 8, 23, 
-8, 24, 8, 
-30, 24, 24, 
-10, 25, 10, 
-30, 25, 25, 1]
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/EntityType: FMS_QUADRILATERAL
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/NumEntities: 20
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/Size: 80
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/Type: FMS_INT32
-DataCollection/Mesh/DomainNames/0/Domains/0/Entities/1/Values: [0, 1, 2, 
-3, 3, 4, 
-5, 6, 6, 
-7, 8, 9, 
-9, 10, 11, 
-12, 12, 13, 
-14, 0, 15, 
-16, 17, 1, 
-17, 18, 19, 
-20, 2, 20, 
-21, 22, 22, 
-23, 24, 4, 
-24, 25, 26, 
-27, 5, 27, 
-28, 29, 29, 
-30, 31, 7, 
-31, 32, 33, 
-34, 8, 34, 
-35, 36, 36, 
-37, 38, 10, 
-38, 39, 40, 
-41, 11, 41, 
-42, 43, 43, 
-44, 45, 13, 
-45, 46, 47, 
-48, 14, 48, 
-49, 15]
-DataCollection/Mesh/Components/0/Name: volume
-DataCollection/Mesh/Components/0/Dimension: 2
-DataCollection/Mesh/Components/0/NumEntities: 20
-DataCollection/Mesh/Components/0/Coordinates: Coords
-DataCollection/Mesh/Components/0/NumParts: 1
-DataCollection/Mesh/Components/0/Parts/0/DomainName: Domain
-DataCollection/Mesh/Components/0/Parts/0/DomainID: 0
-DataCollection/Mesh/Components/0/Parts/0/FullDomain: Yes
-DataCollection/Mesh/Components/0/Relations/Size: 0
-DataCollection/Mesh/Components/0/Relations/Type: FMS_UINT64
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -38,7 +38,7 @@ PROJECT_NAME           = "MFEM"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.

-PROJECT_NUMBER         = v4.3.1
+PROJECT_NUMBER         = v4.2.1

 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -766,7 +766,6 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                         @MFEM_SOURCE_DIR@/mesh \
                         @MFEM_SOURCE_DIR@/fem \
                         @MFEM_SOURCE_DIR@/examples \
-                         @MFEM_SOURCE_DIR@/examples/caliper \
                         @MFEM_SOURCE_DIR@/examples/amgx \
                         @MFEM_SOURCE_DIR@/examples/ginkgo \
                         @MFEM_SOURCE_DIR@/examples/hiop \
@@ -779,12 +778,9 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                         @MFEM_SOURCE_DIR@/miniapps/electromagnetics \
                         @MFEM_SOURCE_DIR@/miniapps/gslib \
                         @MFEM_SOURCE_DIR@/miniapps/meshing \
-                         @MFEM_SOURCE_DIR@/miniapps/mtop \
                         @MFEM_SOURCE_DIR@/miniapps/navier \
                         @MFEM_SOURCE_DIR@/miniapps/nurbs \
                         @MFEM_SOURCE_DIR@/miniapps/performance \
-                         @MFEM_SOURCE_DIR@/miniapps/shifted \
-                         @MFEM_SOURCE_DIR@/miniapps/solvers \
                         @MFEM_SOURCE_DIR@/miniapps/tools \
                         @MFEM_SOURCE_DIR@/miniapps/toys

@@ -42,10 +42,8 @@ namespace mfem {
 * - MFEM_FORALL macro in forall.hpp
 *
 * <H3>Example codes</H3>
- * - <a class="el" href="ex0_8cpp_source.html">Example 0</a>: simplest example, nodal H1 FEM for the Laplace problem
- * - <a class="el" href="ex0p_8cpp_source.html">Example 0p</a>: simplest parallel example, nodal H1 FEM for the Laplace problem
- * - <a class="el" href="examples_2ex1_8cpp_source.html">Example 1</a>: nodal H1 FEM for the Laplace problem (same discretization as ex0 but with more sophisticated options)
- * - <a class="el" href="examples_2ex1p_8cpp_source.html">Example 1p</a>: parallel nodal H1 FEM for the Laplace problem (same discretization as ex0p but with more sophisticated options)
+ * - <a class="el" href="examples_2ex1_8cpp_source.html">Example 1</a>: nodal H1 FEM for the Laplace problem
+ * - <a class="el" href="examples_2ex1p_8cpp_source.html">Example 1p</a>: parallel nodal H1 FEM for the Laplace problem
 * - <a class="el" href="ex2_8cpp_source.html">Example 2</a>: vector FEM for linear elasticity
 * - <a class="el" href="ex2p_8cpp_source.html">Example 2p</a>: parallel vector FEM for linear elasticity
 * - <a class="el" href="ex3_8cpp_source.html">Example 3</a>: Nedelec H(curl) FEM for the definite Maxwell problem
@@ -94,10 +92,6 @@ namespace mfem {
 * - <a class="el" href="ex26p_8cpp_source.html">Example 26p</a>: parallel multigrid preconditioner for the Laplace problem using nodal H1 FEM
 * - <a class="el" href="ex27_8cpp_source.html">Example 27</a>: boundary conditions for the Laplace problem
 * - <a class="el" href="ex27p_8cpp_source.html">Example 27p</a>: parallel boundary conditions for the Laplace problem
- * - <a class="el" href="ex28_8cpp_source.html">Example 28</a>: sliding contact in elasticity
- * - <a class="el" href="ex28p_8cpp_source.html">Example 28p</a>: parallel sliding contact in elasticity
- * - <a class="el" href="ex29_8cpp_source.html">Example 29</a>: Laplace solve on a 3D-embedded surface
- * - <a class="el" href="ex29p_8cpp_source.html">Example 29p</a>: parallel Laplace solve on a 3D-embedded surface
 *
 * <H4>AmgX Examples</H4>
 * - Variants of Examples
@@ -105,12 +99,6 @@ namespace mfem {
 *   <a class="el" href="examples_2amgx_2ex1p_8cpp_source.html">1p</a>,
 *   demonstrating the use of MFEM's \link amgxsolver.hpp AmgX integration\endlink.
 *
- * <H4>Caliper Examples</H4>
- * - Variants of Example
- *   <a class="el" href="examples_2caliper_2ex1_8cpp_source.html">1</a> and
- *   <a class="el" href="examples_2caliper_2ex1p_8cpp_source.html">1p</a>,
- *   demonstrating the use of MFEM's \link annotation.hpp Ginkgo integration\endlink.
- *
 * <H4>Ginkgo Examples</H4>
 * - Variants of Example
 *   <a class="el" href="examples_2ginkgo_2ex1_8cpp_source.html">1</a>,
@@ -188,10 +176,6 @@ namespace mfem {
 * - <a class="el" href="findpts_8cpp_source.html">Find Points</a>: evaluate grid function in physical space, <a class="el" href="findpts_8cpp_source.html">serial</a> and <a class="el" href="pfindpts_8cpp_source.html">parallel</a> versions
 * - <a class="el" href="field-diff_8cpp_source.html">Field Diff</a>: compare grid functions on different meshes
 * - <a class="el" href="field-interp_8cpp_source.html">Field Interp</a>: transfer a grid functions between meshes
- * - <a class="el" href="distance_8cpp_source.html">Distance</a>: finite element distance function solver
- * - <a class="el" href="diffusion_8cpp_source.html">Shifted Diffusion</a>: shifted boundary diffusion solver
- * - <a class="el" href="distance_8cpp_source.html">Block Solvers</a>: comparison of saddle point system solvers
- * - <a class="el" href="parheat_8cpp_source.html">Optimization gradients</a>: Gradients of PDE-constrained function
 * - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Laplace problem
 * - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Laplace problem
 *
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -10,7 +10,6 @@
 # CONTRIBUTING.md for details.

 list(APPEND ALL_EXE_SRCS
-  ex0.cpp
  ex1.cpp
  ex2.cpp
  ex3.cpp
@@ -35,13 +34,10 @@ list(APPEND ALL_EXE_SRCS
  ex25.cpp
  ex26.cpp
  ex27.cpp
-  ex28.cpp
-  ex29.cpp
  )

 if (MFEM_USE_MPI)
  list(APPEND ALL_EXE_SRCS
-    ex0p.cpp
    ex1p.cpp
    ex2p.cpp
    ex3p.cpp
@@ -68,8 +64,6 @@ if (MFEM_USE_MPI)
    ex25p.cpp
    ex26p.cpp
    ex27p.cpp
-    ex28p.cpp
-    ex29p.cpp
    )
 endif()

@@ -85,9 +79,6 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})

  set(THIS_TEST_OPTIONS "-no-vis")
-  if (${TEST_NAME} MATCHES "ex0p?")
-    set(THIS_TEST_OPTIONS)
-  endif()
  if (${TEST_NAME} MATCHES "ex10p*")
    list(APPEND THIS_TEST_OPTIONS "-tf" "5")
  elseif(${TEST_NAME} MATCHES "ex15p*")
@@ -108,34 +99,6 @@ foreach(SRC_FILE ${ALL_EXE_SRCS})
  endif()
 endforeach()

-# Add CUDA/HIP tests.
-set(DEVICE_EXAMPLES
-    # serial examples with device support:
-    ex1 ex3 ex4 ex5 ex6 ex9 ex22 ex24 ex25 ex26
-    # parallel examples with device support:
-    ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex22p ex24p ex25p ex26p)
-set(MFEM_TEST_DEVICE)
-if (MFEM_USE_CUDA)
-  set(MFEM_TEST_DEVICE "cuda")
-elseif (MFEM_USE_HIP)
-  set(MFEM_TEST_DEVICE "hip")
-endif()
-if (MFEM_TEST_DEVICE)
-  foreach(TEST_NAME ${DEVICE_EXAMPLES})
-    set(THIS_TEST_OPTIONS "-no-vis" "-d" "${MFEM_TEST_DEVICE}")
-    if (NOT (${TEST_NAME} MATCHES ".*p$"))
-      add_test(NAME ${TEST_NAME}_${MFEM_TEST_DEVICE}_ser
-        COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-    elseif (MFEM_USE_MPI)
-      add_test(NAME ${TEST_NAME}_${MFEM_TEST_DEVICE}_np=${MFEM_MPI_NP}
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
-
 # If STRUMPACK is enabled, add a test run that uses it.
 if (MFEM_USE_STRUMPACK)
  add_test(NAME ex11p_strumpack_np=${MFEM_MPI_NP}
@@ -184,10 +147,6 @@ if (MFEM_USE_SUNDIALS)
  add_subdirectory(sundials)
 endif()

-if(MFEM_USE_CALIPER)
-  add_subdirectory(caliper)
-endif()
-
 # Include the examples/superlu directory if SUPERLU is enabled.
 if (MFEM_USE_SUPERLU)
  add_subdirectory(superlu)
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -157,7 +157,7 @@ int main(int argc, char *argv[])
      delete_fec = true;
   }
   ParFiniteElementSpace fespace(&pmesh, fec);
-   HYPRE_BigInt size = fespace.GlobalTrueVSize();
+   HYPRE_Int size = fespace.GlobalTrueVSize();
   if (myid == 0)
   {
      cout << "Number of finite element unknowns: " << size << endl;
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+# Copyright (c) 2010-2020, Lawrence Livermore National Security, LLC. Produced
 # at the Lawrence Livermore National Laboratory. All Rights reserved. See files
 # LICENSE and NOTICE for details. LLNL-CODE-806117.
 #
@@ -1,51 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-set(CALIPER_EXAMPLES_SRCS)
-
-list(APPEND CALIPER_EXE_SRCS
-    ex1.cpp
-    )
-
-if (MFEM_USE_MPI)
-  list(APPEND CALIPER_EXE_SRCS
-      ex1p.cpp
-      )
-endif()
-
-
-# Include the source directory where mfem.hpp and mfem-performance.hpp are.
-include_directories(BEFORE ${PROJECT_BINARY_DIR})
-
-# Add one executable per cpp file
-set(PREFIX caliper_)
-add_mfem_examples(CALIPER_EXE_SRCS ${PREFIX})
-
-# Add a test for each example
-foreach(SRC_FILE ${CALIPER_EXE_SRCS})
-  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-
-  set(THIS_TEST_OPTIONS "-no-vis")
-
-  if (NOT (${TEST_NAME} MATCHES ".*p$"))
-    add_test(NAME ${TEST_NAME}_ser
-      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
-  else()
-    add_test(NAME ${TEST_NAME}_np=${MFEM_MPI_NP}
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-      ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-      ${MPIEXEC_POSTFLAGS})
-  endif()
-endforeach()
-
-
@@ -1,18 +0,0 @@
-                    Finite Element Discretization Library
-                                   __
-                       _ __ ___   / _|  ___  _ __ ___
-                      | '_ ` _ \ | |_  / _ \| '_ ` _ \
-                      | | | | | ||  _||  __/| | | | | |
-                      |_| |_| |_||_|   \___||_| |_| |_|
-
-                               https://mfem.org
-
-This directory contains modifications of the example codes that illustrate the
-use of MFEM features based on the Caliper performance profiling library.
-
-To build these examples, make sure that MFEM is configured with the option
-"MFEM_USE_CALIPER = YES", see the top-level INSTALL file for details (version
-2.5.0 of Caliper is recommended, though older versions may work too).
-
-We recommend comparing the original example codes with the corresponding files
-in the current directory.
@@ -1,270 +0,0 @@
-//                                MFEM Example 1
-//                             Caliper Modification
-//
-// Compile with: make ex1
-//
-// Sample runs:  ex1 -m ../data/square-disc.mesh
-//               ex1 -m ../data/star.mesh
-//               ex1 -m ../data/star-mixed.mesh
-//               ex1 -m ../data/escher.mesh
-//               ex1 -m ../data/fichera.mesh
-//               ex1 -m ../data/fichera-mixed.mesh
-//               ex1 -m ../data/toroid-wedge.mesh
-//               ex1 -m ../data/periodic-annulus-sector.msh
-//               ex1 -m ../data/periodic-torus-sector.msh
-//               ex1 -m ../data/square-disc-p2.vtk -o 2
-//               ex1 -m ../data/square-disc-p3.mesh -o 3
-//               ex1 -m ../data/square-disc-nurbs.mesh -o -1
-//               ex1 -m ../data/star-mixed-p2.mesh -o 2
-//               ex1 -m ../data/disc-nurbs.mesh -o -1
-//               ex1 -m ../data/pipe-nurbs.mesh -o -1
-//               ex1 -m ../data/fichera-mixed-p2.mesh -o 2
-//               ex1 -m ../data/star-surf.mesh
-//               ex1 -m ../data/square-disc-surf.mesh
-//               ex1 -m ../data/inline-segment.mesh
-//               ex1 -m ../data/amr-quad.mesh
-//               ex1 -m ../data/amr-hex.mesh
-//               ex1 -m ../data/fichera-amr.mesh
-//               ex1 -m ../data/mobius-strip.mesh
-//               ex1 -m ../data/mobius-strip.mesh -o -1 -sc
-//
-// Device sample runs:
-//               ex1 -pa -d cuda
-//               ex1 -pa -d raja-cuda
-//               ex1 -pa -d occa-cuda
-//               ex1 -pa -d raja-omp
-//               ex1 -pa -d occa-omp
-//               ex1 -pa -d ceed-cpu
-//             * ex1 -pa -d ceed-cuda
-//               ex1 -pa -d ceed-cuda:/gpu/cuda/shared
-//               ex1 -m ../data/beam-hex.mesh -pa -d cuda
-//               ex1 -m ../data/beam-tet.mesh -pa -d ceed-cpu
-//               ex1 -m ../data/beam-tet.mesh -pa -d ceed-cuda:/gpu/cuda/ref
-//
-// Description: This example is a copy of Example 1 instrumented with the
-//              Caliper performance profilinh library. Any option supported by
-//              the Caliper ConfigManager can be passed to the code using a
-//              configuration string after -p or --caliper flag. For more
-//              information, see the Caliper documentation.
-//
-// Examples: ex1 --caliper runtime-report
-//           ex1 --caliper runtime-report,mem.highwatermark
-//
-// The first run will return the default report. The second run will also output
-// the memory high-water mark and time spent in MPI routines.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // Define Caliper ConfigManager
-   cali::ConfigManager mgr;
-   // Caliper instrumentation
-   MFEM_PERF_FUNCTION;
-
-   // 1. Parse command-line options.
-   const char *mesh_file = "../../data/star.mesh";
-   int order = 1;
-   bool static_cond = false;
-   bool pa = false;
-   const char *device_config = "cpu";
-   bool visualization = true;
-   const char* cali_config = "runtime-report";
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&cali_config, "-p", "--caliper",
-                  "Caliper configuration string.");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   // 2. Enable hardware devices such as GPUs, and programming models such as
-   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
-   Device device(device_config);
-   device.Print();
-
-   // Caliper configuration
-   mgr.add(cali_config);
-   mgr.start();
-
-   // 3. Read the mesh from the given mesh file. We can handle triangular,
-   //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes with
-   //    the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-
-   // 4. Refine the mesh to increase the resolution. In this example we do
-   //    'ref_levels' of uniform refinement. We choose 'ref_levels' to be the
-   //    largest number that gives a final mesh with no more than 50,000
-   //    elements.
-   {
-      int ref_levels =
-         (int)floor(log(50000./mesh.GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         mesh.UniformRefinement();
-      }
-   }
-
-   // 5. Define a finite element space on the mesh. Here we use continuous
-   //    Lagrange finite elements of the specified order. If order < 1, we
-   //    instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   bool delete_fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-      delete_fec = true;
-   }
-   else if (mesh.GetNodes())
-   {
-      fec = mesh.GetNodes()->OwnFEC();
-      delete_fec = false;
-      cout << "Using isoparametric FEs: " << fec->Name() << endl;
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-      delete_fec = true;
-   }
-   FiniteElementSpace fespace(&mesh, fec);
-   cout << "Number of finite element unknowns: "
-        << fespace.GetTrueVSize() << endl;
-
-   // 6. Determine the list of true (i.e. conforming) essential boundary dofs.
-   //    In this example, the boundary conditions are defined by marking all
-   //    the boundary attributes from the mesh as essential (Dirichlet) and
-   //    converting them to a list of true dofs.
-   Array<int> ess_tdof_list;
-   if (mesh.bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(mesh.bdr_attributes.Max());
-      ess_bdr = 1;
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 7. Set up the linear form b(.) which corresponds to the right-hand side of
-   //    the FEM linear system, which in this case is (1,phi_i) where phi_i are
-   //    the basis functions in the finite element fespace.
-   MFEM_PERF_BEGIN("Set up the linear form");
-   LinearForm b(&fespace);
-   ConstantCoefficient one(1.0);
-   b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   b.Assemble();
-   MFEM_PERF_END("Set up the linear form");
-
-   // 8. Define the solution vector x as a finite element grid function
-   //    corresponding to fespace. Initialize x with initial guess of zero,
-   //    which satisfies the boundary conditions.
-   GridFunction x(&fespace);
-   x = 0.0;
-
-   // 9. Set up the bilinear form a(.,.) on the finite element space
-   //    corresponding to the Laplacian operator -Delta, by adding the Diffusion
-   //    domain integrator.
-   MFEM_PERF_BEGIN("Set up the bilinear form");
-   BilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
-   a.AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 10. Assemble the bilinear form and the corresponding linear system,
-   //     applying any necessary transformations such as: eliminating boundary
-   //     conditions, applying conforming constraints for non-conforming AMR,
-   //     static condensation, etc.
-   if (static_cond) { a.EnableStaticCondensation(); }
-   a.Assemble();
-
-   OperatorPtr A;
-   Vector B, X;
-   a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);
-   MFEM_PERF_END("Set up the bilinear form");
-
-   cout << "Size of linear system: " << A->Height() << endl;
-
-   // 11. Solve the linear system A X = B.
-   if (!pa)
-   {
-      MFEM_PERF_SCOPE("Solve A X=B (FA)");
-#ifndef MFEM_USE_SUITESPARSE
-      // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
-      GSSmoother M((SparseMatrix&)(*A));
-      PCG(*A, M, B, X, 1, 200, 1e-12, 0.0);
-#else
-      // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
-      UMFPackSolver umf_solver;
-      umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
-      umf_solver.SetOperator(*A);
-      umf_solver.Mult(B, X);
-#endif
-   }
-   else // Jacobi preconditioning in partial assembly mode
-   {
-      MFEM_PERF_SCOPE("Solve A X=B (PA)");
-      if (UsesTensorBasis(fespace))
-      {
-         OperatorJacobiSmoother M(a, ess_tdof_list);
-         PCG(*A, M, B, X, 1, 400, 1e-12, 0.0);
-      }
-      else
-      {
-         CG(*A, B, X, 1, 400, 1e-12, 0.0);
-      }
-   }
-   // 12. Recover the solution as a finite element grid function.
-   a.RecoverFEMSolution(X, b, x);
-
-   // 13. Save the refined mesh and the solution. This output can be viewed later
-   //     using GLVis: "glvis -m refined.mesh -g sol.gf".
-   MFEM_PERF_BEGIN("Save the results");
-   ofstream mesh_ofs("refined.mesh");
-   mesh_ofs.precision(8);
-   mesh.Print(mesh_ofs);
-   ofstream sol_ofs("sol.gf");
-   sol_ofs.precision(8);
-   x.Save(sol_ofs);
-   MFEM_PERF_END("Save the results");
-   // 14. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << mesh << x << flush;
-   }
-
-   // 15. Free the used memory.
-   if (delete_fec)
-   {
-      delete fec;
-   }
-
-   // Flush output
-   mgr.flush();
-
-   return 0;
-}
@@ -1,299 +0,0 @@
-//                       MFEM Example 1 - Parallel Version
-//                             Caliper Modification
-//
-// Compile with: make ex1p
-//
-// Sample runs:  mpirun -np 4 ex1p -m ../data/square-disc.mesh
-//               mpirun -np 4 ex1p -m ../data/star.mesh
-//               mpirun -np 4 ex1p -m ../data/star-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/escher.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera.mesh
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed.mesh
-//               mpirun -np 4 ex1p -m ../data/toroid-wedge.mesh
-//               mpirun -np 4 ex1p -m ../data/periodic-annulus-sector.msh
-//               mpirun -np 4 ex1p -m ../data/periodic-torus-sector.msh
-//               mpirun -np 4 ex1p -m ../data/square-disc-p2.vtk -o 2
-//               mpirun -np 4 ex1p -m ../data/square-disc-p3.mesh -o 3
-//               mpirun -np 4 ex1p -m ../data/square-disc-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/star-mixed-p2.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/disc-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/pipe-nurbs.mesh -o -1
-//               mpirun -np 4 ex1p -m ../data/ball-nurbs.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/fichera-mixed-p2.mesh -o 2
-//               mpirun -np 4 ex1p -m ../data/star-surf.mesh
-//               mpirun -np 4 ex1p -m ../data/square-disc-surf.mesh
-//               mpirun -np 4 ex1p -m ../data/inline-segment.mesh
-//               mpirun -np 4 ex1p -m ../data/amr-quad.mesh
-//               mpirun -np 4 ex1p -m ../data/amr-hex.mesh
-//               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh
-//               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh -o -1 -sc
-//
-// Device sample runs:
-//               mpirun -np 4 ex1p -pa -d cuda
-//               mpirun -np 4 ex1p -pa -d occa-cuda
-//               mpirun -np 4 ex1p -pa -d raja-omp
-//               mpirun -np 4 ex1p -pa -d ceed-cpu
-//             * mpirun -np 4 ex1p -pa -d ceed-cuda
-//               mpirun -np 4 ex1p -pa -d ceed-cuda:/gpu/cuda/shared
-//               mpirun -np 4 ex1p -m ../data/beam-tet.mesh -pa -d ceed-cpu
-//
-// Description: This example is a copy of Example 1 instrumented with the
-//              Caliper performance profilinh library. Any option supported by
-//              the Caliper ConfigManager can be passed to the code using a
-//              configuration string after -p or --caliper flag. For more
-//              information, see the Caliper documentation.
-//
-// Examples:  mpirun -np 4 ex1p --caliper runtime-report
-//            mpirun -np 4 ex1p --caliper runtime-report,mem.highwatermark,mpi-report
-//
-// The first run will return the default report. The second run will also output
-// the memory high-water mark and time spent in MPI routines.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Initialize MPI.
-   int num_procs, myid;
-   MPI_Init(&argc, &argv);
-   MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
-   MPI_Comm_rank(MPI_COMM_WORLD, &myid);
-   // Define Caliper ConfigManager
-   cali::ConfigManager mgr;
-   // Caliper instrumentation
-   MFEM_PERF_FUNCTION;
-
-   // 2. Parse command-line options.
-   const char *mesh_file = "../../data/star.mesh";
-   int order = 1;
-   bool static_cond = false;
-   bool pa = false;
-   const char *device_config = "cpu";
-   bool visualization = true;
-   const char* cali_config = "runtime-report";
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh",
-                  "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order",
-                  "Finite element order (polynomial degree) or -1 for"
-                  " isoparametric space.");
-   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
-                  "--no-static-condensation", "Enable static condensation.");
-   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
-                  "--no-partial-assembly", "Enable Partial Assembly.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&cali_config, "-p", "--caliper",
-                  "Caliper configuration string.");
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   // 3. Enable hardware devices such as GPUs, and programming models such as
-   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
-   Device device(device_config);
-   if (myid == 0) { device.Print(); }
-
-   // Caliper configuration
-   mgr.add(cali_config);
-   mgr.start();
-
-   // 4. Read the (serial) mesh from the given mesh file on all processors.  We
-   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
-   //    and volume meshes with the same code.
-   Mesh mesh(mesh_file, 1, 1);
-   int dim = mesh.Dimension();
-
-   // 5. Refine the serial mesh on all processors to increase the resolution. In
-   //    this example we do 'ref_levels' of uniform refinement. We choose
-   //    'ref_levels' to be the largest number that gives a final mesh with no
-   //    more than 10,000 elements.
-   {
-      int ref_levels =
-         (int)floor(log(10000./mesh.GetNE())/log(2.)/dim);
-      for (int l = 0; l < ref_levels; l++)
-      {
-         mesh.UniformRefinement();
-      }
-   }
-
-   // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
-   //    this mesh further in parallel to increase the resolution. Once the
-   //    parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-   {
-      int par_ref_levels = 2;
-      for (int l = 0; l < par_ref_levels; l++)
-      {
-         pmesh.UniformRefinement();
-      }
-   }
-
-   // 7. Define a parallel finite element space on the parallel mesh. Here we
-   //    use continuous Lagrange finite elements of the specified order. If
-   //    order < 1, we instead use an isoparametric/isogeometric space.
-   FiniteElementCollection *fec;
-   bool delete_fec;
-   if (order > 0)
-   {
-      fec = new H1_FECollection(order, dim);
-      delete_fec = true;
-   }
-   else if (pmesh.GetNodes())
-   {
-      fec = pmesh.GetNodes()->OwnFEC();
-      delete_fec = false;
-      if (myid == 0)
-      {
-         cout << "Using isoparametric FEs: " << fec->Name() << endl;
-      }
-   }
-   else
-   {
-      fec = new H1_FECollection(order = 1, dim);
-      delete_fec = true;
-   }
-   ParFiniteElementSpace fespace(&pmesh, fec);
-   HYPRE_BigInt size = fespace.GlobalTrueVSize();
-   if (myid == 0)
-   {
-      cout << "Number of finite element unknowns: " << size << endl;
-   }
-
-   // 8. Determine the list of true (i.e. parallel conforming) essential
-   //    boundary dofs. In this example, the boundary conditions are defined
-   //    by marking all the boundary attributes from the mesh as essential
-   //    (Dirichlet) and converting them to a list of true dofs.
-   Array<int> ess_tdof_list;
-   if (pmesh.bdr_attributes.Size())
-   {
-      Array<int> ess_bdr(pmesh.bdr_attributes.Max());
-      ess_bdr = 1;
-      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
-   }
-
-   // 9. Set up the parallel linear form b(.) which corresponds to the
-   //    right-hand side of the FEM linear system, which in this case is
-   //    (1,phi_i) where phi_i are the basis functions in fespace.
-   MFEM_PERF_BEGIN("Set up the linear form");
-   ParLinearForm b(&fespace);
-   ConstantCoefficient one(1.0);
-   b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   b.Assemble();
-   MFEM_PERF_END("Set up the linear form");
-
-   // 10. Define the solution vector x as a parallel finite element grid function
-   //     corresponding to fespace. Initialize x with initial guess of zero,
-   //     which satisfies the boundary conditions.
-   ParGridFunction x(&fespace);
-   x = 0.0;
-
-   // 11. Set up the parallel bilinear form a(.,.) on the finite element space
-   //     corresponding to the Laplacian operator -Delta, by adding the Diffusion
-   //     domain integrator.
-   MFEM_PERF_BEGIN("Set up the bilinear form");
-   ParBilinearForm a(&fespace);
-   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
-   a.AddDomainIntegrator(new DiffusionIntegrator(one));
-
-   // 12. Assemble the parallel bilinear form and the corresponding linear
-   //     system, applying any necessary transformations such as: parallel
-   //     assembly, eliminating boundary conditions, applying conforming
-   //     constraints for non-conforming AMR, static condensation, etc.
-   if (static_cond) { a.EnableStaticCondensation(); }
-   a.Assemble();
-
-   OperatorPtr A;
-   Vector B, X;
-   a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);
-   MFEM_PERF_END("Set up the bilinear form");
-   // 13. Solve the linear system A X = B.
-   //     * With full assembly, use the BoomerAMG preconditioner from hypre.
-   //     * With partial assembly, use Jacobi smoothing, for now.
-   {
-      MFEM_PERF_SCOPE("Solve A X=B");
-      Solver *prec = NULL;
-      if (pa)
-      {
-         if (UsesTensorBasis(fespace))
-         {
-            prec = new OperatorJacobiSmoother(a, ess_tdof_list);
-         }
-      }
-      else
-      {
-         prec = new HypreBoomerAMG;
-      }
-      CGSolver cg(MPI_COMM_WORLD);
-      cg.SetRelTol(1e-12);
-      cg.SetMaxIter(2000);
-      cg.SetPrintLevel(1);
-      if (prec) { cg.SetPreconditioner(*prec); }
-      cg.SetOperator(*A);
-      cg.Mult(B, X);
-      delete prec;
-   }
-   // 14. Recover the parallel grid function corresponding to X. This is the
-   //     local finite element solution on each processor.
-   a.RecoverFEMSolution(X, b, x);
-
-   // 15. Save the refined mesh and the solution in parallel. This output can
-   //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
-   MFEM_PERF_BEGIN("Save the results");
-   {
-      ostringstream mesh_name, sol_name;
-      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
-      sol_name << "sol." << setfill('0') << setw(6) << myid;
-
-      ofstream mesh_ofs(mesh_name.str().c_str());
-      mesh_ofs.precision(8);
-      pmesh.Print(mesh_ofs);
-
-      ofstream sol_ofs(sol_name.str().c_str());
-      sol_ofs.precision(8);
-      x.Save(sol_ofs);
-   }
-   MFEM_PERF_END("Save the results");
-   // 16. Send the solution by socket to a GLVis server.
-   if (visualization)
-   {
-      char vishost[] = "localhost";
-      int  visport   = 19916;
-      socketstream sol_sock(vishost, visport);
-      sol_sock << "parallel " << num_procs << " " << myid << "\n";
-      sol_sock.precision(8);
-      sol_sock << "solution\n" << pmesh << x << flush;
-   }
-
-   // 17. Free the used memory.
-   if (delete_fec)
-   {
-      delete fec;
-   }
-   // Flush output before MPI_finalize
-   mgr.flush();
-   MPI_Finalize();
-
-   return 0;
-}
@@ -1,76 +0,0 @@
-# Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
-# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
-# LICENSE and NOTICE for details. LLNL-CODE-806117.
-#
-# This file is part of the MFEM library. For more information and source code
-# availability visit https://mfem.org.
-#
-# MFEM is free software; you can redistribute it and/or modify it under the
-# terms of the BSD-3 license. We welcome feedback and contributions, see file
-# CONTRIBUTING.md for details.
-
-# Use the MFEM build directory
-MFEM_DIR ?= ../..
-MFEM_BUILD_DIR ?= ../..
-SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/examples/caliper,)
-CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
-# Use the MFEM install directory
-# MFEM_INSTALL_DIR = ../../mfem
-# CONFIG_MK = $(MFEM_INSTALL_DIR)/share/mfem/config.mk
-
-MFEM_LIB_FILE = mfem_is_not_built
-include $(CONFIG_MK)
-
-SEQ_EXAMPLES = ex1
-PAR_EXAMPLES = ex1p
-
-ifeq ($(MFEM_USE_MPI),NO)
-   EXAMPLES = $(SEQ_EXAMPLES)
-else
-   EXAMPLES = $(PAR_EXAMPLES) $(SEQ_EXAMPLES)
-endif
-
-.SUFFIXES:
-.SUFFIXES: .o .cpp .mk
-.PHONY: all clean clean-build clean-exec
-
-# Remove built-in rule
-%: %.cpp
-
-# Replace the default implicit rule for *.cpp files
-%: $(SRC)%.cpp $(MFEM_LIB_FILE) $(CONFIG_MK)
-	$(MFEM_CXX) $(MFEM_FLAGS) $< -o $@ $(MFEM_LIBS)
-
-all: $(EXAMPLES)
-
-MFEM_TESTS = EXAMPLES
-include $(MFEM_TEST_MK)
-
-# Testing: Parallel vs. serial runs
-RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) $(MFEM_MPI_NP)
-%-test-par: %
-	@$(call mfem-test,$<, $(RUN_MPI), Parallel example)
-%-test-seq: %
-	@$(call mfem-test,$<,, Serial example)
-
-# Testing: Specific execution options
-ex1-test-seq: ex1
-	@$(call mfem-test,$<,, Caliper serial example)
-ex1p-test-par: ex1p
-	@$(call mfem-test,$<, $(RUN_MPI), Caliper parallel example)
-
-# Testing: "test" target and mfem-test* variables are defined in config/test.mk
-
-# Generate an error message if the MFEM library is not built and exit
-$(MFEM_LIB_FILE):
-	$(error The MFEM library is not built)
-
-clean: clean-build clean-exec $(SUBDIRS_CLEAN)
-
-clean-build:
-	rm -f *.o *~ $(SEQ_EXAMPLES) $(PAR_EXAMPLES)
-	rm -rf *.dSYM *.TVD.*breakpoints
-
-clean-exec:
-	@rm -f refined.mesh displaced.mesh mesh.* ex5.mesh
-	@rm -f sphere_refined.* sol.* sol_u.* sol_p.* sol_r.* sol_i.*
@@ -0,0 +1,340 @@
+// Compile with: make drl_shock_wave
+//
+// drl_shock_wave -o 2 -m ../data/inline-quad.mesh
+// for multi agent local, set the mesh to use 20x20 grid because that is what 
+// was used for training.
+
+#include "mfem.hpp"
+#include <fstream>
+#include <iostream>
+#include "multi_agent_local_refiner.hpp"
+
+#define MFEM_USE_RLLIB
+#ifdef MFEM_USE_RLLIB
+#include <Python.h>
+#include "numpy/arrayobject.h"
+#endif
+
+using namespace std;
+using namespace mfem;
+
+#define alpha 2.0/3.0
+
+double exact_vel(const Vector &x)
+{
+   double xv = x(0), yv = x(1);
+   double rv = xv*xv + yv*yv;
+   if (rv > 0) { rv = pow(rv, 0.5); };
+   double theta = atan2(yv, xv);
+   if (theta < 0.0) { theta += 2*M_PI; }
+   return pow(rv, alpha)*sin(alpha*theta);
+}
+
+int main(int argc, char *argv[])
+{
+   // 1. Parse command-line options.
+   const char *mesh_file = "lshape.mesh";
+   int order = 2;
+   bool pa = false;
+   const char *device_config = "cpu";
+   bool visualization = true;
+   int jobid = 0;
+   double error_threshold = 0.10;
+   double max_elem_error = 5.0e-3;
+   int refinement_levels = 2;
+
+
+#ifdef MFEM_USE_RLLIB
+   Py_Initialize();
+   import_array(); // numpy init
+#endif
+
+   OptionsParser args(argc, argv);
+   args.AddOption(&mesh_file, "-m", "--mesh",
+                  "Mesh file to use.");
+   args.AddOption(&order, "-o", "--order",
+                  "Finite element order (polynomial degree).");
+   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
+                  "--no-partial-assembly", "Enable Partial Assembly.");
+   args.AddOption(&device_config, "-d", "--device",
+                  "Device configuration string, see Device::Configure().");
+   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
+                  "--no-visualization",
+                  "Enable or disable GLVis visualization.");
+   args.AddOption(&jobid, "-j", "--jobid",
+                  "slurb_jobid.");
+   args.AddOption(&error_threshold, "-err", "--err",
+                  "Total error fraction for zz or max_elem_error for policy.");
+   args.AddOption(&refinement_levels, "-r", "--ref",
+                 "Refinement levels");
+ 
+   args.Parse();
+   if (!args.Good())
+   {
+      args.PrintUsage(cout);
+      return 1;
+   }
+   args.PrintOptions(cout);
+
+   // 2. Enable hardware devices such as GPUs, and programming models such as
+   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
+   Device device(device_config);
+   device.Print();
+
+   // 3. Read the mesh from the given mesh file. We can handle triangular,
+   //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes with
+   //    the same code.
+   Mesh mesh(mesh_file, 1, 1);
+   int dim = mesh.Dimension();
+   int sdim = mesh.SpaceDimension();
+
+   mesh.SetCurvature(2);
+
+   // 4. Since a NURBS mesh can currently only be refined uniformly, we need to
+   //    convert it to a piecewise-polynomial curved mesh. First we refine the
+   //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
+   if (mesh.NURBSext)
+   {
+      for (int i = 0; i < 2; i++)
+      {
+         mesh.UniformRefinement();
+      }
+      mesh.SetCurvature(2);
+   }
+   else {
+      // mesh.UniformRefinement();
+      //mesh.UniformRefinement();
+      for (int i = 0; i < refinement_levels; i++)
+      {
+         mesh.UniformRefinement();
+      }
+      mesh.EnsureNCMesh();
+   }
+
+   // 5. Define a finite element space on the mesh. The polynomial order is
+   //    one (linear) by default, but this can be changed on the command line.
+   H1_FECollection fec(order, dim);
+   FiniteElementSpace fespace(&mesh, &fec);
+
+   // Create 0-order L2 gridfunction to hold errors
+   L2_FECollection fec0(0, dim);
+   FiniteElementSpace fes0(&mesh, &fec0);
+   GridFunction err(&fes0);
+
+   // 6. As in Example 1, we set up bilinear and linear forms corresponding to
+   //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
+   //    problem yet, this will be done in the main loop.
+   BilinearForm a(&fespace);
+   if (pa)
+   {
+      a.SetAssemblyLevel(AssemblyLevel::PARTIAL);
+      a.SetDiagonalPolicy(Operator::DIAG_ONE);
+   }
+   LinearForm b(&fespace);
+
+   ConstantCoefficient rhs(0.0);
+   ConstantCoefficient one(1.0);
+   FunctionCoefficient exact(exact_vel);
+
+   BilinearFormIntegrator *integ = new DiffusionIntegrator(one);
+   a.AddDomainIntegrator(integ);
+   int int_order = 8;
+   int geom_type = mesh.GetElementBaseGeometry(0);
+   DomainLFIntegrator* dlfi = new DomainLFIntegrator(rhs);
+   dlfi->SetIntRule(&IntRules.Get(geom_type, int_order));
+   b.AddDomainIntegrator(dlfi);
+
+   // 7. The solution vector x and the associated finite element grid function
+   //    will be maintained over the AMR iterations. We initialize it to zero.
+   GridFunction x(&fespace);
+   x = 0.0;
+
+   // 8. All boundary attributes will be used for essential (Dirichlet) BC.
+   MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,
+               "Boundary attributes required in the mesh.");
+   Array<int> ess_bdr(mesh.bdr_attributes.Max());
+   ess_bdr = 1;
+
+   // 9. Connect to GLVis.
+   char vishost[] = "localhost";
+   int  visport   = 19916;
+   socketstream sol_sock;
+   socketstream err_sock;
+   if (visualization)
+   {
+      sol_sock.open(vishost, visport);
+      err_sock.open(vishost, visport);
+   }
+
+   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   //     that uses the ComputeElementFlux method of the DiffusionIntegrator to
+   //     recover a smoothed flux (gradient) that is subtracted from the element
+   //     flux to get an error indicator. We need to supply the space for the
+   //     smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
+   FiniteElementSpace flux_fespace(&mesh, &fec, sdim);
+   ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
+   //KellyErrorEstimator estimator2(*integ, x, flux_fespace);
+   //estimator.SetAnisotropic();
+
+   // 11. A refiner selects and refines elements based on a refinement strategy.
+   //     The strategy here is to refine elements with errors larger than a
+   //     fraction of the maximum element error. Other strategies are possible.
+   //     The refiner will call the given error estimator.
+
+   bool zz = false;
+#if 0
+   ThresholdRefiner refiner(estimator);
+   refiner.SetTotalErrorFraction(error_threshold);
+   zz = true;
+#else
+   MAL_DRLRefiner refiner(x, error_threshold);
+#endif
+
+   bool derefine = false;
+   ThresholdDerefiner derefiner(estimator);
+   derefiner.SetThreshold(0.05);
+   derefiner.SetNCLimit(0);
+
+   string errorfilename;
+   errorfilename = to_string(jobid) + "_lshape_error.txt";
+   ofstream myfile;
+   myfile.open(errorfilename, ofstream::in | ofstream::out | ofstream::app);
+
+
+   // 12. The main AMR loop. In each iteration we solve the problem on the
+   //     current mesh, visualize the solution, and refine the mesh.
+   const int max_dofs = 200000;
+   for (int it = 0; it < 6; it++)
+   {
+      int cdofs = fespace.GetTrueVSize();
+      cout << "\nAMR iteration " << it << endl;
+      cout << "Number of unknowns: " << cdofs << endl;
+
+      // 13. Assemble the right-hand side.
+      b.Assemble();
+
+      // 14. Set Dirichlet boundary values in the GridFunction x.
+      //     Determine the list of Dirichlet true DOFs in the linear system.
+      Array<int> ess_tdof_list;
+      x.ProjectBdrCoefficient(exact, ess_bdr);
+      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
+
+      // 15. Assemble the stiffness matrix.
+      a.Assemble();
+      
+      // 16. Create the linear system: eliminate boundary conditions, constrain
+      //     hanging nodes and possibly apply other transformations. The system
+      //     will be solved for true (unconstrained) DOFs only.
+      OperatorPtr A;
+      Vector B, X;
+
+      const int copy_interior = 1;
+      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
+
+      // 17. Solve the linear system A X = B.
+      if (!pa)
+      {
+#ifndef MFEM_USE_SUITESPARSE
+         // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
+         GSSmoother M((SparseMatrix&)(*A));
+         PCG(*A, M, B, X, 3, 200, 1e-12, 0.0);
+#else
+         // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
+         UMFPackSolver umf_solver;
+         umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+         umf_solver.SetOperator(*A);
+         umf_solver.Mult(B, X);
+#endif
+      }
+      else // Diagonal preconditioning in partial assembly mode.
+      {
+         OperatorJacobiSmoother M(a, ess_tdof_list);
+         PCG(*A, M, B, X, 3, 2000, 1e-12, 0.0);
+      }
+
+      // 18. After solving the linear system, reconstruct the solution as a
+      //     finite element GridFunction. Constrained nodes are interpolated
+      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
+      a.RecoverFEMSolution(X, b, x);
+
+      // Compute error against exact solution
+
+      x.ComputeElementL2Errors(exact, err);
+      int int_order = std::max(20 - it, 2*order+1);
+      double error;
+      error = err.Norml2();
+
+      if (derefine) {
+         myfile << error_threshold << " " << cdofs << " " << error << endl;
+      }
+      else {
+         myfile << -error_threshold << " " << cdofs << " " << error << endl;
+      }
+
+      // 19. Send solution by socket to the GLVis server.
+      if (visualization && sol_sock.good())
+      {
+         sol_sock.precision(8);
+         sol_sock << "solution\n" << mesh << x << flush;
+      }
+      if (visualization && err_sock.good())
+      {
+         err_sock.precision(8);
+         err_sock << "solution\n" << mesh << err << flush;
+      }
+
+      if (cdofs > max_dofs)
+      {
+         cout << "Reached the maximum number of dofs. Stop." << endl;
+         break;
+      }
+
+      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      //     estimator to obtain element errors, then it selects elements to be
+      //     refined and finally it modifies the mesh. The Stop() method can be
+      //     used to determine if a stopping criterion was met.
+
+      refiner.Apply(mesh);
+      if (refiner.Stop())
+      {
+         cout << "Stopping criterion satisfied. Stop." << endl;
+         break;
+      }
+      fespace.Update();fes0.Update();x.Update();err.Update();
+      a.Update();b.Update();
+
+      if (derefine) {
+         derefiner.Apply(mesh);
+         fespace.Update();fes0.Update();x.Update();err.Update();
+         a.Update();b.Update();
+      }
+e
+      {
+         string solname = to_string(jobid) + "_lshape_amr" + to_string(it) + ".gf";
+         ofstream sol_ofs(solname);
+         x.Save(sol_ofs);
+      }
+
+      {
+         string meshname = to_string(jobid) + "_lshape_amr" + to_string(it) + ".mesh";
+         ofstream mesh_ofs(meshname);
+         mesh_ofs.precision(14);
+         mesh.Print(mesh_ofs);
+      }
+   }
+   myfile.close();
+
+
+   {
+      ofstream sol_ofs("lshape_amr.gf");
+      x.Save(sol_ofs);
+   }
+
+   {
+      ofstream mesh_ofs("lshape_amr.mesh");
+      mesh_ofs.precision(14);
+      mesh.Print(mesh_ofs);
+   }
+
+   return 0;
+}
@@ -0,0 +1,330 @@
+// Compile with: make drl_shock_wave
+//
+// drl_shock_wave -o 2 -m ../data/inline-quad.mesh
+// for multi agent local, set the mesh to use 20x20 grid because that is what 
+// was used for training.
+
+#include "mfem.hpp"
+#include <fstream>
+#include <iostream>
+#include "drl_shock_wave.hpp"
+#include "multi_agent_local_refiner.hpp"
+
+#define MFEM_USE_RLLIB
+#ifdef MFEM_USE_RLLIB
+#include <Python.h>
+#include "numpy/arrayobject.h"
+#endif
+
+using namespace std;
+using namespace mfem;
+
+double bdry_function(const Vector& x)
+{
+   return 0.0; // default
+}
+
+int main(int argc, char *argv[])
+{
+   // 1. Parse command-line options.
+   const char *mesh_file = "../data/inline-quad.mesh";
+   int order = 2;
+   bool pa = false;
+   const char *device_config = "cpu";
+   bool visualization = true;
+   int jobid = 0;
+
+#ifdef MFEM_USE_RLLIB
+   Py_Initialize();
+   import_array(); // numpy init
+#endif
+
+   OptionsParser args(argc, argv);
+   args.AddOption(&mesh_file, "-m", "--mesh",
+                  "Mesh file to use.");
+   args.AddOption(&order, "-o", "--order",
+                  "Finite element order (polynomial degree).");
+   args.AddOption(&pa, "-pa", "--partial-assembly", "-no-pa",
+                  "--no-partial-assembly", "Enable Partial Assembly.");
+   args.AddOption(&device_config, "-d", "--device",
+                  "Device configuration string, see Device::Configure().");
+   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
+                  "--no-visualization",
+                  "Enable or disable GLVis visualization.");
+   args.AddOption(&jobid, "-j", "--jobid",
+                  "slurb_jobid.");
+   args.Parse();
+   if (!args.Good())
+   {
+      args.PrintUsage(cout);
+      return 1;
+   }
+   args.PrintOptions(cout);
+
+   // 2. Enable hardware devices such as GPUs, and programming models such as
+   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
+   Device device(device_config);
+   device.Print();
+
+   // 3. Read the mesh from the given mesh file. We can handle triangular,
+   //    quadrilateral, tetrahedral, hexahedral, surface and volume meshes with
+   //    the same code.
+   Mesh mesh(mesh_file, 1, 1);
+   int dim = mesh.Dimension();
+   int sdim = mesh.SpaceDimension();
+
+   mesh.SetCurvature(2);
+
+   // 4. Since a NURBS mesh can currently only be refined uniformly, we need to
+   //    convert it to a piecewise-polynomial curved mesh. First we refine the
+   //    NURBS mesh a bit more and then project the curvature to quadratic Nodes.
+   if (mesh.NURBSext)
+   {
+      for (int i = 0; i < 2; i++)
+      {
+         mesh.UniformRefinement();
+      }
+      mesh.SetCurvature(2);
+   }
+   else {
+      // mesh.UniformRefinement();
+      //mesh.UniformRefinement();
+      mesh.EnsureNCMesh();
+   }
+
+   // 5. Define a finite element space on the mesh. The polynomial order is
+   //    one (linear) by default, but this can be changed on the command line.
+   H1_FECollection fec(order, dim);
+   FiniteElementSpace fespace(&mesh, &fec);
+
+   // Create 0-order L2 gridfunction to hold errors
+   L2_FECollection fec0(0, dim);
+   FiniteElementSpace fes0(&mesh, &fec0);
+   GridFunction err(&fes0);
+
+   // 6. As in Example 1, we set up bilinear and linear forms corresponding to
+   //    the Laplace problem -\Delta u = 1. We don't assemble the discrete
+   //    problem yet, this will be done in the main loop.
+   BilinearForm a(&fespace);
+   if (pa)
+   {
+      a.SetAssemblyLevel(AssemblyLevel::PARTIAL);
+      a.SetDiagonalPolicy(Operator::DIAG_ONE);
+   }
+   LinearForm b(&fespace);
+
+   FunctionCoefficient bdry(bdry_function);
+   FunctionCoefficient rhs(layer2_laplace);
+   FunctionCoefficient exact(layer2_exsol);
+   ConstantCoefficient one(1.0);
+
+   BilinearFormIntegrator *integ = new DiffusionIntegrator(one);
+   a.AddDomainIntegrator(integ);
+   int int_order = 8;
+   int geom_type = mesh.GetElementBaseGeometry(0);
+   DomainLFIntegrator* dlfi = new DomainLFIntegrator(rhs);
+   dlfi->SetIntRule(&IntRules.Get(geom_type, int_order));
+   b.AddDomainIntegrator(dlfi);
+
+   // 7. The solution vector x and the associated finite element grid function
+   //    will be maintained over the AMR iterations. We initialize it to zero.
+   GridFunction x(&fespace);
+   x = 0.0;
+
+   // 8. All boundary attributes will be used for essential (Dirichlet) BC.
+   MFEM_VERIFY(mesh.bdr_attributes.Size() > 0,
+               "Boundary attributes required in the mesh.");
+   Array<int> ess_bdr(mesh.bdr_attributes.Max());
+   ess_bdr = 1;
+
+   // 9. Connect to GLVis.
+   char vishost[] = "localhost";
+   int  visport   = 19916;
+   socketstream sol_sock;
+   socketstream err_sock;
+   if (visualization)
+   {
+      sol_sock.open(vishost, visport);
+      err_sock.open(vishost, visport);
+   }
+
+   // 10. Set up an error estimator. Here we use the Zienkiewicz-Zhu estimator
+   //     that uses the ComputeElementFlux method of the DiffusionIntegrator to
+   //     recover a smoothed flux (gradient) that is subtracted from the element
+   //     flux to get an error indicator. We need to supply the space for the
+   //     smoothed flux: an (H1)^sdim (i.e., vector-valued) space is used here.
+   FiniteElementSpace flux_fespace(&mesh, &fec, sdim);
+   ZienkiewiczZhuEstimator estimator(*integ, x, flux_fespace);
+   //KellyErrorEstimator estimator2(*integ, x, flux_fespace);
+   //estimator.SetAnisotropic();
+
+   // 11. A refiner selects and refines elements based on a refinement strategy.
+   //     The strategy here is to refine elements with errors larger than a
+   //     fraction of the maximum element error. Other strategies are possible.
+   //     The refiner will call the given error estimator.
+
+#if 0
+   ThresholdRefiner refiner(estimator);
+   refiner.SetTotalErrorFraction(0.10);
+#else
+   MAL_DRLRefiner refiner(x);
+   //DRLRefiner refiner(x);
+#endif
+  
+#if 0
+   x.ProjectCoefficient(exact);
+   refiner.Apply(mesh);
+   fespace.Update();
+   fes0.Update();
+   x.Update();
+   x.ProjectCoefficient(exact);
+   refiner.Apply(mesh);
+   fespace.Update();
+   fes0.Update();
+   x.Update();
+   {
+      ofstream sol_ofs("sol.gf");
+      x.Save(sol_ofs);
+   }
+   {
+      ofstream mesh_ofs("amr.mesh");
+      mesh_ofs.precision(14);
+      mesh.Print(mesh_ofs);
+   }
+   MFEM_ABORT(" ");
+#endif
+
+   // 12. The main AMR loop. In each iteration we solve the problem on the
+   //     current mesh, visualize the solution, and refine the mesh.
+   const int max_dofs = 20000;
+   for (int it = 0; it < 4; it++)
+   {
+      int cdofs = fespace.GetTrueVSize();
+      cout << "\nAMR iteration " << it << endl;
+      cout << "Number of unknowns: " << cdofs << endl;
+
+      // 13. Assemble the right-hand side.
+      b.Assemble();
+
+      // 14. Set Dirichlet boundary values in the GridFunction x.
+      //     Determine the list of Dirichlet true DOFs in the linear system.
+      Array<int> ess_tdof_list;
+      x.ProjectBdrCoefficient(exact, ess_bdr);
+      fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
+
+      // 15. Assemble the stiffness matrix.
+      a.Assemble();
+      
+      // 16. Create the linear system: eliminate boundary conditions, constrain
+      //     hanging nodes and possibly apply other transformations. The system
+      //     will be solved for true (unconstrained) DOFs only.
+      OperatorPtr A;
+      Vector B, X;
+
+      const int copy_interior = 1;
+      a.FormLinearSystem(ess_tdof_list, x, b, A, X, B, copy_interior);
+
+      // 17. Solve the linear system A X = B.
+      if (!pa)
+      {
+#ifndef MFEM_USE_SUITESPARSE
+         // Use a simple symmetric Gauss-Seidel preconditioner with PCG.
+         GSSmoother M((SparseMatrix&)(*A));
+         PCG(*A, M, B, X, 3, 200, 1e-12, 0.0);
+#else
+         // If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
+         UMFPackSolver umf_solver;
+         umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
+         umf_solver.SetOperator(*A);
+         umf_solver.Mult(B, X);
+#endif
+      }
+      else // Diagonal preconditioning in partial assembly mode.
+      {
+         OperatorJacobiSmoother M(a, ess_tdof_list);
+         PCG(*A, M, B, X, 3, 2000, 1e-12, 0.0);
+      }
+
+      // 18. After solving the linear system, reconstruct the solution as a
+      //     finite element GridFunction. Constrained nodes are interpolated
+      //     from true DOFs (it may therefore happen that x.Size() >= X.Size()).
+      a.RecoverFEMSolution(X, b, x);
+
+      // Compute error against exact solution
+
+      x.ComputeElementL2Errors(exact, err);
+
+      // 19. Send solution by socket to the GLVis server.
+      if (visualization && sol_sock.good())
+      {
+         sol_sock.precision(8);
+         sol_sock << "solution\n" << mesh << x << flush;
+      }
+      if (visualization && err_sock.good())
+      {
+         err_sock.precision(8);
+         err_sock << "solution\n" << mesh << err << flush;
+      }
+
+      if (cdofs > max_dofs || it == 3)
+      {
+         cout << "Reached the maximum number of dofs. Stop." << endl;
+         break;
+      }
+
+      // 20. Call the refiner to modify the mesh. The refiner calls the error
+      //     estimator to obtain element errors, then it selects elements to be
+      //     refined and finally it modifies the mesh. The Stop() method can be
+      //     used to determine if a stopping criterion was met.
+
+      refiner.Apply(mesh);
+      if (refiner.Stop())
+      {
+         cout << "Stopping criterion satisfied. Stop." << endl;
+         break;
+      }
+
+      // 21. Update the space to reflect the new state of the mesh. Also,
+      //     interpolate the solution x so that it lies in the new space but
+      //     represents the same function. This saves solver iterations later
+      //     since we'll have a good initial guess of x in the next step.
+      //     Internally, FiniteElementSpace::Update() calculates an
+      //     interpolation matrix which is then used by GridFunction::Update().
+      fespace.Update();
+      fes0.Update();
+      x.Update();
+      err.Update();
+
+      {
+         string solname = to_string(jobid) + "_amrsol" + to_string(it) + ".gf";
+         ofstream sol_ofs(solname);
+         x.Save(sol_ofs);
+      }
+
+      {
+         string meshname = to_string(jobid) + "_amr" + to_string(it) + ".mesh";
+         ofstream mesh_ofs(meshname);
+         mesh_ofs.precision(14);
+         mesh.Print(mesh_ofs);
+      }
+
+      // 22. Inform also the bilinear and linear forms that the space has
+      //     changed.
+      a.Update();
+      b.Update();
+   }
+
+
+   {
+      ofstream sol_ofs("amrsol.gf");
+      x.Save(sol_ofs);
+   }
+
+   {
+      ofstream mesh_ofs("amr.mesh");
+      mesh_ofs.precision(14);
+      mesh.Print(mesh_ofs);
+   }
+
+   return 0;
+}
@@ -0,0 +1,136 @@
+#include "mfem.hpp"
+#include <fstream>
+#include <iostream>
+
+using namespace mfem;
+using namespace std;
+
+const double alpha =  200.0; // standard params
+const double center = -0.05;
+const double radius = 0.7;
+template<typename T> T sqr(T x) { return x*x; }
+double layer2_exsol(Vector &p)
+{
+   double x = p(0), y = p(1);
+   double r = sqrt(sqr(x - center) + sqr(y - center));
+   return atan(alpha * (r - radius));
+}
+
+void layer2_exgrad(const Vector &p, Vector &grad)
+{
+   double x = p(0), y = p(1);
+   double r = sqrt(sqr(x - center) + sqr(y - center));
+   double u = r * (sqr(alpha) * sqr(r - radius) + 1);
+   grad(0) = alpha * (x - center) / u;
+   grad(1) = alpha * (y - center) / u;
+}
+
+double layer2_laplace(Vector &p)
+{
+   double x = p(0), y = p(1);
+   double r = sqr(y - center) + sqr(x - center);
+   double u = sqr(alpha) * sqr(sqrt(r) - radius) + 1;
+
+   return 2 * pow(alpha,3) * (sqrt(r) - radius) * sqr(y - center) / (r * sqr(u))
+          + alpha * sqr(y - center) / (pow(r, 1.5) * u)
+          - 2 * alpha / (sqrt(r) * u)
+          + 2 * pow(alpha,3) * (sqrt(r) - radius) * sqr(x - center) / (r * sqr(u))
+          + alpha * sqr(x - center) / (pow(r, 1.5) * u);
+}
+
+static double safeSqrt(double x)
+{
+   if (x < 0.0)
+      return -sqrt(-x);
+   else
+      return sqrt(x);
+}
+
+double CalculateH10Error(GridFunction *sol, VectorCoefficient *exgrad,
+                         Array<double> *elemError, Array<int> *elemRef,
+                         int intOrder)
+{
+   const FiniteElementSpace *fes = sol->FESpace();
+   Mesh* mesh = fes->GetMesh();
+
+   Vector e_grad, a_grad, el_dofs, q_grad;
+   DenseMatrix dshape, dshapet, Jinv;
+   Array<int> vdofs;
+   const FiniteElement *fe;
+   ElementTransformation *transf;
+
+   int dim = mesh->Dimension();
+   e_grad.SetSize(dim);
+   a_grad.SetSize(dim);
+   q_grad.SetSize(dim);
+   Jinv.SetSize(dim);
+
+   double error = 0.0;
+   if (elemError) elemError->SetSize(mesh->GetNE());
+   if (elemRef)   elemRef->SetSize(mesh->GetNE());
+
+   for (int i = 0; i < mesh->GetNE(); i++)
+   {
+      fe = fes->GetFE(i);
+      int fdof = fe->GetDof();
+      transf = mesh->GetElementTransformation(i);
+      el_dofs.SetSize(fdof);
+      dshape.SetSize(fdof, dim);
+      dshapet.SetSize(fdof, dim);
+
+      fes->GetElementVDofs(i, vdofs);
+      for (int k = 0; k < fdof; k++)
+         if (vdofs[k] >= 0)
+            el_dofs(k) =  (*sol)(vdofs[k]);
+         else
+            el_dofs(k) = -(*sol)(-1-vdofs[k]);
+
+      const IntegrationRule &ir = IntRules.Get(fe->GetGeomType(), intOrder);
+
+      double el_err = 0.0, a_dxyz[3] = { 0, 0, 0 };
+      for (int j = 0; j < ir.GetNPoints(); j++)
+      {
+         const IntegrationPoint &ip = ir.IntPoint(j);
+
+         transf->SetIntPoint(&ip);
+         CalcInverse(transf->Jacobian(), Jinv);
+         double w = ip.weight * transf->Weight();
+
+         exgrad->Eval(e_grad, *transf, ip);
+
+         fe->CalcDShape(ip, dshape);
+         Mult(dshape, Jinv, dshapet);
+         dshapet.MultTranspose(el_dofs, a_grad);
+
+         e_grad -= a_grad;
+         el_err += w * (e_grad * e_grad);
+
+         transf->Jacobian().MultTranspose(e_grad, q_grad);
+         for (int k = 0; k < dim; k++)
+         {
+            a_dxyz[k] += w * (q_grad[k] * q_grad[k]);
+         }
+      }
+
+      error += el_err;
+      if (elemError)
+         (*elemError)[i] = sqrt(fabs(el_err));
+
+      if (elemRef)
+      {
+         double sum = 0;
+         for (int k = 0; k < dim; k++)
+            sum += a_dxyz[k];
+
+         const double thresh = 0.2 * 3/dim;
+         int ref = 0;
+         for (int k = 0; k < dim; k++)
+            if (a_dxyz[k] / sum > thresh)
+               ref |= (1 << k);
+
+         (*elemRef)[i] = ref;
+      }
+   }
+
+   return safeSqrt(error);
+}
@@ -1,81 +0,0 @@
-//                                MFEM Example 0
-//
-// Compile with: make ex0
-//
-// Sample runs:  ex0
-//               ex0 -m ../data/fichera.mesh
-//               ex0 -m ../data/square-disc.mesh -o 2
-//
-// Description: This example code demonstrates the most basic usage of MFEM to
-//              define a simple finite element discretization of the Laplace
-//              problem -Delta u = 1 with zero Dirichlet boundary conditions.
-//              General 2D/3D mesh files and finite element polynomial degrees
-//              can be specified by command line options.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command line options
-   const char *mesh_file = "../data/star.mesh";
-   int order = 1;
-
-   OptionsParser args(argc, argv);
-   args.AddOption(&mesh_file, "-m", "--mesh", "Mesh file to use.");
-   args.AddOption(&order, "-o", "--order", "Finite element polynomial degree");
-   args.ParseCheck();
-
-   // 2. Read the mesh from the given mesh file, and refine once uniformly.
-   Mesh mesh(mesh_file);
-   mesh.UniformRefinement();
-
-   // 3. Define a finite element space on the mesh. Here we use H1 continuous
-   //    high-order Lagrange finite elements of the given order.
-   H1_FECollection fec(order, mesh.Dimension());
-   FiniteElementSpace fespace(&mesh, &fec);
-   cout << "Number of unknowns: " << fespace.GetTrueVSize() << endl;
-
-   // 4. Extract the list of all the boundary DOFs. These will be marked as
-   //    Dirichlet in order to enforce zero boundary conditions.
-   Array<int> boundary_dofs;
-   fespace.GetBoundaryTrueDofs(boundary_dofs);
-
-   // 5. Define the solution x as a finite element grid function in fespace. Set
-   //    the initial guess to zero, which also sets the boundary conditions.
-   GridFunction x(&fespace);
-   x = 0.0;
-
-   // 6. Set up the linear form b(.) corresponding to the right-hand side.
-   ConstantCoefficient one(1.0);
-   LinearForm b(&fespace);
-   b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   b.Assemble();
-
-   // 7. Set up the bilinear form a(.,.) corresponding to the -Delta operator.
-   BilinearForm a(&fespace);
-   a.AddDomainIntegrator(new DiffusionIntegrator);
-   a.Assemble();
-
-   // 8. Form the linear system A X = B. This includes eliminating boundary
-   //    conditions, applying AMR constraints, and other transformations.
-   SparseMatrix A;
-   Vector B, X;
-   a.FormLinearSystem(boundary_dofs, x, b, A, X, B);
-
-   // 9. Solve the system using PCG with symmetric Gauss-Seidel preconditioner.
-   GSSmoother M(A);
-   PCG(A, M, B, X, 1, 200, 1e-12, 0.0);
-
-   // 10. Recover the solution x as a grid function and save to file. The output
-   //     can be viewed using GLVis as follows: "glvis -m mesh.mesh -g sol.gf"
-   a.RecoverFEMSolution(X, b, x);
-   x.Save("sol.gf");
-   mesh.Save("mesh.mesh");
-
-   return 0;
-}
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Ketan Mittal	b442aaa349	add lshape example	2021-07-13 13:17:58 -07:00
Ketan Mittal	cbc4632fb8	mergin with gslib and other changes to streamline eval	2021-06-17 11:52:38 -07:00
Ketan Mittal	0186022c01	adding python and DRLfiner for multi agent local(MAL)	2021-06-11 13:36:47 -07:00
Ketan Mittal	dd8f8f2124	adding shock wave example from AMR paper by Cerveny et al	2021-06-11 11:29:38 -07:00
Robert W. Anderson	6640970f50	add NIST arctan test problem, parameterize bdry cond with problem num	2021-04-22 18:02:36 -07:00
Robert W. Anderson	f5ab281afa	add MMS exact solution to ex6, and error computation and visualization	2021-04-22 12:18:52 -07:00
Robert W. Anderson	d665bbf5b7	clean up	2021-04-21 22:42:53 -07:00
Robert W. Anderson	31b838f103	some temporary changes to example 6 to test the DRLRefiner	2021-04-21 22:42:33 -07:00
Robert W. Anderson	046d01c30e	symmetrize the criterion with mirroring operations	2021-04-21 22:41:46 -07:00
Robert W. Anderson	c688a208d6	clean up debug code	2021-04-21 16:17:42 -07:00
Robert W. Anderson	eafb5c8ba0	ex0 and ex6 seem to be working	2021-04-07 17:09:40 -07:00
Robert W. Anderson	bb8345e76c	add python script for rllib policy eval	2021-03-29 16:39:23 -07:00