unit KronMult methods

.binder/environment.yml

@@ -1,12 +0,0 @@
-# extends https://github.com/jupyterhub/repo2docker/blob/main/repo2docker/buildpacks/conda/environment.yml
-# see https://mybinder.readthedocs.io/en/latest/using/config_files.html#environment-yml-install-a-conda-environment
-channels:
-- conda-forge
-dependencies:
-- xeus-cling=0.13.0
-- xwidgets=0.26.0
-# NOTE: it's possible these aren't needed for the lab frontend
-- widgetsnbextension=3.5.1
-- pip
-- pip:
-  - glvis==0.3.2

.binder/postBuild

@@ -1,26 +0,0 @@
-#!/bin/bash
-
-set -e
-
-# cling is installed here (in bin) and will look in {dir}/include and {dir}/lib
-# without extra intervention (jk it doesn't look in {dir}/lib unless something
-# has been #included from {dir}/include first...)
-install_dir=/srv/conda/envs/notebook
-mkdir -p $install_dir
-
-# build and install mfem, which is the directory we start in
-make serial SHARED=YES -j8
-make install PREFIX=$install_dir
-
-# install xeus-glvis
-git clone https://github.com/GLVis/xeus-glvis.git
-pushd xeus-glvis
-make install prefix=$install_dir
-popd
-
-# install jupyter-lab extension
-jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
-jupyter labextension install glvis-jupyter
-
-# fixup kernelspec, we could probably do this from sh but ¯\_(ツ)_/¯
-python .binder/update_kernel_env.py

.binder/update_kernel_env.py

@@ -1,14 +0,0 @@
-# Update the LD_LIBRARY_PATH of the C++14 kernel so it can find mfem without
-# extra pragma cling statements
-
-import json
-
-kernelspec = "/srv/conda/envs/notebook/share/jupyter/kernels/xcpp14/kernel.json"
-
-with open(kernelspec, "r") as f:
-    obj = json.load(f)
-
-obj["env"] = {"LD_LIBRARY_PATH": "/srv/conda/envs/notebook/lib"}
-
-with open(kernelspec, "w") as f:
-    json.dump(obj, f)

.github/workflows/mfem-analysis.yml

@@ -82,9 +82,9 @@ jobs:
       uses: mfem/github-actions/build-mfem@v2.0
       with:
         os: ${{ runner.os }}
-        target: opt
+        target: optim
         codecov: NO
-        mpi: par
+        mpi: parallel
         build-system: make
         hypre-dir: ${{ env.HYPRE_TOP_DIR }}
         metis-dir: ${{ env.METIS_TOP_DIR }}

.github/workflows/repo-check.yml

@@ -63,7 +63,7 @@ jobs:
         exit 1
 
   code-style:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-16.04 # needed for astyle 2.05.1
 
     steps:
     - name: checkout mfem
@@ -71,7 +71,7 @@ jobs:
 
     - name: get astyle
       run: |
-        sudo apt-get install astyle=3.1-1ubuntu2
+        sudo apt-get install astyle=2.05.1-0ubuntu1
 
     - name: style check
       run: |
@@ -105,9 +105,6 @@ jobs:
 
     - name: branch-history
       run: |
-        # We override origin to make sure we point to the main repo.
-        # This is to have consistent test results on PRs from forks.
-        git remote remove origin
-        git remote add origin https://github.com/mfem/mfem.git
+        git fetch origin master:master
         git checkout -b gh-actions-branch-history
         ./config/githooks/pre-push --history

.gitignore

@@ -15,19 +15,6 @@
 CMakeCache.txt
 CMakeFiles/
 
-# NSYS files
-*.nsys-rep
-
-# Benchmark files
-*.tex
-*.org
-*.aux
-*.log
-*.gnuplot
-*.table
-*.pdf
-*.png
-
 # Backup files
 *~
 
@@ -64,8 +51,6 @@ examples/ex1[04-9]
 examples/ex1[0-9]p
 examples/ex2[0-9]
 examples/ex2[0-9]p
-examples/ex30
-examples/ex30p
 
 examples/refined.mesh
 examples/displaced.mesh
@@ -238,14 +223,6 @@ miniapps/mtop/ParHeat*
 miniapps/mtop/seqheat
 miniapps/mtop/SeqHeat*
 
-miniapps/autodiff/paradiff
-miniapps/autodiff/seqadiff
-miniapps/autodiff/seqtest
-miniapps/autodiff/par_example
-miniapps/autodiff/seq_example
-miniapps/autodiff/seq_test
-miniapps/autodiff/Exampl*
-
 miniapps/navier/navier_mms
 miniapps/navier/navier_kovasznay
 miniapps/navier/navier_kovasznay_vs
@@ -275,7 +252,6 @@ 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
@@ -311,30 +287,15 @@ miniapps/solvers/ParaView
 miniapps/solvers/mesh.*
 miniapps/solvers/sol.*
 
-miniapps/parelag/MultilevelHcurlHdivSolver
-miniapps/parelag/*.mesh
-
 # Unit test binary and outputs
 tests/unit/output_meshes
 tests/unit/unit_tests
 tests/unit/punit_tests
-tests/unit/cunit_tests
-tests/unit/pcunit_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
-
-# Benchmark binaries
-tests/benchmarks/bench_ceed
-tests/benchmarks/bench_solvers
-tests/benchmarks/bench_linext
-tests/benchmarks/bench_lor_assembly
-tests/benchmarks/bench_tmop
-tests/benchmarks/bench_vector
-tests/benchmarks/bench_virtuals
 
 # Test script output
 tests/scripts/*.err
@@ -352,6 +313,3 @@ build-*/*
 # PETSc automated build
 petsc-build/*
 pkg.gitcommit
-
-# Jupyter Notebook Checkpoints
-.ipynb_checkpoints

.gitlab-ci.yml

@@ -13,84 +13,242 @@
 # at Lawrence Livermore National Laboratory (LLNL). This entire pipeline is
 # LLNL-specific!
 
+# We define the following GitLab pipeline variables:
+#
+# BUILD_ROOT:
+# The path to the shared resources between all jobs. For example, external
+# repositories like 'tests' and 'tpls' are cloned here. Also, 'tpls' is built
+# once for all targets, so that build happen here. The BUILD_ROOT is unique to
+# the pipeline, preventing any form of concurrency with other pipelines. This
+# also means that the BUILD_ROOT directory will never be cleaned.
+# TODO: add a clean-up mechanism
+#
+# 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
+# the option to manually ask for rebaselining from another branch if necessary.
+#
+# MFEM_ALLOC_NAME:
+# On LLNL's quartz, there is only one allocation shared among jobs in order to
+# save time and resources. This allocation has to be uniquely named so that we
+# are sure to retrieve it.
+#
+# TPLS_REPO & TESTS_REPO:
+# Git repositories used in the pipeline
+#
+# ARTIFACTS_DIR:
+# Directory used to place artifacts.
 
-# 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.
+variables:
+  BUILD_ROOT: ${CI_BUILDS_DIR}/MFEM/${CI_PROJECT_NAME}_${CI_COMMIT_REF_SLUG}_${CI_PIPELINE_ID}
+  AUTOTEST_ROOT: ${CI_BUILDS_DIR}/MFEM
+  REBASELINE: "NO"
+  AUTOTEST: "NO"
+  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
+
+# 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 and setup_baseline phases to download content outside of mfem
 #   directory.
-# - Allocate/Release is where quartz resource are allocated/released once for all.
+# - Allocate/Release is where quartz resources are allocated/released once for all.
 # - Build and Test is where we build and MFEM for multiple toolchains.
 # - Baseline_checks gathers baseline-type test suites execution
 # - Baseline_publish, only available on master, allows to update baseline
 #   results
 stages:
-  - sub-pipelines
+  - setup
+  - q_allocate_resources
+  - q_build_and_test
+  - q_release_resources
+  - l_build_and_test
+  - c_build_and_test
+  - setup_baseline
+  - baseline_check
+  - baseline_to_autotest
+  - baseline_publish
 
-variables:
-  CUSTOM_CI_BUILDS_DIR: "/usr/workspace/mfem/gitlab-runner"
-  USER_CI_TOP_DIR: "${CUSTOM_CI_BUILDS_DIR}/${GITLAB_USER_LOGIN}"
-  SHARED_REPOS_DIR: "${USER_CI_TOP_DIR}/repos"
-  AUTOTEST_ROOT: "${SHARED_REPOS_DIR}"
-  # MFEM_DATA_DIR is setup in '.gitlab/configs/setup-build-and-test.yml' and
-  # used in '.gitlab/configs/<machine>-config.yml':
-  MFEM_DATA_DIR: "${SHARED_REPOS_DIR}/mfem-data"
-
-# 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
-# the option to manually ask for rebaselining from another branch if necessary.
-  REBASELINE: "NO"
-  AUTOTEST: "NO"
-  # AUTOTEST_COMMIT: used only when AUTOTEST is set to YES.
-  # * If AUTOTEST_COMMIT is NOT set to NO, reporting jobs will commit their
-  #   files to the MFEM/autotest repo.
-  # * If AUTOTEST_COMMIT is set to NO, reporting jobs will NOT commit their
-  #   files to the MFEM/autotest repo. Instead they will just show the contents
-  #   of the report files and remove them.
-  AUTOTEST_COMMIT: "YES"
-
-# Trigger subpipelines:
-quartz-build-and-test:
-  stage: sub-pipelines
+# setup clones the mfem/data repo in ${BUILD_ROOT}. The build_and_test script
+# then symlinks the repo to the parent directory of the MFEM source directory.
+# Unit tests that depend on the mfem/data repo will then detect that this
+# directory is present and be enabled.
+setup:
+  tags:
+    - shell
+    - quartz
+  stage: setup
   variables:
-    # Explicitly pass down values that we want to be able to set when triggering
-    # pipelines manually or using scheduling
-    AUTOTEST: "${AUTOTEST}"
-    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
-  trigger:
-    include: .gitlab/quartz-build-and-test.yml
-    strategy: depend
+    GIT_STRATEGY: none
+  script:
+    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
+    - if [ ! -d data ]; then git clone ${MFEM_DATA_REPO}; fi
+  needs: []
 
-quartz-baseline:
-  stage: sub-pipelines
+# 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.
+setup_baseline:
+  tags:
+    - shell
+    - quartz
+  stage: setup_baseline
   variables:
-    # Explicitly pass down values that we want to be able to set when triggering
-    # pipelines manually or using scheduling
-    REBASELINE: "${REBASELINE}"
-    AUTOTEST: "${AUTOTEST}"
-    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
-  trigger:
-    include: .gitlab/quartz-baseline.yml
-    strategy: depend
+    GIT_STRATEGY: none
+  script:
+    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
+    - if [ ! -d "tpls" ]; then git clone ${TPLS_REPO}; fi
+    - 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: []
 
-lassen-build-and-test:
-  stage: sub-pipelines
-  variables:
-    # Explicitly pass down values that we want to be able to set when triggering
-    # pipelines manually or using scheduling
-    AUTOTEST: "${AUTOTEST}"
-    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
-  trigger:
-    include: .gitlab/lassen-build-and-test.yml
-    strategy: depend
+.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
 
-corona-build-and-test:
-  stage: sub-pipelines
+.build_toss_3_x86_64_ib_corona_script:
+  script:
+    - srun -p mi60 -t 15 -N 1 tests/gitlab/build_and_test
+
+# 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:
+  script:
+    - lalloc 1 -W 30 -q pdebug tests/gitlab/build_and_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_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
+  # 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}"
+  # post
+  mkdir ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}
+  if [[ -s ${_glob_err} ]]
+  then
+    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}
+    exit 1;
+  elif [[ ! -f ${_base_patch} && ! -f ${_base_out} ]]
+  then
+    echo "Something went WRONG in ${BASELINE_TEST}:";
+    echo "Either ${_base_patch} or ${_base_out} should exists";
+    exit 1;
+  elif [[ -f ${_base_patch} ]]
+  then
+    echo "${BASELINE_TEST}: Differences found, patch generated"
+    cp ${_base_patch} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_patch}
+  elif [[ -f ${_base_out} ]]
+  then
+    echo "${BASELINE_TEST}: Differences found, replacement file generated"
+    cp ${_base_out} ${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/${_base_out}
+  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
+  fi
+  if [[ ! -s ${_base_diff} ]]
+  then
+    echo "${BASELINE_TEST}: PASSED"
+    true
+  else
+    echo "${BASELINE_TEST}: FAILED"
+    false
+  fi
+
+# Actual templates for baseline checks
+.baselinecheck_mfem:
+  stage: baseline_check
   variables:
-    # Explicitly pass down values that we want to be able to set when triggering
-    # pipelines manually or using scheduling
-    AUTOTEST: "${AUTOTEST}"
-    AUTOTEST_COMMIT: "${AUTOTEST_COMMIT}"
-  trigger:
-    include: .gitlab/corona-build-and-test.yml
-    strategy: depend
+    BASELINE_TEST: baseline
+    ADDITIONAL_DIR: ${BUILD_ROOT}/tpls
+  script:
+    - *baseline_script
+  artifacts:
+    when: always
+    paths:
+      - ${ARTIFACTS_DIR}
+  allow_failure: true
+
+.samplebaselinecheck_mfem:
+  stage: baseline_check
+  variables:
+    BASELINE_TEST: sample-runs-baseline
+    ADDITIONAL_DIR: ""
+  script:
+    - *baseline_script
+  timeout: 4h
+  artifacts:
+    when: always
+    paths:
+      - ${ARTIFACTS_DIR}
+  allow_failure: true
+
+# This job can only be manually triggered on a pipeline for master branch, or if
+# the pipeline was triggered with REBASELINE="YES"
+.rebaseline_mfem:
+  stage: baseline_publish
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "YES"'
+      when: manual
+  script:
+    - export PATCH_FILE=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}.patch
+    - export FULL_FILE=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}.out
+    - export DIFF_FILE=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}.diff
+    - cd ${BUILD_ROOT}/tests
+    - |
+      if [[ ! -f "${DIFF_FILE}" ]]
+      then
+          echo "Nothing to be done: no relevant change in baseline"
+          exit 0
+      elif [[ -f "${PATCH_FILE}" ]]
+      then
+          patch "./baseline-${SYS_TYPE}.saved" < "${PATCH_FILE}"
+      elif [[ -f "${FULL_FILE}t" ]]
+      then
+          cp "${FULL_FILE}" "./baseline-${SYS_TYPE}.saved"
+      else
+          echo "File missing: expected ${PATCH_FILE} or ${FULL_FILE}"
+          exit 1
+      fi
+    - git add baseline-${SYS_TYPE}.saved
+    - git commit -m "${SYS_TYPE} rebaselined in GitLab pipeline ${CI_PIPELINE_ID}"
+    - git push origin master
+
+# The list on jobs is defined in machine-specific files.
+include:
+  - local: .gitlab/quartz.yml
+  - local: .gitlab/lassen.yml

.gitlab/README.md

@@ -1,94 +0,0 @@
-                    Finite Element Discretization Library
-                                   __
-                       _ __ ___   / _|  ___  _ __ ___
-                      | '_ ` _ \ | |_  / _ \| '_ ` _ \
-                      | | | | | ||  _||  __/| | | | | |
-                      |_| |_| |_||_|   \___||_| |_| |_|
-
-                               https://mfem.org
-
-
-This directory contains most of the GitLab CI configuration. MFEM runs both PR
-and nightly testing on GitLab.
-
-# Structure
-
-## Top level
-
-The root configuration file is `.gitlab-ci.yml` at the root of MFEM repo.
-This file only defines one stage, in which we trigger several
-sub-pipelines.
-
-We use sub-pipelines to isolate the test for one combination of `machine`
-and `test type`.
-
-Machines typically include:
-
-* Quartz: Intel bi-socket x86
-* Lassen: Power9 + Nvidia GPU
-* Corona: AMD GPU
-
-Test types include:
-
-* Build and test: Spack driven build of dependencies, mfem build, mfem
-  test
-* Baseline: Script driven build of dependencies, thorough testing
-
-⚠️ The sub-pipeline design allows to add a new machine or a new test type without
-altering the scheduling, execution and displaying of the others.
-
-## Sub-pipelines
-
-Each file is this directory is the root configuration file for one
-sub-pipeline. The naming reflects the corresponding couple (`machine`,
-`test_type`).
-
-Those files define the *stages* and the *jobs* for the sub-pipeline. They
-also contain any configuration that cannot be shared. For the most part
-though, the configuration is shared and is placed in `.gitlab/configs`.
-
-We try to keep scripts out of the CI config and share them among similar
-jobs. They are gathered in `.gitlab/scripts`.
-
-## Scripts
-
-Scripts specific to the CI only are in `.gitlab/scripts`. It is best practice
-to keep scripts outside the CI configuration (no bash scripts embedded in a
-yaml file) because it helps with readability, maintenance and also with
-transition to another CI system.
-
-⚠️ Most of the scripts there are driven by environment variables and do not have a
-usage function. This should be improved.
-
-
-# More testing
-
-## Adding a new target to a build_and_test pipeline
-
-`build_and_test` pipelines rely on Spack to install dependencies. Spack is
-driven by Uberenv which helps freezing Spack configuration: the goal being to
-point to specific commit in Spack and isolate its configuration so that it is
-not influenced by the user environment. More documentation about this can be
-found in `tests/gitlab`.
-
-In the end, the MFEM target for which to build the dependencies is expressed
-with a spack spec of MFEM, within the limits permitted by the MFEM spack
-package.
-
-In any build-and-test sub-pipeline a job basically consists in defining the
-spack spec to use. Adding a job on quartz for example resumes to:
-
-```yaml
-<job_name>:
-  variables:
-    SPEC: "<spack_spec>"
-  extends: .build_and_test_on_quartz
-```
-
-The remaining and non trivial work is to make sure this spec is working. To
-test a spec before adding it, or reproduce a CI configuration, please refer to
-`tests/gitlab/reproduce-ci-jobs-interactively.md`.
-
-⚠️ It is assumed that the spack spec applies to `mfem@develop`. That's why in the
-CI all the specs start with the compiler or the variants to apply to mfem. The
-mechanism still works with a full spec.

.gitlab/configs/common.yml

@@ -1,36 +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.
-
-# We define the following GitLab pipeline variables:
-variables:
-
-# The path to the shared resource between all jobs. For example, external
-# repositories like 'tests' and 'tpls' are cloned here. Also, 'tpls' is built
-# once for all targets, so that build happen here. The BUILD_ROOT is unique to
-# the pipeline, preventing any form of concurrency with other pipelines. This
-# also means that the BUILD_ROOT directory will never be cleaned.
-# TODO: add a clean-up mechanism
-  BUILD_ROOT: ${USER_CI_TOP_DIR}/${CI_PROJECT_NAME}-${MACHINE_NAME}-pipeline-${CI_PIPELINE_ID}
-
-# On LLNL's quartz, there is only one allocation shared among jobs in order to
-# save time and resource. This allocation has to be uniquely named so that we
-# are sure to retrieve it.
-  ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
-
-# Git repositories used in the pipeline
-  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
-
-# Directory used to place artifacts.
-  ARTIFACTS_DIR: artifacts
-  SLURM_OVERLAP: 1

.gitlab/configs/corona-config.yml

@@ -1,59 +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.
-
-# GitLab pipeline configuration for the Corona machine at LLNL
-variables:
-  MACHINE_NAME: corona
-
-.on_corona:
-  tags:
-    - shell
-    - corona
-  rules:
-    # Don’t run corona jobs if...
-    # Note: This makes corona an "opt-in" machine. To activate builds on corona
-    # for a given GitLab clone of MFEM, go to Setting/CI-CD/variables, and set
-    # "ON_CORONA" to "ON". An LC account on for corona is required to trigger a
-    # pipeline there.
-    - if: '$CI_COMMIT_BRANCH =~ /_cnone/ || $ON_CORONA != "ON"'
-      when: never
-    # Don’t run autotest update if...
-    - if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
-      when: never
-    # Report success on success status
-    - if: '$CI_JOB_NAME =~ /report_job_success/ && $AUTOTEST == "YES"'
-      when: on_success
-    # Report failure on failure status
-    - if: '$CI_JOB_NAME =~ /report_job_failure/ && $AUTOTEST == "YES"'
-      when: on_failure
-    # Always release resource
-    - if: '$CI_JOB_NAME =~ /release_resource/'
-      when: always
-    # Always cleanup
-    - if: '$CI_JOB_NAME =~ /cleanup/'
-      when: always
-    # Default is to run if previous stage succeeded
-    - when: on_success
-
-# Spack helped builds
-# Generic corona build job, extending build script
-.build_and_test_on_corona:
-  extends: [.on_corona]
-  stage: build_and_test
-  script:
-    # THREADS is used by 'tests/gitlab/build_and_test', run below
-    - export THREADS=12
-    - echo ${ALLOC_NAME}
-    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
-    - echo ${JOBID}
-    - echo ${MFEM_DATA_DIR}
-    - echo ${SPEC}
-    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 15 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data

.gitlab/configs/lassen-config.yml

@@ -1,49 +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.
-
-# GitLab pipelines configurations for the Lassen machine at LLNL
-variables:
-  MACHINE_NAME: lassen
-
-.on_lassen:
-  tags:
-    - shell
-    - lassen
-  rules:
-    - if: '$CI_COMMIT_BRANCH =~ /_lnone/ || $ON_LASSEN == "OFF"' #run except if ...
-      when: never
-    # Don't run autotest update if...
-    - if: '$CI_JOB_NAME =~ /report/ && $AUTOTEST != "YES"'
-      when: never
-    # Report success on success status
-    - if: '$CI_JOB_NAME =~ /report_job_success/ && $AUTOTEST == "YES"'
-      when: on_success
-    # Report failure on failure status
-    - if: '$CI_JOB_NAME =~ /report_job_failure/ && $AUTOTEST == "YES"'
-      when: on_failure
-    # Always cleanup
-    - if: '$CI_JOB_NAME =~ /cleanup/'
-      when: always
-    - when: on_success
-
-# 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_and_test_on_lassen:
-  extends: [.on_lassen]
-  stage: build_and_test
-  script:
-    - echo ${MFEM_DATA_DIR}
-    - echo ${SPEC}
-    # Next script uses 'THREADS': leaving it empty --> it uses 'make all -j'
-    - lalloc 1 -W 30 -q pdebug --atsdisable tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
-  needs: [setup]

.gitlab/configs/quartz-config.yml

@@ -1,55 +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.
-
-# GitLab pipelines configurations for the Quartz machine at LLNL
-variables:
-  MACHINE_NAME: quartz
-
-.on_quartz:
-  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 =~ /report/ && $AUTOTEST != "YES"'
-      when: never
-    # Report success on success status
-    - if: '$CI_JOB_NAME =~ /report_job_success/ && $AUTOTEST == "YES"'
-      when: on_success
-    # Report failure on failure status
-    - if: '$CI_JOB_NAME =~ /report_job_failure/ && $AUTOTEST == "YES"'
-      when: on_failure
-    # Always release resource
-    - if: '$CI_JOB_NAME =~ /release_resource/'
-      when: always
-    # Always cleanup
-    - if: '$CI_JOB_NAME =~ /cleanup/'
-      when: always
-    # Default is to run if previous stage succeeded
-    - when: on_success
-
-# Spack helped builds
-# Generic quartz build job, extending build script
-.build_and_test_on_quartz:
-  extends: [.on_quartz]
-  stage: build_and_test
-  script:
-    # THREADS is used by 'tests/gitlab/build_and_test', run below
-    - export THREADS=12
-    - echo ${ALLOC_NAME}
-    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
-    - echo ${JOBID}
-    - echo ${MFEM_DATA_DIR}
-    - echo ${SPEC}
-    - srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 30 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data

.gitlab/configs/report-build-and-test.yml

@@ -1,81 +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.
-
-# Jobs report
-.report_job_success:
-  script:
-    - echo ${MACHINE_NAME}
-    - echo ${AUTOTEST}
-    - echo ${AUTOTEST_COMMIT}
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - cd ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # Report SUCCESS while holding the file lock on 'autotest.lock'.
-        # The next script uses the following environment variables:
-        # - MACHINE_NAME, AUTOTEST_ROOT, AUTOTEST_COMMIT
-        # - CI_COMMIT_REF_SLUG, CI_PROJECT_DIR, CI_PIPELINE_URL
-        # It also calls the script '.gitlab/scripts/safe_create_rundir'.
-        ${CI_PROJECT_DIR}/.gitlab/scripts/report_build_and_test_success
-        err=$?
-        # sleep for a period to allow NFS to propagate the above changes;
-        # clearly, there is no guarantee that other NFS clients will see the
-        # changes even after the timeout
-        sleep 10
-        exit $err
-      ) 9> autotest.lock
-
-.report_job_failure:
-  script:
-    - echo ${MACHINE_NAME}
-    - echo ${AUTOTEST}
-    - echo ${AUTOTEST_COMMIT}
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - cd ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # Report FAILURE while holding the file lock on 'autotest.lock'.
-        # The next script uses the following environment variables:
-        # - MACHINE_NAME, AUTOTEST_ROOT, AUTOTEST_COMMIT
-        # - CI_COMMIT_REF_SLUG, CI_PROJECT_DIR, CI_PIPELINE_URL
-        # It also calls the script '.gitlab/scripts/safe_create_rundir'.
-        ${CI_PROJECT_DIR}/.gitlab/scripts/report_build_and_test_failure
-        err=$?
-        # sleep for a period to allow NFS to propagate the above changes;
-        # clearly, there is no guarantee that other NFS clients will see the
-        # changes even after the timeout
-        sleep 10
-        exit $err
-      ) 9> autotest.lock

.gitlab/configs/setup-baseline.yml

@@ -1,72 +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.
-
-# The setup_baseline job 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.
-setup_baseline:
-  tags:
-    - shell
-    - quartz
-  stage: setup
-  variables:
-    GIT_STRATEGY: none
-  script:
-    #
-    # Setup ${BUILD_ROOT}/tpls and ${BUILD_ROOT}/tests:
-    #
-    - echo "MACHINE_NAME = ${MACHINE_NAME}"
-    - echo "REBASELINE = ${REBASELINE}"
-    - echo "AUTOTEST = ${AUTOTEST}"
-    - echo "AUTOTEST_COMMIT = ${AUTOTEST_COMMIT}"
-    - echo "BUILD_ROOT ${BUILD_ROOT}"
-    - mkdir -p ${BUILD_ROOT} && cd ${BUILD_ROOT}
-    - if [ ! -d "tpls" ]; then git clone ${TPLS_REPO}; fi
-    - if [ ! -d "tests" ]; then git clone ${TESTS_REPO}; fi
-    - cd tpls && git pull && cd ..
-    - cd tests && git pull origin && cd ..
-    #
-    # Setup ${AUTOTEST_ROOT}/autotest:
-    #
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - mkdir -p ${AUTOTEST_ROOT} && cd ${AUTOTEST_ROOT}
-    - command -v flock || echo "Required command 'flock' not found"
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # clone/update the autotest repo while holding the file lock on
-        # 'autotest.lock'
-        err=0
-        if [[ ! -d "autotest" ]]; then
-          git clone ${AUTOTEST_REPO}
-        else
-          cd autotest && git pull && cd ..
-        fi || err=1
-        # sleep for a period to allow NFS to propagate the above changes;
-        # clearly, there is no guarantee that other NFS clients will see the
-        # changes even after the timeout
-        sleep 10
-        exit $err
-      ) 9> autotest.lock

.gitlab/configs/setup-build-and-test.yml

@@ -1,94 +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.
-
-# Setup clones the mfem/data repo in ${SHARED_REPOS_DIR}. The build_and_test
-# script then symlinks the repo to the parent directory of the MFEM source
-# directory. Unit tests that depend on the mfem/data repo will then detect that
-# this directory is present and be enabled.
-setup:
-  tags:
-    - shell
-    - quartz
-  stage: setup
-  variables:
-    GIT_STRATEGY: none
-  script:
-    #
-    # Setup MFEM_DATA_DIR=${SHARED_REPOS_DIR}/mfem-data, see '.gitlab-ci.yml'
-    # and '.gitlab/configs/<machine>-config.yml'
-    #
-    - echo "MACHINE_NAME = ${MACHINE_NAME}"
-    - echo "AUTOTEST = ${AUTOTEST}"
-    - echo "AUTOTEST_COMMIT = ${AUTOTEST_COMMIT}"
-    - echo "SHARED_REPOS_DIR ${SHARED_REPOS_DIR}"
-    - mkdir -p ${SHARED_REPOS_DIR} && cd ${SHARED_REPOS_DIR}
-    - command -v flock || echo "Required command 'flock' not found"
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/mfem-data.lock' ..."
-        # try to get an excusive lock on fd 9 (mfem-data.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/mfem-data.lock'"
-        date
-        # clone/update the mfem/data repo while holding the file lock on
-        # 'mfem-data.lock'
-        err=0
-        if [[ ! -d "mfem-data" ]]; then
-          git clone ${MFEM_DATA_REPO} "mfem-data"
-        else
-          cd "mfem-data" && git pull && cd ..
-        fi || err=1
-        # sleep for a period to allow NFS to propagate the above changes;
-        # clearly, there is no guarantee that other NFS clients will see the
-        # changes even after the timeout
-        sleep 10
-        exit $err
-      ) 9> mfem-data.lock
-    #
-    # Setup ${AUTOTEST_ROOT}/autotest:
-    #
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - mkdir -p ${AUTOTEST_ROOT} && cd ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # clone/update the autotest repo while holding the file lock on
-        # 'autotest.lock'
-        err=0
-        if [[ ! -d "autotest" ]]; then
-          git clone ${AUTOTEST_REPO}
-        else
-          cd autotest && git pull && cd ..
-        fi || err=1
-        # sleep for a period to allow NFS to propagate the above changes;
-        # clearly, there is no guarantee that other NFS clients will see the
-        # changes even after the timeout
-        sleep 10
-        exit $err
-      ) 9> autotest.lock

.gitlab/corona-build-and-test.yml

@@ -1,67 +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.
-
-stages:
-  - setup
-  - allocate_resource
-  - build_and_test
-  - release_resource_and_report
-
-# Slurm shared allocation
-allocate_resource:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_corona
-  stage: allocate_resource
-  script:
-    - echo ${ALLOC_NAME}
-    - salloc --exclusive --nodes=1 --partition=mi60 --time=30 --no-shell --job-name=${ALLOC_NAME}
-  timeout: 6h
-  needs: [setup]
-
-# Build and test jobs, simply provide a spec
-rocm_gcc_8.3.1:
-  variables:
-    SPEC: "@develop%gcc@8.3.1+rocm amdgpu_target=gfx906"
-  extends: .build_and_test_on_corona
-  needs: [allocate_resource]
-
-# Release slurm allocation
-release_resource:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_corona
-  stage: release_resource_and_report
-  script:
-    - echo ${ALLOC_NAME}
-    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
-    - echo ${JOBID}
-    - ([[ -n "${JOBID}" ]] && scancel ${JOBID})
-  needs: [rocm_gcc_8.3.1]
-
-# Jobs report
-report_job_success:
-  stage: release_resource_and_report
-  extends:
-    - .on_corona
-    - .report_job_success
-
-report_job_failure:
-  stage: release_resource_and_report
-  extends:
-    - .on_corona
-    - .report_job_failure
-
-include:
-  - local: .gitlab/configs/common.yml
-  - local: .gitlab/configs/corona-config.yml
-  - local: .gitlab/configs/setup-build-and-test.yml
-  - local: .gitlab/configs/report-build-and-test.yml

.gitlab/lassen.yml

@@ -9,31 +9,25 @@
 # terms of the BSD-3 license. We welcome feedback and contributions, see file
 # CONTRIBUTING.md for details.
 
-stages:
-  - setup
-  - build_and_test
-  - report
+# GitLab pipelines configurations for the Lassen machine at LLNL
+
+.on_lassen:
+  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
+.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"
+    SPEC: "%xl@16.1.1.8 +mpi +cuda cuda_arch=sm_70"
   extends: .build_and_test_on_lassen
-
-# Jobs report
-report_job_success:
-  stage: report
-  extends:
-    - .on_lassen
-    - .report_job_success
-
-report_job_failure:
-  stage: report
-  extends:
-    - .on_lassen
-    - .report_job_failure
-
-include:
-  - local: .gitlab/configs/common.yml
-  - local: .gitlab/configs/lassen-config.yml
-  - local: .gitlab/configs/setup-build-and-test.yml
-  - local: .gitlab/configs/report-build-and-test.yml

.gitlab/quartz-baseline.yml

@@ -1,133 +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.
-
-variables:
-  BASELINE_TEST: baseline
-
-stages:
-  - setup
-  - baseline_check
-  - baseline_report
-  - cleanup
-  - baseline_publish
-
-baselinecheck_mfem_intel_quartz:
-  extends: [.on_quartz]
-  stage: baseline_check
-  variables:
-    # TPLS_DIR is used in .gitlab/scripts/baseline to provide the tpls location
-    # when call the runtest script in MFEM test repo.
-    # Note: the value must be consistent with the setup performed in
-    #       .gitlab/configs/setup-baseline.yml.
-    TPLS_DIR: ${BUILD_ROOT}/tpls
-  script:
-    - echo ${BUILD_ROOT}
-    - echo ${TPLS_DIR}
-    # Used by the tests in MFEM/tests:
-    - export MFEM_TEST_NP=32
-    # The next script uses the following environment variables:
-    # * BASELINE_TEST, SYS_TYPE, CI_PROJECT_DIR, ARTIFACTS_DIR,
-    # * BUILD_ROOT, TPLS_DIR, MACHINE_NAME
-    - .gitlab/scripts/baseline
-  artifacts:
-    when: always
-    paths:
-      - ${ARTIFACTS_DIR}
-  allow_failure: true
-
-cleanup:
-  extends: .on_quartz
-  stage: cleanup
-  variables:
-    GIT_STRATEGY: none
-  script:
-    - echo "BUILD_ROOT=${BUILD_ROOT}"
-    - rm -rf "${BUILD_ROOT}" || true
-
-report_baseline:
-  extends: [.on_quartz]
-  stage: baseline_report
-  script:
-    - echo ${MACHINE_NAME}
-    - echo ${AUTOTEST}
-    - echo ${AUTOTEST_COMMIT}
-    - echo "AUTOTEST_ROOT ${AUTOTEST_ROOT}"
-    - cd ${AUTOTEST_ROOT}
-    - |
-      (
-        date
-        echo "Waiting to aquire lock on '$PWD/autotest.lock' ..."
-        # try to get an excusive lock on fd 9 (autotest.lock) repeating the try
-        # every 5 seconds; simply using no timeout, i.e. 'flock 9', causes the
-        # command to hang indefinitely sometimes, so we use the timeout & retry
-        # as a workaround; we may want to add a counter for the number of
-        # retries to interrupt a potential infinite loop
-        while ! flock -w 5 9; do
-          true
-        done
-        echo "Aquired lock on '$PWD/autotest.lock'"
-        date
-        # ----------------------
-        cd ${AUTOTEST_ROOT}/autotest || \
-          { echo "Invalid 'autotest' dir: ${AUTOTEST_ROOT}/autotest"; exit 1; }
-        mkdir -p ${MACHINE_NAME}
-        rundir="${MACHINE_NAME}/$(date +%Y-%m-%d)-gitlab-${BASELINE_TEST}-${CI_COMMIT_REF_SLUG}"
-        rundir=$(${CI_PROJECT_DIR}/.gitlab/scripts/safe_create_rundir ${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 ${rundir}/${BASELINE_TEST}.err ]]; then
-          cp ${rundir}/${BASELINE_TEST}.err ${rundir}/autotest-email.html
-        fi
-        printf "%s\n" "" "Pipeline URL:" "$CI_PIPELINE_URL" \
-          >> ${rundir}/pipeline.txt
-        msg="GitLab CI log for ${BASELINE_TEST} on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
-        if [[ "$AUTOTEST_COMMIT" != "NO" ]]; then
-          git pull && \
-          git add ${rundir} && \
-          git commit -m "${msg}" && \
-          git push origin master
-        else
-          for file in ${rundir}/*; do
-            echo "------------------------------"
-            echo "Content of '$file'"
-            echo "******************************"
-            cat $file
-            echo "******************************"
-          done
-          rm -rf ${rundir} || true
-        fi
-        err=$?
-        # ----------------------
-        # sleep for a period to allow NFS to propagate the above changes;
-        # clearly, there is no guarantee that other NFS clients will see the
-        # changes even after the timeout
-        sleep 10
-        exit $err
-      ) 9> autotest.lock
-
-baselinepublish_mfem_quartz:
-  extends: [.on_quartz]
-  stage: baseline_publish
-  rules:
-    # - if: '$CI_COMMIT_BRANCH == "master" || $REBASELINE == "YES"'
-    - if: '$REBASELINE == "YES"'
-      when: manual
-  script:
-    - echo ${BUILD_ROOT}
-    - echo ${PWD}
-    - echo ${ARTIFACTS_DIR}
-    - ls -lA ${ARTIFACTS_DIR}
-    - .gitlab/scripts/rebaseline
-
-include:
-  - local: .gitlab/configs/common.yml
-  - local: .gitlab/configs/quartz-config.yml
-  - local: .gitlab/configs/setup-baseline.yml

.gitlab/quartz-build-and-test.yml

@@ -1,99 +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.
-
-stages:
-  - setup
-  - allocate_resource
-  - build_and_test
-  - release_resource_and_report
-
-# Allocate
-allocate_resource:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  stage: allocate_resource
-  script:
-    - echo ${ALLOC_NAME}
-    - salloc --exclusive --nodes=1 --partition=pdebug --time=30 --no-shell --job-name=${ALLOC_NAME}
-  timeout: 6h
-
-# GitLab jobs for the Quartz machine at LLNL
-debug_ser_gcc_4_9_3:
-  variables:
-    SPEC: "%gcc@4.9.3 +debug~mpi"
-  extends: .build_and_test_on_quartz
-
-debug_ser_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0 +debug~mpi"
-  extends: .build_and_test_on_quartz
-
-debug_par_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0 +debug+mpi"
-  extends: .build_and_test_on_quartz
-
-opt_ser_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0 ~mpi"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0:
-  variables:
-    SPEC: "%gcc@6.1.0"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0_sundials:
-  variables:
-    SPEC: "%gcc@6.1.0 +sundials"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0_petsc:
-  variables:
-    SPEC: "%gcc@6.1.0 +petsc ^petsc+mumps"
-  extends: .build_and_test_on_quartz
-
-opt_par_gcc_6_1_0_pumi:
-  variables:
-    SPEC: "%gcc@6.1.0 +pumi"
-  extends: .build_and_test_on_quartz
-
-# Release
-release_resource:
-  variables:
-    GIT_STRATEGY: none
-  extends: .on_quartz
-  stage: release_resource_and_report
-  script:
-    - echo ${ALLOC_NAME}
-    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
-    - echo ${JOBID}
-    - ([[ -n "${JOBID}" ]] && scancel ${JOBID})
-
-# Jobs report
-report_job_success:
-  stage: release_resource_and_report
-  extends:
-    - .on_quartz
-    - .report_job_success
-
-report_job_failure:
-  stage: release_resource_and_report
-  extends:
-    - .on_quartz
-    - .report_job_failure
-
-include:
-  - local: .gitlab/configs/common.yml
-  - local: .gitlab/configs/quartz-config.yml
-  - local: .gitlab/configs/setup-build-and-test.yml
-  - local: .gitlab/configs/report-build-and-test.yml

.gitlab/quartz.yml

@@ -0,0 +1,166 @@
+# 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.
+
+# GitLab pipelines configurations for the Quartz machine at LLNL
+
+.on_quartz:
+  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
+
+# Allocate
+q_allocate_resources:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_allocate_resources
+  script:
+    - salloc --exclusive --nodes=1 --partition=pdebug --time=30 --no-shell --job-name=${ALLOC_NAME}
+  timeout: 6h
+
+# Release
+q_release_resources:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_release_resources
+  script:
+    - export JOBID=$(squeue -h --name=${ALLOC_NAME} --format=%A)
+    - ([[ -n "${JOBID}" ]] && scancel ${JOBID})
+
+# Release
+q_report_success:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_release_resources
+  script:
+    - echo "Can only run if all the quartz jobs passed"
+    - rundir="gitlab/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
+    - cd ${AUTOTEST_ROOT}/autotest && git pull
+    - mkdir -p ${rundir}
+    - echo "The Quartz jobs were successful" > ${rundir}/gitlab.out
+    - git add ${rundir}
+    - git commit -am "Gitlab CI log for baseline on quartz with intel ($(date +%Y-%m-%d))"
+    - git push origin master
+
+q_report_failure:
+  variables:
+    GIT_STRATEGY: none
+  extends: .on_quartz
+  stage: q_release_resources
+  script:
+    - echo "Runs if there was at least one failure on quartz"
+    - rundir="gitlab/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
+    - cd ${AUTOTEST_ROOT}/autotest && git pull
+    - mkdir -p ${rundir}
+    - echo "There was an error while running CI on Quartz" > ${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
+
+# 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
+  needs: [setup]
+
+# Build MFEM
+debug_ser_gcc_4_9_3:
+  variables:
+    SPEC: "%gcc@4.9.3 +debug~mpi"
+  extends: .build_and_test_on_quartz
+
+debug_ser_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0 +debug~mpi"
+  extends: .build_and_test_on_quartz
+
+debug_par_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0 +debug+mpi"
+  extends: .build_and_test_on_quartz
+
+opt_ser_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0 ~mpi"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0:
+  variables:
+    SPEC: "%gcc@6.1.0"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0_sundials:
+  variables:
+    SPEC: "%gcc@6.1.0 +sundials"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0_petsc:
+  variables:
+    SPEC: "%gcc@6.1.0 +petsc ^petsc+mumps"
+  extends: .build_and_test_on_quartz
+
+opt_par_gcc_6_1_0_pumi:
+  variables:
+    SPEC: "%gcc@6.1.0 +pumi"
+  extends: .build_and_test_on_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:
+    - rundir="quartz/$(date +%Y-%m-%d)-github-${CI_COMMIT_REF_SLUG}"
+    - cd ${AUTOTEST_ROOT}/autotest && git pull
+    - mkdir -p ${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
+        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
+
+baselinepublish_mfem_quartz:
+  extends: [.on_quartz, .rebaseline_mfem]
+  needs: [baselinecheck_mfem_intel_quartz]

.gitlab/scripts/baseline

@@ -1,88 +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.
-
-# locals
-glob_err=${BASELINE_TEST}.err
-base=${BASELINE_TEST}-${SYS_TYPE}
-base_diff=${base}.diff
-base_patch=${base}.patch
-base_out=${base}.out
-artifacts_path=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}
-
-# prepare
-cd ${BUILD_ROOT} || \
-  { echo "Invalid BUILD_ROOT=$BUILD_ROOT"; exit 1; }
-ln -snf ${CI_PROJECT_DIR} mfem
-cd tests
-[[ -d _${BASELINE_TEST} ]] && rm -rf _${BASELINE_TEST}
-mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
-
-# run
-if [[ "${MACHINE_NAME}" == "quartz" || "${MACHINE_NAME}" == "ruby" ]]; then
-  srun --nodes=1 -p pdebug ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
-elif [[ ${MACHINE_NAME} == "corona" ]]; then
-  srun --nodes=1 -t 60 -p mi60 ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
-elif [[ ${MACHINE_NAME} == "lassen" ]]; then
-  lalloc 1 -q pdebug ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
-else
-  echo "Unknown machine: MACHINE_NAME=$MACHINE_NAME"
-  exit 1
-fi
-
-# post
-mkdir ${artifacts_path}
-
-if [[ -s ${glob_err} ]]
-then
-  echo "ERROR during ${BASELINE_TEST} execution";
-  echo "Here is the ${glob_err} file content";
-  cat ${glob_err}
-  cp ${glob_err} ${artifacts_path}/${glob_err}
-  exit 1;
-elif [[ ! -f ${base_patch} && ! -f ${base_out} ]]
-then
-  echo "Something went WRONG in ${BASELINE_TEST}:";
-  echo "Either ${base_patch} or ${base_out} should exists";
-  exit 1;
-elif [[ -f ${base_patch} ]]
-then
-  echo "${BASELINE_TEST}: Differences found, patch generated"
-  cp ${base_patch} ${artifacts_path}/${base_patch}
-elif [[ -f ${base_out} ]]
-then
-  echo "${BASELINE_TEST}: Differences found, replacement file generated"
-  cp ${base_out} ${artifacts_path}/${base_out}
-fi
-
-if [[ -f ${BASELINE_TEST}.out ]]; then
-  cp ${BASELINE_TEST}.out ${artifacts_path}
-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} ${artifacts_path}/${base_diff}
-  # We create a .err file, because that's how we signal that there was a diff.
-  cp ${base_diff} ${artifacts_path}/gitlab-${BASELINE_TEST}-${MACHINE_NAME}.err
-fi
-
-if [[ ! -s ${base_diff} ]]
-then
-  echo "${BASELINE_TEST}: PASSED"
-  true
-else
-  echo "${BASELINE_TEST}: FAILED"
-  false
-fi

.gitlab/scripts/rebaseline

@@ -1,49 +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.
-
-# There will be collision between corona and quartz baselines.
-# Once the corresponding files have been generated, we can switch to machine
-# specific ref.
-ARTIFACT_PATH=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}
-#ARTIFACT_PATH=${CI_PROJECT_DIR}/${ARTIFACTS_DIR}/baseline-${SYS_TYPE}-${MACHINE_NAME}
-
-PATCH_FILE=${ARTIFACT_PATH}.patch
-FULL_FILE=${ARTIFACT_PATH}.out
-DIFF_FILE=${ARTIFACT_PATH}.diff
-
-# There will be collision between corona and quartz baselines.
-# Once the corresponding files have been generated, we can switch to machine
-# specific ref.
-SAVED_NAME=baseline-${SYS_TYPE}.saved
-#SAVED_NAME=baseline-${SYS_TYPE}-${MACHINE_NAME}.saved
-
-cd ${BUILD_ROOT}/tests
-
-if [[ ! -f "${DIFF_FILE}" ]]
-then
-    echo "Nothing to be done: no relevant change in baseline"
-    exit 0
-elif [[ -f "${PATCH_FILE}" ]]
-then
-    patch "${SAVED_NAME}" < "${PATCH_FILE}"
-elif [[ -f "${FULL_FILE}" ]]
-then
-    cp "${FULL_FILE}" "${SAVED_NAME}"
-else
-    echo "File missing: expected ${PATCH_FILE} or ${FULL_FILE}"
-    exit 1
-fi
-
-git add "${SAVED_NAME}"
-git commit -m "${SYS_TYPE} (${MACHINE_NAME}) rebaselined in GitLab pipeline ${CI_PIPELINE_ID}"
-git push origin master

.gitlab/scripts/report_build_and_test_failure

@@ -1,45 +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.
-
-echo "Runs if there was at least one failure on ${MACHINE_NAME}"
-
-cd ${AUTOTEST_ROOT}/autotest || \
-  { echo "Invalid 'autotest' dir: ${AUTOTEST_ROOT}/autotest"; exit 1; }
-mkdir -p ${MACHINE_NAME}
-
-rundir="${MACHINE_NAME}/$(date +%Y-%m-%d)-gitlab-ci-${CI_COMMIT_REF_SLUG}"
-rundir=$(${CI_PROJECT_DIR}/.gitlab/scripts/safe_create_rundir $rundir)
-
-printf "%s\n" "Some 'build-and-test' jobs on ${MACHINE_NAME} FAILED." \
-  "Pipeline URL:" "$CI_PIPELINE_URL" > ${rundir}/gitlab.err
-
-msg="GitLab CI log for build-and-test on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
-
-# Create 'autotest-email.html' to indicate failure:
-cp ${rundir}/gitlab.err ${rundir}/autotest-email.html
-
-if [[ "$AUTOTEST_COMMIT" != "NO" ]]; then
-  git pull && \
-  git add ${rundir} && \
-  git commit -m "${msg}" && \
-  git push origin master
-else
-  for file in ${rundir}/*; do
-    echo "------------------------------"
-    echo "Content of '$file'"
-    echo "******************************"
-    cat $file
-    echo "******************************"
-  done
-  rm -rf ${rundir} || true
-fi

.gitlab/scripts/report_build_and_test_success

@@ -1,42 +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.
-
-echo "Can only run if all the ${MACHINE_NAME} jobs passed"
-
-cd ${AUTOTEST_ROOT}/autotest || \
-  { echo "Invalid 'autotest' dir: ${AUTOTEST_ROOT}/autotest"; exit 1; }
-mkdir -p ${MACHINE_NAME}
-
-rundir="${MACHINE_NAME}/$(date +%Y-%m-%d)-gitlab-ci-${CI_COMMIT_REF_SLUG}"
-rundir=$(${CI_PROJECT_DIR}/.gitlab/scripts/safe_create_rundir $rundir)
-
-printf "%s\n" "The 'build-and-test' jobs on ${MACHINE_NAME} were SUCCESSFUL." \
-  "Pipeline URL:" "$CI_PIPELINE_URL" > ${rundir}/gitlab.out
-
-msg="GitLab CI log for build-and-test on ${MACHINE_NAME} ($(date +%Y-%m-%d))"
-
-if [[ "$AUTOTEST_COMMIT" != "NO" ]]; then
-  git pull && \
-  git add ${rundir} && \
-  git commit -m "${msg}" && \
-  git push origin master
-else
-  for file in ${rundir}/*; do
-    echo "------------------------------"
-    echo "Content of '$file'"
-    echo "******************************"
-    cat $file
-    echo "******************************"
-  done
-  rm -rf ${rundir} || true
-fi

.gitlab/scripts/safe_create_rundir

@@ -1,42 +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.
-
-# This script takes a seed for a directory name and appends it with a counter
-# incremented until it can create a new directory with it.
-
-# Usage:
-#
-# Expects 1 argument: a string that is use as a seed for the directory name.
-#
-# > rundir="desired_name"
-# > rundir=$(./safe_create_rundir $rundir)
-
-set -o errexit
-set -o nounset
-
-rundir=${1:-""}
-if [[ -z ${rundir} ]]; then
-  >&2 echo "The script expects a string as argument for directory creation."
-  exit 1
-fi
-
-if ! mkdir ${rundir}; then
-  n=1
-  while ! mkdir ${rundir}_${n}
-  do
-    n=$((n+1))
-  done
-  rundir=${rundir}_${n}
-fi
-
-echo $rundir

CHANGELOG

@@ -8,154 +8,40 @@
                                https://mfem.org
 
 
-Version 4.3.1 (development)
+Version 4.2.1 (development)
 ===========================
-- More explicit and consistent formating of the output of iterative solvers
-  with the new IterativeSolver::PrintLevel options. See linalg/solvers.hpp.
+- 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 automatic differentiation. Users can select between native
-  implementation and external library implementation during configuration. One
-  parallel and two serial examples are implemented in the miniapps/autodiff/
-  directory.
+- Memory management:
+  * 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
+    MemoryManager::SetUmpireDevice2AllocatorName.
+  * Added HOST_PINNED MemoryType and a pinned host allocator for CUDA and HIP.
 
-- GridFunctionCoefficient (and the related vector, gradient, divergence, and
-  curl classes) now work properly with LORDiscretization and LORSolver.
+- Added support for Caliper: a library to integrate performance profiling
+  capabilities into applications. See examples/caliper for more details.
 
-- Added support for mesh preprocessing to resolve fine scale problem data
-  before simulation. This feature uses adaptive mesh refinement to control the
-  associated data oscillation error. See the new Example 30/30p.
+- Added support for explicit vectorization in the high-performance templated
+  code for Fujitsu's A64FX ARM microprocessor architecture.
 
-- Switched from Artistic Style (astyle) version 2.05.1 to version 3.1 for code
-  formatting. See the "make style" target.
+- Added AlgebraicCeedSolver that does matrix-free algebraic p-multigrid for
+  diffusion problems with the Ceed backend.
 
-- Split the fem/fe.?pp files into separate files in the new fem/fe/ directory
-  to simplify and clarify the organization of FiniteElement classes.
-
-- Added support for hr-adaptivity using TMOP-based error estimator.
-
-- Coefficient::SetTime now propagates the new time into internally stored
-  Coefficient objects.
-
-- Added initial support for google-benchmarks in the tests/benchmarks directory.
-  It can be enabled with MFEM_USE_BENCHMARK=YES.
-
-- Added Binder (mybinder.org) configuration files for C++ MFEM Jupyter Notebooks
-  with inline GLVis visualization as well as a new examples/jupyter/ directory
-  with a sample notebook based on Example 1. Implementation based on xeus-cling,
-  github.com/jupyter-xeus/xeus-cling + xeus-glvis, github.com/GLVis/xeus-glvis.
-
-- Added 'double' atomicAdd implementation for previous versions of CUDA.
-
-- 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.
-
-- Gmsh meshes where all elements have zero physical tag (the default Gmsh
-  output format if no physical groups are defined) are now successfully loaded,
-  and elements are reassigned attribute number 1.
-
-- Added new miniapps that use the ParELAG library, its hybrid smoothers, and the
-  hierarchy of spaces created by the element-based AMG (AMGe) methodology in
-  ParELAG to build multigrid solvers for H(curl) and H(div) forms. See the
-  miniapps/parelag directory for more details.
-
-- Fixed several MinGW build issues on Windows.
-
-- Remove the 'u' flag in the ar command, to update all files in the archive,
-  avoiding file name collisions from different subdirectories.
-
-- Added initial TMOP-based capabilities for surface fitting and tangential
-  relaxation in the mesh-optimizer and pmesh-optimizer miniapps.
-
-- Added ParMesh Adjaceny Set (adjset) creation support to the Conduit Mesh
-  Blueprint MFEM wrapper functions in ConduitDataCollection.
-
-- Added full assembly / device support for the LinearForm integrators:
-  * DomainLF: L(v) := (f, v)
-  * VectorDomainLF: L(v) := ((f1,...,fn), (v1,...,vn))
-  * DomainLFGrad: L(v) := (f,grad v)
-  * VectorDomainLFGrad:  L(v) := ((f1x,f1y,f1z,...,fnx,fny,fnz),grad(v1,...,vn))
-  It can be enabled by setting the linear assembly level to
-  'LinearAssemblyLevel::FULL' with the 'LinearForm::SetAssemblyLevel' method.
-
-- `HypreParVector` and `Vector` now support move semantics, and the copy
-  constructor for `HypreParVector` now copies the local vector data.
-
-- The HPC versions of ex1 and ex1p (in miniapps/performance) now support
-  runtime selection of either 2D or 3D meshes.
-
-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 new options for the mesh-explorer miniapp to visualize the actual
+  element attributes in parallel meshes while retaining the visualization of
+  the domain decomposition.
 
 - Introduced solver interface for linear problems with constraints, a few
   concrete solvers that implement the interface, and a demonstration of their
@@ -166,18 +52,19 @@ Linear and nonlinear solvers
   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 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.
 
-- 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 a new miniapp for computing (signed) distance functions to a point
+  source or zero level set. See miniapps/shifted/distance.cpp.
 
-- 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.
@@ -185,17 +72,6 @@ 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.
-
-- Implemented an adaptive linear solver tolerance option for NewtonSolver based
-  on the algorithm of Eisenstat and Walker.
-
-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.
-
 - 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
@@ -204,26 +80,113 @@ Meshing improvements
   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 support for 1D non-conforming meshes (which can be useful for parallel
+  load balancing and derefinement).
+
+- Added a "scaled Jacobian" visualization option in the Mesh Explorer miniapp to
+  help identify elements with poor mesh quality.
+
+- Added support for the "BR2" discontinuous Galerkin discretization for
+  diffusion via DGDiffusionBR2Integrator (see Example 14/14p).
+
+- Generalized the Multigrid class to support non-geometric multigrid. The
+  previous functionality, based on FiniteElementSpaceHierarchy, is now available
+  in the derived class GeometricMultigrid.
+
+- Upgraded the Catch unit test framework from version 2.13.0 to version 2.13.2.
+
+- The TMOP mesh optimization algorithms were extended to GPU:
+   - QualityMetric #1, #2, #7 and #77 are available in 2D, #302, #303, #315
+     and #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 a new command line boolean option (`--all`) to the unit tests to launch
+  *all* non-regression tests.
+
+- 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.
+
+- Implemented a filter method for the Navier miniapp to stabilize highly
+  turbulent flows in direct numerical simulation.
+
+- Added HIP support to the CMake build system.
+
+- 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 partial assembly and device support to Example 25/25p, with diagonal
+  preconditioning.
+
+- Implemented a variable step-size IMEX (VSSIMEX) method for the Navier miniapp.
 
 - 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 convective and skew-symmetric integrators for the nonlinear term in the
+  Navier-Stokes equations.
+
+- 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.
+
+- Changed the interface for the error estimator.
+
+- Implemented the Kelly error indicator for scalar-valued problems, supported
+  in serial and parallel builds.
+
+- 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.
+
+- 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.
 
 - 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.
 
+- Testing improvements:
+  * Transitioned from Travis to GitHub Action for testing/CI on GitHub.
+  * Effectively remove Travis from CI.
+  * Use Spack (and Uberenv) to automate TPL building in LLNL GitLab tests.
+  * Added a set of suggested git hooks for developers in config/githooks.
+
+- 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, 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.
+
 - Meshes consisting of any type of elements (including mixed meshes) can be
   converted to all-simplex meshes using Mesh::MakeSimplicial.
 
@@ -236,133 +199,42 @@ Meshing improvements
   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 support for transferring dual fields between high-order and low-order
+  refined finite element spaces using the transposed versions of the
+  L2ProjectionGridTransfer operators. This functionality is illustrated in the
+  lor-transfer miniapp.
+
+- 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 and may not work in more general settings.
+
+- Added support for transferring fields (primary and dual) between high-order
+  and low-order refined H1 finite element spaces using the
+  L2ProjectionH1GridTransfer operators. This functionality is demonstrated
+  through the lor-transfer miniapp when run with the -h1 option.
+
+- 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.
 
 - 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.
-
-- 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.
-
-- 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 VTK meshes in XML format.
-
 - Added makefile rule to generate TAGS table for vi or Emacs users.
 
-- Added HIP support to the CMake build system.
-
-- Various other simplifications, extensions, and bugfixes in the code.
-
 API changes
 -----------
 - Added an abstract interface `mfem::FaceRestriction` for `H1FaceRestriction`
@@ -372,11 +244,20 @@ API changes
   `mfem::FaceRestriction::AddMultTranspose` should replace previous calls to
   `mfem::FaceRestriction::MultTranspose`.
 
+libCEED integration improvements
+--------------------------------
+- Refactor the libCEED integration
+
+- Add support for VectorCoefficient with libCEED backends.
+
+- Add support for ConvectionIntegrator, and VectorConvectionNLFIntegrator with
+  libCEED backends.
+
 
 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
@@ -458,6 +339,9 @@ Linear and nonlinear solvers
   matrix with the function HypreParMatrixFromBlocks. This could be useful for
   solving block systems with parallel direct solvers such as STRUMPACK.
 
+- Added CUDA support for SUNDIALS ODE integrators. See the updated SUNDIALS
+  modification of Example 9/9p.
+
 - Added wrappers for hypre's flexible GMRES solver and the new parallel ILU
   preconditioner. The latter requires hypre version 2.19.0 or later.
 
@@ -568,7 +452,7 @@ 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

CITATION.cff

@@ -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

CMakeLists.txt

@@ -16,7 +16,7 @@ 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)
+if (MFEM_USE_GINKGO) 
   set(CMAKE_CXX_STANDARD 14)
 endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
@@ -54,7 +54,7 @@ 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 ${PROJECT_BINARY_DIR})
@@ -90,11 +90,6 @@ include("${CMAKE_CURRENT_SOURCE_DIR}/config/XSDKDefaults.cmake")
 
 # Enable languages.
 enable_language(CXX)
-if (MINGW)
-   # MinGW GCC does not expose the functions jn/_jn, yn/_yn (used in Example
-   # 25/25p) unless we use '-std=gnu++11':
-   set(CMAKE_CXX_EXTENSIONS ON)
-endif()
 if (MFEM_USE_CUDA)
    if (MFEM_USE_HIP)
       message(FATAL_ERROR " *** MFEM_USE_HIP cannot be combined with MFEM_USE_CUDA.")
@@ -107,7 +102,7 @@ if (MFEM_USE_CUDA)
    endif()
    enable_language(CUDA)
    set(CMAKE_CUDA_STANDARD 11)
-   if (MFEM_USE_GINKGO)
+   if (MFEM_USE_GINKGO) 
      set(CMAKE_CUDA_STANDARD 14)
    endif()
    set(CMAKE_CUDA_STANDARD_REQUIRED ON)
@@ -251,12 +246,6 @@ 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 ${OpenMP_CXX_LIBRARIES})
-  if(APPLE)
-    # On macOS, the compiler needs additional help to find the <omp.h> header.
-    # See issue #2642 for more information.
-    include_directories(${OpenMP_CXX_INCLUDE_DIRS})
-  endif(APPLE)
 endif()
 
 # SuiteSparse (before SUNDIALS which may depend on KLU)
@@ -338,11 +327,7 @@ if (MFEM_USE_AMGX)
 endif()
 
 if (MFEM_USE_CONDUIT)
-    find_package(Conduit REQUIRED conduit relay blueprint)
-endif()
-
-if (MFEM_USE_FMS)
-    find_package(FMS REQUIRED fms)
+    find_package(Conduit REQUIRED conduit relay blueprint )
 endif()
 
 # Axom/Sidre
@@ -372,12 +357,6 @@ if (MFEM_USE_HIOP)
   # find_package updates HIOP_FOUND, HIOP_INCLUDE_DIRS, HIOP_LIBRARIES
 endif()
 
-# CoDiPack package
-if (MFEM_USE_CODIPACK)
-  find_package(CODIPACK REQUIRED)
-  # find_package updates CODIPACK_FOUND, CODIPACK_INCLUDE_DIRS, CODIPACK_LIBRARIES
-endif()
-
 # OCCA
 if (MFEM_USE_OCCA)
    find_package(OCCA REQUIRED)
@@ -393,11 +372,6 @@ if (MFEM_USE_UMPIRE)
    find_package(UMPIRE REQUIRED)
 endif()
 
-# GOOGLE-BENCHMARK
-if (MFEM_USE_BENCHMARK)
-   find_package(Benchmark REQUIRED)
-endif()
-
 # Caliper
 if (MFEM_USE_CALIPER)
   find_package(Caliper REQUIRED)
@@ -426,11 +400,6 @@ if (MFEM_USE_MKL_CPARDISO)
   endif()
 endif()
 
-# PARELAG
-if (MFEM_USE_PARELAG)
-   find_package(PARELAG REQUIRED)
-endif()
-
 # MFEM_TIMER_TYPE
 if (NOT DEFINED MFEM_TIMER_TYPE)
   if (APPLE)
@@ -454,11 +423,10 @@ 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 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 HYPRE BLAS LAPACK SuperLUDist METIS SuiteSparse SUNDIALS PETSC
+    SLEPC MESQUITE MUMPS STRUMPACK AXOM CONDUIT Ginkgo GNUTLS GSLIB NETCDF
     MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE ADIOS2
-    CUSPARSE MKL_CPARDISO AMGX CALIPER CODIPACK BENCHMARK PARELAG MPI_CXX)
-
+    CUSPARSE MKL_CPARDISO AMGX CALIPER)
 # Add all *_FOUND libraries in the variable TPL_LIBRARIES.
 set(TPL_LIBRARIES "")
 set(TPL_INCLUDE_DIRS "")
@@ -477,9 +445,6 @@ 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}")
@@ -522,9 +487,13 @@ set(MFEM_INSTALL_DIR ${CMAKE_INSTALL_PREFIX} CACHE PATH
 # Declaring the library
 mfem_add_library(mfem ${SOURCES} ${HEADERS} ${MASTER_HEADERS})
 # message(STATUS "TPL_LIBRARIES = ${TPL_LIBRARIES}")
-target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
+if (CMAKE_VERSION VERSION_GREATER 2.8.11)
+  target_link_libraries(mfem PUBLIC ${TPL_LIBRARIES})
+else()
+  target_link_libraries(mfem ${TPL_LIBRARIES})
+endif()
 if (MINGW)
-  target_link_libraries(mfem PRIVATE ws2_32)
+  target_link_libraries(mfem ws2_32)
 endif()
 set_target_properties(mfem PROPERTIES VERSION "${mfem_VERSION}")
 set_target_properties(mfem PROPERTIES SOVERSION "${mfem_VERSION}")
@@ -563,21 +532,15 @@ endif()
 set(MFEM_CUSTOM_TARGET_PREFIX CACHE STRING "")
 
 #-------------------------------------------------------------------------------
-# Examples, miniapps, benchmarks and testing
+# Examples, miniapps, and testing
 #-------------------------------------------------------------------------------
 
-# Enable testing and benchmarks if required
+# Enable testing if required
 if (MFEM_ENABLE_TESTING)
   enable_testing()
   set(MFEM_ALL_TESTS_TARGET_NAME tests)
   add_mfem_target(${MFEM_ALL_TESTS_TARGET_NAME} OFF)
   add_subdirectory(tests EXCLUDE_FROM_ALL)
-
-  # Create a target for all benchmarks and, optionally, enable it.
-  set(MFEM_ALL_BENCHMARKS_TARGET_NAME benchmarks)
-  add_mfem_target(${MFEM_ALL_BENCHMARKS_TARGET_NAME}
-                  ${MFEM_ENABLE_GOOGLE_BENCHMARKS})
-  add_subdirectory(tests/benchmarks EXCLUDE_FROM_ALL)
 endif()
 
 # Define a target that all examples and miniapps will depend on.
@@ -587,11 +550,7 @@ add_custom_target(${MFEM_EXEC_PREREQUISITES_TARGET_NAME})
 # Create a target for all examples and, optionally, enable it.
 set(MFEM_ALL_EXAMPLES_TARGET_NAME examples)
 add_mfem_target(${MFEM_ALL_EXAMPLES_TARGET_NAME} ${MFEM_ENABLE_EXAMPLES})
-if (MFEM_ENABLE_EXAMPLES)
-  add_subdirectory(examples) #install examples if enabled
-else()
-  add_subdirectory(examples EXCLUDE_FROM_ALL)
-endif()
+add_subdirectory(examples EXCLUDE_FROM_ALL)
 
 # Create a target for all miniapps and, optionally, enable it.
 set(MFEM_ALL_MINIAPPS_TARGET_NAME miniapps)
@@ -601,7 +560,6 @@ add_subdirectory(miniapps EXCLUDE_FROM_ALL)
 # Target to build all executables, i.e. everything.
 add_custom_target(exec)
 add_dependencies(exec
-  ${MFEM_ALL_BENCHMARKS_TARGET_NAME}
   ${MFEM_ALL_EXAMPLES_TARGET_NAME}
   ${MFEM_ALL_MINIAPPS_TARGET_NAME}
   ${MFEM_ALL_TESTS_TARGET_NAME})

CODE_OF_CONDUCT.md

@@ -1,133 +0,0 @@
-# MFEM Code of Conduct
-
-## Our Pledge
-
-We as members, contributors, and leaders pledge to make participation in our
-community a harassment-free experience for everyone, regardless of age, body
-size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
-nationality, personal appearance, race, caste, color, religion, or sexual
-identity and orientation.
-
-We pledge to act and interact in ways that contribute to an open, welcoming,
-diverse, inclusive, and healthy community.
-
-## Our Standards
-
-Examples of behavior that contributes to a positive environment for our
-community include:
-
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
-  and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the overall
-  community
-
-Examples of unacceptable behavior include:
-
-* The use of sexualized language or imagery, and sexual attention or advances of
-  any kind
-* Trolling, insulting or derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email address,
-  without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
-  professional setting
-
-## Enforcement Responsibilities
-
-Community leaders are responsible for clarifying and enforcing our standards of
-acceptable behavior and will take appropriate and fair corrective action in
-response to any behavior that they deem inappropriate, threatening, offensive,
-or harmful.
-
-Community leaders have the right and responsibility to remove, edit, or reject
-comments, commits, code, wiki edits, issues, and other contributions that are
-not aligned to this Code of Conduct, and will communicate reasons for moderation
-decisions when appropriate.
-
-## Scope
-
-This Code of Conduct applies within all community spaces, and also applies when
-an individual is officially representing the community in public spaces.
-Examples of representing our community include using an official e-mail address,
-posting via an official social media account, or acting as an appointed
-representative at an online or offline event.
-
-## Enforcement
-
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at mfem@llnl.gov.
-All complaints will be reviewed and investigated promptly and fairly.
-
-All community leaders are obligated to respect the privacy and security of the
-reporter of any incident. Anyone involved in the reported behavior will recuse
-themselves from the investigation and decision making about the resolution of
-the complaint.
-
-## Enforcement Guidelines
-
-Community leaders will follow these Community Impact Guidelines in determining
-the consequences for any action they deem in violation of this Code of Conduct:
-
-### 1. Correction
-
-**Community Impact**: Use of inappropriate language or other behavior deemed
-unprofessional or unwelcome in the community.
-
-**Consequence**: A private, written warning from community leaders, providing
-clarity around the nature of the violation and an explanation of why the
-behavior was inappropriate. A public apology may be requested.
-
-### 2. Warning
-
-**Community Impact**: A violation through a single incident or series of
-actions.
-
-**Consequence**: A warning with consequences for continued behavior. No
-interaction with the people involved, including unsolicited interaction with
-those enforcing the Code of Conduct, for a specified period of time. This
-includes avoiding interactions in community spaces as well as external channels
-like social media. Violating these terms may lead to a temporary or permanent
-ban.
-
-### 3. Temporary Ban
-
-**Community Impact**: A serious violation of community standards, including
-sustained inappropriate behavior.
-
-**Consequence**: A temporary ban from any sort of interaction or public
-communication with the community for a specified period of time. No public or
-private interaction with the people involved, including unsolicited interaction
-with those enforcing the Code of Conduct, is allowed during this period.
-Violating these terms may lead to a permanent ban.
-
-### 4. Permanent Ban
-
-**Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior, harassment of an
-individual, or aggression toward or disparagement of classes of individuals.
-
-**Consequence**: A permanent ban from any sort of public interaction within the
-community.
-
-## Attribution
-
-This Code of Conduct is adapted from the [Contributor Covenant][homepage],
-version 2.1, available at
-[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
-
-Community Impact Guidelines were inspired by
-[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
-
-For answers to common questions about this code of conduct, see the FAQ at
-[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
-[https://www.contributor-covenant.org/translations][translations].
-
-[homepage]: https://www.contributor-covenant.org
-[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
-[Mozilla CoC]: https://github.com/mozilla/diversity
-[FAQ]: https://www.contributor-covenant.org/faq
-[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

@@ -21,9 +21,6 @@ documentation; new examples and miniapps; HPC performance improvements; etc.
 MFEM is distributed under the terms of the BSD-3 license. All new contributions
 must be made under this license.
 
-Note also that MFEM has a [Code of Conduct](CODE_OF_CONDUCT.md). By participating
-in the MFEM community, you agree to abide by its rules.
-
 If you plan on contributing to MFEM, consider reviewing the
 [issue tracker](https://github.com/mfem/mfem/issues) first to check if a thread
 already exists for your desired feature or the bug you ran into. Use a pull
@@ -45,7 +42,6 @@ back to them before issuing pull requests:
   - [New Feature Development](#new-feature-development)
   - [Developer Guidelines](#developer-guidelines)
   - [Pull Requests](#pull-requests)
-  - [MFEM PR Rules](#mfem-pr-rules)
   - [Pull Request Checklist](#pull-request-checklist)
   - [Master/Next Workflow](#masternext-workflow)
   - [Releases](#releases)
@@ -71,9 +67,8 @@ Origin](#developers-certificate-of-origin-11) at the end of this file.*
   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) and
-  follow the [MFEM PR Rules](#mfem-pr-rules).
+- 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
   the `ready-for-review` label.
 - PRs are treated similarly to journal submission with an "editor" assigning two
@@ -102,6 +97,7 @@ The MFEM source code has the following structure:
   .
   ├── config
   │   ├── cmake
+  │   │    └── ...
   │   └── githooks
   ├── data
   ├── doc
@@ -110,14 +106,12 @@ The MFEM source code has the following structure:
   │   ├── caliper
   │   ├── ginkgo
   │   ├── hiop
-  │   ├── jupyter
   │   ├── petsc
   │   ├── pumi
   │   ├── sundials
   |   └── superlu
   ├── fem
   │   ├── ceed
-  │   ├── fe
   │   ├── qinterp
   │   └── tmop
   ├── general
@@ -126,7 +120,6 @@ The MFEM source code has the following structure:
   ├── mesh
   ├── miniapps
   │   ├── adjoint
-  │   ├── autodiff
   │   ├── common
   │   ├── electromagnetics
   │   ├── gslib
@@ -134,20 +127,18 @@ The MFEM source code has the following structure:
   │   ├── mtop
   │   ├── navier
   │   ├── nurbs
-  │   ├── parelag
   │   ├── performance
   │   ├── shifted
   │   ├── solvers
   │   ├── tools
   │   └── toys
   └── tests
-      ├── benchmarks
       ├── convergence
       ├── gitlab
-      ├── mem_manager
       ├── par-mesh-format
       ├── scripts
       └── unit
+          └── ...
 ```
 
 #### Main directories and classes
@@ -333,22 +324,15 @@ Before you can start, you need a GitHub account, here are a few suggestions:
     change the code by default.
 
 - Code specifics
-  - All new public, protected, and private classes, methods, data members, and
-    functions have Doxygen-style documentation in source comments.
-  - In addition to arguments and functionality, documentation should include the
-    current limitations of the code, any background information that is
-    implicitly assumed in the implementation, and the ownership and lifetime
-    of data.
+  - All significant new classes, methods and functions have Doxygen-style
+    documentation in source comments.
   - Consistent code styling is enforced with `make style` in the top-level
     directory. This requires [Artistic Style](http://astyle.sourceforge.net) (we
-    specifically use version 3.1). See also the file `config/mfem.astylerc`.
+    specifically use version 2.05.1). See also the file `config/mfem.astylerc`.
   - Use `mfem::out` and `mfem::err` instead of `std::cout` and `std::cerr` in
     internal library code. (You can use `std` in examples and miniapps.)
   - When manually resolving conflicts during a merge, make sure to mention the
     conflicted files in the commit message.
-  - All significant new features and changes should be documented in CHANGELOG.
-  - New examples and miniapps should have documentation on the MFEM webpage.
-
 
 ### Pull Requests
 
@@ -414,83 +398,6 @@ Before you can start, you need a GitHub account, here are a few suggestions:
 - If triggered, track the status of the LLNL GitLab tests. If failing, ask
   one of the _LLNL developers_ for details.
 
-
-### MFEM PR Rules
-
-The Pull Request (PR) approval process in MFEM is similar to the approval of papers in a peer-reviewed journal. In particular:
-
-1. There is an MFEM board of "editors" that evaluates new PRs and assigns "reviewers" for each PR.
-
-2. The assigned reviewers are responsible to carefully review and test the proposed PR.
-
-3. A PR can be (manually) merged in the *next* branch only if 2 of the assigned reviewers have approved it and it has passed internal testing. This merge can be performed by any of the assigned reviewers or by any of the editors.
-
-4. A PR can be merged in the *master* branch only if it has been tested successfully for a week in *next* and an editor has (optionally) taken a final look. This merge can be performed only by one of the editors.
-
-#### Responsibilities of Editors
-
-The current list of MFEM editors is:
-
-- @v-dobrev (Veselin Dobrev)
-- @tzanio (Tzanio Kolev)
-- @pazner (Will Pazner)
-- @mlstowell (Mark Stowell)
-
-**The responsibilities of the editors are:**
-
-1. To assign appropriate milestone and labels for new PRs, e.g. *bugfix*, *minor*, *api-change*, *high-impact*, etc.
-
-2. To assign at least 2 reviewers for new PRs. An editor can also be a reviewer. The editor, reviewers, and author should be listed as "Assignees" on the GitHub PR page. After assignment, the `in-review` label should be added.
-
-3. To complete the initial PR evaluation and assignments in a timely manner: 1 week from submission.
-
-4. To assist reviewers when they need help with their reviews (but also to stay out of the way when they don't).
-
-5. To remind the reviewers about timely completion of their review.
-
-6. To take a final look and complete the PR merge in *master*. The final look step is optional and shouldn't take more than 3 days.
-
-7. The assignment of bugfixes should be expedited proportional to their importance, e.g. in some cases the editor can assign much shorter review window.
-
-#### Responsibilities of Reviewers
-
-Everyone on the MFEM team can be asked to serve as a reviewer on a PR in their area of expertise.
-
-**The responsibilities of the reviewers are:**
-
-1. To let the editors know if the proposed assignment is not a good match for them.
-
-2. To communicate with the PR author, provide feedback and work with them to resolve issues.
-
-3. To ensure the quality of the PR by making sure that the code adheres to the [Developer Guidelines](#developer-guidelines), e.g. all methods, data members, and functions have documentation, including data ownership and lifetime, new examples/miniapps have a corresponding PR in mfem/web, major features have `CHANGELOG` entries, etc.
-
-3. To seek help from the editors in case of difficulties.
-
-4. To complete the review in a timely manner: 3 weeks from assignment.
-
-5. To test the PR thoroughly before merging in *next*. The PR author is also encouraged to perform testing and inform the reviewers about the results.
-
-6. To monitor the PR impact on the testing in the *next* branch and alert the editors that the PR is ready for merging in *master*.
-
-7. The review of bugfixes should be expedited proportional to their importance. The review window can be much less than three weeks in such cases.
-
-#### Responsibilities of Authors
-
-Authors should clearly indicate when a PR is ready for review (before that the PR should be marked as `Draft` or `[WIP]`).
-
-**The responsibilities of the authors are:**
-
-1. To follow the instructions and PR checklist in the `CONTRIBUTING.md` document in the MFEM repository.
-
-2. To respond to reviewer feedback in a timely manner.
-
-3. Authors are encouraged to perform testing and inform the reviewers about the results.
-
-4. Authors can use the "Reviewers" section of the GitHub PR page to suggest reviewers, but the "Assignees" section will show who the editor has assigned to do the reviews.
-
-5. To indicate when the PR is ready for review by adding the `ready-for-review` label.
-
-
 ### Pull Request Checklist
 
 Before a PR can be merged, it should satisfy the following:
@@ -544,9 +451,7 @@ Before a PR can be merged, it should satisfy the following:
      - [ ] The miniapps go at the end of the page, and are usually listed only under a specific "Application (PDE)" category.
      - [ ] Add a short description of the miniapp in the "Extensive Examples" section of `features.md`.
 - [ ] New capability:
-   - [ ] All new public, protected, and private classes, methods, data members, and functions have full Doxygen-style documentation in source comments. Documentation should include descriptions of member data, function arguments and return values, template parameters, and prerequisites for calling new functions.
-   - [ ] Pointer arguments and return values must specify whether ownership is being transferred or lent with the call.
-   - [ ] Any new functions should include descriptions of their intended use e.g. for internal use only, user-facing, etc., along with references to example code whenever possible/appropriate.
+   - [ ] All significant new classes, methods and functions have Doxygen-style documentation in source comments.
    - [ ] Consider adding new sample runs in existing examples to highlight the new capability.
    - [ ] Consider saving cool simulation pictures with the new capability in the Confluence gallery (LLNL only) or submitting them, via pull request, to the gallery section of the `mfem/web` repo.
    - [ ] If this is a major new feature, consider mentioning it in the short summary inside `README` *(rare)*.
@@ -557,7 +462,6 @@ Before a PR can be merged, it should satisfy the following:
 - [ ] (LLNL only) After merging:
    - [ ] Update internal tests to include the new features.
 
-
 ### Master/Next Workflow
 
 MFEM uses a `master`/`next`-branch workflow as described below:
@@ -649,10 +553,8 @@ MFEM uses a `master`/`next`-branch workflow as described below:
     - Update version and shortlinks in `src/index.md` and `src/download.md`.
     -  Use [cloc-1.62.pl](http://cloc.sourceforge.net/) and `ls -lh` to estimate the SLOC and the tarball size in `src/download.md`.
 
-
 ## LLNL Workflow
 
-
 ### Mirroring on Bitbucket
 
 - The GitHub `master` and `next` branches are mirrored to the LLNL institutional
@@ -672,17 +574,16 @@ MFEM uses a `master`/`next`-branch workflow as described below:
   - `mfem:gh-next` -- Bleeding-edge development version, may be broken, use at
      your own risk.
 
-
 ### Mirroring on GitLab
 
 - MFEM repository is also mirrored on the LLNL GitLab instance, in a
   semi-automated manner.
 
 - This instance is meant to complete CI testing with tests on Livermore
-  Computing systems. GitLab pipeline status is reported in the corresponding
+  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.
+- In Gitlab pipelines, TPLs (dependencies) are built using Spack, driven by Uberenv.
 
 - No change to the MFEM repo can be made on this instance.
 
@@ -695,7 +596,6 @@ 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
@@ -707,7 +607,6 @@ 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.
 - Tests on the `next` branch are currently scheduled to run each night.
 
-
 ### Windows smoke test
 We use Appveyor to test building with the MS Visual C++ compiler in a Windows
 environment, as well as to test the CMake build. See the `.appveyor` file and the
@@ -717,7 +616,6 @@ build logs at
 CMake is used to generate the MSVC Project files and drive the build.  A release
 and debug build is performed with a simple run of `ex1` to verify the executable.
 
-
 ### Tests at LLNL
 
 - We mirror the `master` and `next` branches internally (to `gh-master` and

INSTALL

@@ -459,22 +459,10 @@ MFEM_USE_UMPIRE = YES/NO
    discovery, provision, and management of memory on machines with multiple
    memory devices like NUMA and GPUs.
 
-MFEM_USE_BENCHMARK = YES/NO
-   Enables support for Google Benchmark, a library to support the benchmarking
-   of functions, in the tests/benchmarks directory.
-
 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.
 
-MFEM_USE_CODIPACK = YES/NO
-  Enable automatic differentiation using the CoDiPack library.
-  www.scicomp.uni-kl.de/codi/
-
-MFEM_USE_ADFORWARD = YES/NO
-  Enable forward mode for AD packages. This option is valid
-  only if the AD package supports two modes (backward/forward).
-
 MFEM_USE_CUDA = YES/NO
    Enables support for CUDA devices in MFEM. CUDA is a parallel computing
    platform and programming model for general computing on graphical processing
@@ -486,7 +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
@@ -528,18 +516,6 @@ MFEM_USE_CALIPER = YES/NO
    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_USE_PARELAG = YES/NO
-   Enables the miniapps that use the ParELAG library. MFEM does not currently
-   use ParELAG. In fact, ParELAG is dependent on MFEM. Therefore, this option
-   currently only concerns the miniapps.
-
 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.
@@ -564,9 +540,8 @@ The specific libraries and their options are:
   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,
+            HYPRE >= 2.20.0 for '--enable-mixedint' support.
 
 - METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
   MFEM_USE_METIS_5 = YES (default is to use METIS 4).
@@ -640,7 +615,7 @@ The specific libraries and their options are:
   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.
+  Versions: Ginkgo >= 1.4.0. 
 
 - AmgX (optional), used when MFEM_USE_AMGX = YES.
   URL: https://github.com/NVIDIA/AMGX
@@ -709,12 +684,7 @@ 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 >= 0.4.6.
-
-- CoDiPack (optiobal), used with MFEM_USE_CODIPACK = YES
-  URL: https://www.scicomp.uni-kl.de/codi/
-  Options: CODIPACK_OPT
-  Versions: 1.9.3
+  Versions: HIOP >= 0.4.
 
 - 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
@@ -752,10 +722,10 @@ The specific libraries and their options are:
   Versions: libCEED >= 0.8.
 
 - RAJA (optional), used when MFEM_USE_RAJA = YES.
-  Beginning with MFEM v4.3, only RAJA v0.14.0+ is supported.
+  Beginning with MFEM v4.3, only RAJA v0.13.0+ is supported.
   URL: https://github.com/LLNL/RAJA
   Options: RAJA_DIR, RAJA_OPT, RAJA_LIB.
-  Versions: RAJA >= 0.14.0.
+  Versions: RAJA >= 0.13.0.
 
 - Caliper (optional), used when MFEM_USE_CALIPER = YES.
   URL: https://github.com/LLNL/Caliper
@@ -766,12 +736,7 @@ The specific libraries and their options are:
   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 >= 3.0.0.
-
-- Benchmark, used when MFEM_USE_BENCHMARK = YES.
-  URL: https://github.com/google/benchmark
-  Options: BENCHMARK_DIR, BENCHMARK_LIB.
-  Versions: Benchmark >= 1.5.6.
+  Versions: Umpire >= 2.0.0.
 
 - MPFR (optional), used when MFEM_USE_MPFR = YES.
   URL: http://mpfr.org, it depends on the GMP library: https://gmplib.org
@@ -788,15 +753,6 @@ 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.
-
-- ParELAG, used when MFEM_USE_PARELAG = YES.
-  URL: https://github.com/LLNL/parelag
-  Options: PARELAG_DIR, PARELAG_OPT, PARELAG_LIB.
-
 Building with CMake
 ===================
 The MFEM build system consists of two steps: configuration and compilation.
@@ -921,8 +877,6 @@ MFEM_USE_MPFR
 MFEM_USE_ZLIB
 MFEM_USE_PUMI
 MFEM_USE_HIOP
-MFEM_USE_CODIPACK
-MFEM_USE_ADFORWARD
 MFEM_USE_CUDA
 MFEM_USE_OCCA
 MFEM_USE_CEED
@@ -930,9 +884,6 @@ MFEM_USE_RAJA
 MFEM_USE_UMPIRE
 MFEM_USE_SIDRE
 MFEM_USE_CALIPER
-MFEM_USE_FMS
-MFEM_USE_BENCHMARK
-MFEM_USE_PARELAG
 
 The following options are CMake specific:
 
@@ -982,15 +933,11 @@ The CMake build system adds auto-detection for the following packages/libraries:
  - POSIXCLOCKS
  - PUMI
  - HIOP
- - CoDiPack
  - OCCA
  - RAJA
  - UMPIRE
  - AXOM - Used when MFEM_USE_SIDRE is enabled
  - CALIPER
- - FMS
- - BENCHMARK
- - ParELAG
 
 The following built-in CMake packages are also used:
 
@@ -1008,7 +955,7 @@ 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.
 
@@ -1016,7 +963,7 @@ 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

README

@@ -12,9 +12,6 @@ to enable high-performance scalable finite element discretization research and
 application development on a wide variety of platforms, ranging from laptops to
 supercomputers.
 
-We welcome contributions and feedback from the community. Please see the file
-CONTRIBUTING.md for additional details about our development process.
-
 * For building instructions, see the file INSTALL, or type "make help".
 
 * Copyright and licensing information can be found in files LICENSE and NOTICE.
@@ -22,6 +19,9 @@ CONTRIBUTING.md for additional details about our development process.
 * The best starting point for new users interested in MFEM's features is to
   review the examples and miniapps at https://mfem.org/examples.
 
+* Developers interested in contributing to the library, should read the
+  instructions and documentation in the CONTRIBUTING.md file.
+
 Conceptually, MFEM can be viewed as a finite element toolbox that provides the
 building blocks for developing finite element algorithms in a manner similar to
 that of MATLAB for linear algebra methods. In particular, MFEM provides support

config/XSDKDefaults.cmake

@@ -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()
@@ -283,11 +279,3 @@ ENDIF()
 IF (DEFINED TPL_ENABLE_UMPIRE)
   SET(MFEM_USE_UMPIRE ${TPL_ENABLE_UMPIRE} CACHE BOOL "Enable Umpire" FORCE)
 ENDIF()
-
-IF (DEFINED TPL_ENABLE_BENCHMARK)
-  SET(MFEM_USE_BENCHMARK ${TPL_ENABLE_BENCHMARK} CACHE BOOL "Enable Google-Benchmark" FORCE)
-ENDIF()
-
-IF (DEFINED TPL_ENABLE_PARELAG)
-  SET(MFEM_USE_PARELAG ${TPL_ENABLE_PARELAG} CACHE BOOL "Enable ParELAG" FORCE)
-ENDIF()

config/cmake/MFEMConfig.cmake.in

@@ -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@)
@@ -54,11 +53,7 @@ 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_CODIPACK @MFEM_USE_CODIPACK@)
-set(MFEM_USE_ADFORWARD @MFEM_USE_ADFORWARD@)
 set(MFEM_USE_CALIPER @MFEM_USE_CALIPER@)
-set(MFEM_USE_BENCHMARK @MFEM_USE_BENCHMARK@)
-set(MFEM_USE_PARELAG @MFEM_USE_PARELAG@)
 
 set(MFEM_CXX_COMPILER "@CMAKE_CXX_COMPILER@")
 set(MFEM_CXX_FLAGS "@CMAKE_CXX_FLAGS@")

config/cmake/config.hpp.in

@@ -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
 
@@ -175,13 +172,4 @@
 // Enable interface to the MKL CPardiso library.
 #cmakedefine MFEM_USE_MKL_CPARDISO
 
-// Use forward mode for automatic differentiation
-#cmakedefine MFEM_USE_ADFORWARD
-
-// Enable the use of the CoDiPack library for AD
-#cmakedefine MFEM_USE_CODIPACK
-
-// Enable MFEM functionality based on the Google Benchmark library.
-#cmakedefine MFEM_USE_BENCHMARK
-
 #endif // MFEM_CONFIG_HEADER

config/cmake/modules/FindBenchmark.cmake

@@ -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:
-#   - BENCHMARK_FOUND
-#   - BENCHMARK_LIBRARIES
-#   - BENCHMARK_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(Benchmark BENCHMARK BENCHMARK_DIR
-        "include" "benchmark/benchmark.h"
-        "lib" "benchmark"
-        "Paths to headers required by Google Benchmark."
-        "Libraries required by Google Benchmark.")

config/cmake/modules/FindCODIPACK.cmake

@@ -1,24 +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.
-
-# Automatic differentiation using the CoDiPack library.
-#  www.scicomp.uni-kl.de/codi/
-# Sets the following variables:
-#   - CODIPACK_FOUND
-#   - CODIPACK_INCLUDE_DIRS
-#   - CODIPACK_LIBRARIES
-
-include(MfemCmakeUtilities)
-mfem_find_package(CODIPACK CODIPACK CODIPACK_DIR
-  "include" "codi.h"
-  "lib" ""
-  "Paths to headers required by CODIPACK."
-  "Libraries required by CODIPACK.")

config/cmake/modules/FindFMS.cmake

@@ -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.")

config/cmake/modules/FindPARELAG.cmake

@@ -1,19 +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:
-#   - PARELAG_FOUND
-#   - PARELAG_LIBRARIES
-#   - PARELAG_INCLUDE_DIRS
-
-include(MfemCmakeUtilities)
-mfem_find_package(PARELAG PARELAG PARELAG_DIR "" "" "" ""
-  "Paths to headers required by ParELAG." "Libraries required by ParELAG.")

config/cmake/modules/MfemCmakeUtilities.cmake

@@ -100,8 +100,6 @@ macro(add_mfem_examples EXE_SRCS)
 
     string(REPLACE ".cpp" "" EXE_NAME "${EXE_PREFIX}${SRC_FILENAME}")
     mfem_add_executable(${EXE_NAME} ${SRC_FILE})
-    install(TARGETS ${EXE_NAME}
-            RUNTIME DESTINATION examples)
     add_dependencies(${MFEM_ALL_EXAMPLES_TARGET_NAME} ${EXE_NAME})
     if (EXE_NEEDED_BY)
       add_dependencies(${EXE_NEEDED_BY} ${EXE_NAME})
@@ -766,7 +764,7 @@ function(mfem_export_mk_files)
       MFEM_USE_GNUTLS MFEM_USE_GSLIB MFEM_USE_NETCDF MFEM_USE_PETSC
       MFEM_USE_SLEPC MFEM_USE_MPFR MFEM_USE_SIDRE MFEM_USE_CONDUIT MFEM_USE_PUMI
       MFEM_USE_CUDA MFEM_USE_OCCA MFEM_USE_RAJA MFEM_USE_UMPIRE MFEM_USE_SIMD
-      MFEM_USE_ADIOS2 MFEM_USE_BENCHMARK MFEM_USE_PARELAG)
+      MFEM_USE_ADIOS2)
   foreach(var ${CONFIG_MK_BOOL_VARS})
     if (${var})
       set(${var} YES)

config/config.hpp.in

@@ -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
 
@@ -180,13 +177,4 @@
 // Enable interface to the MKL CPardiso library.
 // #define MFEM_USE_MKL_CPARDISO
 
-// Use forward mode for automatic differentiation
-// #define MFEM_USE_ADFORWARD
-
-// Enable the use of the CoDiPack library for AD
-// #define MFEM_USE_CODIPACK
-
-// Enable functionality based on the Google Benchmark library.
-// #define MFEM_USE_BENCHMARK
-
 #endif // MFEM_CONFIG_HEADER

config/config.mk.in

@@ -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@
@@ -58,10 +57,6 @@ MFEM_USE_UMPIRE        = @MFEM_USE_UMPIRE@
 MFEM_USE_SIMD          = @MFEM_USE_SIMD@
 MFEM_USE_ADIOS2        = @MFEM_USE_ADIOS2@
 MFEM_USE_MKL_CPARDISO  = @MFEM_USE_MKL_CPARDISO@
-MFEM_USE_ADFORWARD     = @MFEM_USE_ADFORWARD@
-MFEM_USE_CODIPACK      = @MFEM_USE_CODIPACK@
-MFEM_USE_BENCHMARK     = @MFEM_USE_BENCHMARK@
-MFEM_USE_PARELAG       = @MFEM_USE_PARELAG@
 
 # Compiler, compile options, and link options
 MFEM_CXX       = @MFEM_CXX@

config/defaults.cmake

@@ -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)
@@ -58,10 +57,6 @@ 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)
-option(MFEM_USE_ADFORWARD "Enable forward mode for AD" OFF)
-option(MFEM_USE_CODIPACK "Enable automatic differentiation (AD) using CoDiPack" OFF)
-option(MFEM_USE_BENCHMARK "Enable Google Benchmark" OFF)
-option(MFEM_USE_PARELAG "Enable ParELAG" OFF)
 
 # Optional overrides for autodetected MPIEXEC and MPIEXEC_NUMPROC_FLAG
 # set(MFEM_MPIEXEC "mpirun" CACHE STRING "Command for running MPI tests")
@@ -78,7 +73,6 @@ set(MFEM_MPI_NP 4 CACHE STRING "Number of processes used for MPI tests")
 option(MFEM_ENABLE_TESTING "Enable the ctest framework for testing" ON)
 option(MFEM_ENABLE_EXAMPLES "Build all of the examples" OFF)
 option(MFEM_ENABLE_MINIAPPS "Build all of the miniapps" OFF)
-option(MFEM_ENABLE_GOOGLE_BENCHMARKS "Build all of the Google benchmarks" OFF)
 
 # Setting CXX/MPICXX on the command line or in user.cmake will overwrite the
 # autodetected C++ compiler.
@@ -102,11 +96,6 @@ 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.")
 
@@ -143,10 +132,10 @@ 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.")
@@ -198,12 +187,6 @@ 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.")
 
@@ -229,25 +212,12 @@ 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(BENCHMARK_DIR "${MFEM_DIR}/../google-benchmark" CACHE PATH
-    "Path to Google Benchmark")
-
-# Provide paths, since ParELAG is dependent on MFEM and MFEM needs to be
-# compiled (or at least cmake needs to succeed) before compiling ParELAG.
-set(PARELAG_DIR "${MFEM_DIR}/../parelag" CACHE PATH "Path to ParELAG")
-set(PARELAG_INCLUDE_DIRS "${PARELAG_DIR}/src;${PARELAG_DIR}/build/src" CACHE
-    STRING "Path to ParELAG headers.")
-set(PARELAG_LIBRARIES "${PARELAG_DIR}/build/src/libParELAG.a" CACHE STRING
-    "The ParELAG library.")
 
 set(BLAS_INCLUDE_DIRS "" CACHE STRING "Path to BLAS headers.")
 set(BLAS_LIBRARIES "" CACHE STRING "The BLAS library.")
 set(LAPACK_INCLUDE_DIRS "" CACHE STRING "Path to LAPACK headers.")
 set(LAPACK_LIBRARIES "" CACHE STRING "The LAPACK library.")
 
-set(CODIPACK_INCLUDE_DIRS "${MFEM_DIR}/../CoDiPack/inlude" CACHE STRING "Path to CoDiPack headers.")
-set(CODIPACK_LIBRARIES "")
-
 # Some useful variables:
 set(CMAKE_SKIP_PREPROCESSED_SOURCE_RULES ON) # Skip *.i rules
 set(CMAKE_SKIP_ASSEMBLY_SOURCE_RULES  ON)    # Skip *.s rules

config/defaults.mk

@@ -59,12 +59,9 @@ HIP_FLAGS = --amdgpu-target=$(HIP_ARCH)
 HIP_XCOMPILER =
 HIP_XLINKER   = -Wl,
 
-# Flags for generating dependencies.
-DEP_FLAGS = -MM -MT
-
 ifneq ($(NOTMAC),)
    AR      = ar
-   ARFLAGS = crv
+   ARFLAGS = cruv
    RANLIB  = ranlib
    PICFLAG = $(XCOMPILER)-fPIC
    SO_EXT  = so
@@ -76,7 +73,7 @@ ifneq ($(NOTMAC),)
 else
    # Silence "has no symbols" warnings on Mac OS X
    AR      = ar
-   ARFLAGS = Scrv
+   ARFLAGS = Scruv
    RANLIB  = ranlib -no_warning_for_no_symbols
    PICFLAG = $(XCOMPILER)-fPIC
    SO_EXT  = dylib
@@ -89,9 +86,6 @@ else
    BUILD_RPATH = $(XLINKER)-undefined,dynamic_lookup
    INSTALL_SOFLAGS = $(subst $1 ,,$(call MAKE_SOFLAGS,$(MFEM_LIB_DIR)))
    INSTALL_RPATH = $(XLINKER)-undefined,dynamic_lookup
-   # Silence unused command line argument warnings when generating dependencies
-   # with mpicxx and clang
-   DEP_FLAGS := -Wno-unused-command-line-argument $(DEP_FLAGS)
 endif
 
 # Set CXXFLAGS to overwrite the default selection of DEBUG_FLAGS/OPTIM_FLAGS
@@ -142,7 +136,6 @@ 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
@@ -157,10 +150,6 @@ MFEM_USE_UMPIRE        = NO
 MFEM_USE_SIMD          = NO
 MFEM_USE_ADIOS2        = NO
 MFEM_USE_MKL_CPARDISO  = NO
-MFEM_USE_ADFORWARD     = NO
-MFEM_USE_CODIPACK      = NO
-MFEM_USE_BENCHMARK     = NO
-MFEM_USE_PARELAG       = NO
 
 # MPI library compile and link flags
 # These settings are used only when building MFEM with MPI + HIP
@@ -185,10 +174,6 @@ 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)
@@ -372,11 +357,6 @@ 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$(CONDUIT_DIR)/include/conduit
@@ -416,11 +396,6 @@ HIOP_DIR = @MFEM_DIR@/../hiop/install
 HIOP_OPT = -I$(HIOP_DIR)/include
 HIOP_LIB = -L$(HIOP_DIR)/lib -lhiop $(LAPACK_LIB)
 
-# CoDiPack
-CODIPACK_DIR = @MFEM_DIR@/../CoDiPack
-CODIPACK_OPT = -I$(CODIPACK_DIR)
-CODIPACK_LIB =
-
 # GSLIB library
 GSLIB_DIR = @MFEM_DIR@/../gslib/build
 GSLIB_OPT = -I$(GSLIB_DIR)/include
@@ -428,7 +403,7 @@ GSLIB_LIB = -L$(GSLIB_DIR)/lib -lgs
 
 # CUDA library configuration
 CUDA_OPT =
-CUDA_LIB = -lcusparse -lnvToolsExt
+CUDA_LIB = -lcusparse
 
 # HIP library configuration (currently not needed)
 HIP_OPT =
@@ -444,11 +419,6 @@ CALIPER_DIR = @MFEM_DIR@/../caliper
 CALIPER_OPT = -I$(CALIPER_DIR)/include
 CALIPER_LIB = $(XLINKER)-rpath,$(CALIPER_DIR)/lib64 -L$(CALIPER_DIR)/lib64 -lcaliper
 
-# BENCHMARK library configuration
-BENCHMARK_DIR = @MFEM_DIR@/../google-benchmark
-BENCHMARK_OPT = -I$(BENCHMARK_DIR)/include
-BENCHMARK_LIB = -L$(BENCHMARK_DIR)/lib -lbenchmark -lpthread
-
 # libCEED library configuration
 CEED_DIR ?= @MFEM_DIR@/../libCEED
 CEED_OPT = -I$(CEED_DIR)/include
@@ -479,11 +449,6 @@ MKL_CPARDISO_LIB = $(XLINKER)-rpath,$(MKL_CPARDISO_DIR)/$(MKL_LIBRARY_SUBDIR)\
    -L$(MKL_CPARDISO_DIR)/$(MKL_LIBRARY_SUBDIR) -l$(MKL_MPI_WRAPPER)\
    -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
 
-# PARELAG library configuration
-PARELAG_DIR = @MFEM_DIR@/../parelag
-PARELAG_OPT = -I$(PARELAG_DIR)/src -I$(PARELAG_DIR)/build/src
-PARELAG_LIB = -L$(PARELAG_DIR)/build/src -lParELAG
-
 # If YES, enable some informational messages
 VERBOSE = NO
 

config/githooks/pre-push

@@ -87,12 +87,12 @@ fi
 ## style check
 #if [[ "${option}" == "--style" || "${option}" == "" ]]; then
 if [[ "${option}" == "--style" ]]; then
-  if which astyle && [[ "$(astyle --version)" == "Artistic Style Version 3.1" ]]; 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 3.1"
+    echo "Warning: astyle not found or version is not 2.05.1"
   fi
 fi
 

config/test.mk

@@ -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

data/inline-pyramid.mesh

@@ -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

data/octahedron.mesh

@@ -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

data/ref-pyramid.mesh

@@ -1,38 +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
-1
-1 7 0 1 2 3 4
-
-boundary
-5
-1 3 3 2 1 0
-2 2 0 1 4
-3 2 1 2 4
-4 2 2 3 4
-5 2 3 0 4
-
-vertices
-5
-3
-0 0 0
-1 0 0
-1 1 0
-0 1 0
-0 0 1

data/star-q3.fms

@@ -1,246 +0,0 @@
-FMS: 100
-DataCollection/Name: star
-DataCollection/NumberOfFieldDescriptors: 1
-DataCollection/FieldDescriptors/0/Name: CoordsDescriptor
-DataCollection/FieldDescriptors/0/ComponentName: volume
-DataCollection/FieldDescriptors/0/Type: 0
-DataCollection/FieldDescriptors/0/FixedOrder/Size: 3
-DataCollection/FieldDescriptors/0/FixedOrder/Type: FMS_UINT64
-DataCollection/FieldDescriptors/0/FixedOrder/Values: [0, 1, 3]
-DataCollection/FieldDescriptors/0/NumDofs: 211
-DataCollection/NumberOfFields: 1
-DataCollection/Fields/0/Name: Coords
-DataCollection/Fields/0/LayoutType: 0
-DataCollection/Fields/0/NumberOfVectorComponents: 2
-DataCollection/Fields/0/FieldDescriptorName: CoordsDescriptor
-DataCollection/Fields/0/Data/Size: 422
-DataCollection/Fields/0/Data/Type: FMS_DOUBLE
-DataCollection/Fields/0/Data/Values: [-0.016886, 1.000000, 0.309017, 
-1.309020, -0.809017, -0.500000, 
--0.809017, -1.618030, 0.309017, 
--0.500000, 1.309020, 0.519420, 
-1.154510, 0.809019, 0.147680, 
--0.095492, -0.654508, -0.415586, 
--1.213520, -1.213520, -0.392210, 
--0.654508, -0.095492, 0.139949, 
-0.809019, 1.154510, 0.660184, 
--0.264063, -0.800064, -0.231060, 
-0.663691, 0.183114, 0.317639, 
-0.543082, 0.598483, 0.345112, 
-0.478298, 0.027703, 0.095229, 
-0.012368, -0.092534, -0.334412, 
--0.313767, -0.140526, -0.293881, 
--0.534056, -0.660290, -0.537646, 
--0.655590, -0.121396, -0.274504, 
--0.346497, -0.296570, 0.004737, 
--0.098835, 0.069287, 0.082675, 
-0.318799, 0.467183, 0.564505, 
-0.595190, 0.846237, 0.671735, 
-1.051500, 1.103010, 0.964008, 
-0.821603, 1.257520, 1.206010, 
-1.142350, 0.975686, 0.781273, 
-0.717257, 0.475684, 0.642352, 
-0.268930, 0.211049, 0.174181, 
-0.039345, -0.147746, -0.177481, 
--0.365164, -0.230328, -0.551503, 
--0.603005, -0.497587, -0.389864, 
--0.757514, -0.706011, -0.675487, 
--0.528946, -0.943851, -1.078690, 
--1.087600, -0.955467, -1.483190, 
--1.348360, -1.483190, -1.348360, 
--1.085930, -0.938010, -0.943851, 
--1.078690, -0.681476, -0.540944, 
--0.757514, -0.706011, -0.540614, 
--0.367058, -0.551503, -0.603005, 
--0.365164, -0.230328, -0.138552, 
--0.206896, 0.174181, 0.039345, 
-0.268468, 0.222269, 0.475684, 
-0.642352, 0.759791, 0.719381, 
-1.142350, 0.975686, 1.257520, 
-1.206010, 0.972837, 0.836119, 
-1.051500, 1.103010, 0.214572, 
-0.407449, 0.288323, 0.449827, 
--0.086700, -0.027358, -0.200560, 
--0.166595, -0.271802, -0.418426, 
--0.426131, -0.551441, -0.096117, 
--0.206969, -0.027946, -0.184969, 
-0.211136, 0.260131, 0.407172, 
-0.430781, 0.718277, 0.885068, 
-0.753103, 0.957692, 0.866273, 
-1.024530, 0.934099, 1.093820, 
-0.348422, 0.524463, 0.404903, 
-0.587376, 0.054525, 0.146431, 
--0.078026, -0.007795, -0.329488, 
--0.302967, -0.488115, -0.439332, 
--0.498515, -0.453527, -0.633059, 
--0.570251, -0.655787, -0.791132, 
--0.802013, -0.956872, -1.094720, 
--1.208560, -1.207720, -1.339910, 
--0.693371, -0.795404, -0.803594, 
--0.945068, -0.464668, -0.631721, 
--0.458968, -0.547876, -0.332878, 
--0.485696, -0.286385, -0.408481, 
-0.053021, -0.058200, 0.110846, 
--0.002086, 0.381384, 0.416784, 
-0.551133, 0.613261, 0.872474, 
-0.901208, 1.038300, 1.084660, 
-0.737459, 0.751250, 0.890002, 
-0.915210, 0.010915, 0.000000, 
-0.951057, 0.951057, 0.587785, 
-1.538840, -0.587785, 0.000000, 
--0.951057, -1.538840, -0.951057, 
--0.015847, 0.475529, 0.951057, 
-0.492248, 1.244950, 1.063310, 
-0.274399, 0.293893, -0.293892, 
--0.296404, -1.063310, -1.244950, 
--0.453865, -0.951057, -0.475529, 
-0.466620, 0.792932, -0.013913, 
--0.748783, -0.497528, 0.021382, 
--0.017158, 0.172591, 0.330125, 
-0.458568, 0.457971, 0.137740, 
-0.299049, 0.588394, 0.667324, 
-0.432341, 0.634346, 0.117322, 
-0.193603, 0.211702, 0.098278, 
--0.199438, -0.077304, -0.082243, 
--0.216296, -0.458634, -0.592374, 
--0.563926, -0.680404, -0.135751, 
--0.302942, -0.469005, -0.453640, 
--0.182727, -0.314240, 0.024270, 
-0.021546, 0.158510, 0.317019, 
-0.485799, 0.492951, 0.792548, 
-0.634038, 0.951057, 0.951057, 
-0.777915, 0.613430, 0.951057, 
-0.951057, 0.793994, 0.635800, 
-1.049020, 1.146990, 1.084480, 
-0.924310, 1.440880, 1.342910, 
-1.380330, 1.221820, 0.948209, 
-0.856297, 0.746293, 0.904802, 
-0.476242, 0.393234, 0.489821, 
-0.391857, 0.194471, 0.075751, 
-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

doc/CodeDocumentation.conf.in

@@ -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
@@ -765,7 +765,6 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/linalg \
                          @MFEM_SOURCE_DIR@/mesh \
                          @MFEM_SOURCE_DIR@/fem \
-                         @MFEM_SOURCE_DIR@/fem/fe \
                          @MFEM_SOURCE_DIR@/examples \
                          @MFEM_SOURCE_DIR@/examples/caliper \
                          @MFEM_SOURCE_DIR@/examples/amgx \
@@ -781,15 +780,13 @@ INPUT                  = @MFEM_SOURCE_DIR@/doc/CodeDocumentation.dox \
                          @MFEM_SOURCE_DIR@/miniapps/gslib \
                          @MFEM_SOURCE_DIR@/miniapps/meshing \
                          @MFEM_SOURCE_DIR@/miniapps/mtop \
-                         @MFEM_SOURCE_DIR@/miniapps/autodiff \
                          @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 \
-                         @MFEM_SOURCE_DIR@/miniapps/parelag
+                         @MFEM_SOURCE_DIR@/miniapps/toys
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

doc/CodeDocumentation.dox

@@ -194,8 +194,6 @@ namespace mfem {
  * - <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
- * - <a class="el" href="par__example_8cpp_source.html">Parallel pLaplacian example using AD</a>: Parallel pLaplacian example
- * - <a class="el" href="seq__example_8cpp_source.html">Serial pLaplacian example using AD</a>: Serial pLaplacian example
  *
  * See also the <a class="el" href="https://mfem.org/examples/">examples documentation</a> online.
  */

examples/CMakeLists.txt

@@ -37,7 +37,6 @@ list(APPEND ALL_EXE_SRCS
   ex27.cpp
   ex28.cpp
   ex29.cpp
-  ex30.cpp
   )
 
 if (MFEM_USE_MPI)
@@ -71,7 +70,6 @@ if (MFEM_USE_MPI)
     ex27p.cpp
     ex28p.cpp
     ex29p.cpp
-    ex30p.cpp
     )
 endif()
 
@@ -82,80 +80,49 @@ include_directories(BEFORE ${PROJECT_BINARY_DIR})
 add_mfem_examples(ALL_EXE_SRCS)
 
 # Add a test for each example
-if (MFEM_ENABLE_TESTING)
-  foreach(SRC_FILE ${ALL_EXE_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+foreach(SRC_FILE ${ALL_EXE_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
 
+  if (NOT (${TEST_NAME} MATCHES "ex0p?"))
     set(THIS_TEST_OPTIONS "-no-vis")
-    if (${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*")
-      list(APPEND THIS_TEST_OPTIONS "-e" "1")
-    elseif(${TEST_NAME} MATCHES "ex27p*")
-      list(APPEND THIS_TEST_OPTIONS "-dg")
-    endif()
-
-    if (NOT (${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()
-
-  # 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}
-          ${MPIEXEC_POSTFLAGS})
-      endif()
-    endforeach()
+  if (${TEST_NAME} MATCHES "ex10p*")
+    list(APPEND THIS_TEST_OPTIONS "-tf" "5")
+  elseif(${TEST_NAME} MATCHES "ex15p*")
+    list(APPEND THIS_TEST_OPTIONS "-e" "1")
+  elseif(${TEST_NAME} MATCHES "ex27p*")
+    list(APPEND THIS_TEST_OPTIONS "-dg")
   endif()
 
-  # If STRUMPACK is enabled, add a test run that uses it.
-  if (MFEM_USE_STRUMPACK)
-    add_test(NAME ex11p_strumpack_np=${MFEM_MPI_NP}
+  if (NOT (${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:ex11p> "-no-vis" "--strumpack"
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
       ${MPIEXEC_POSTFLAGS})
   endif()
+endforeach()
 
-  # If SuperLU_DIST is enabled, add a test run that uses it.
-  if (MFEM_USE_SUPERLU)
-    add_test(NAME ex11p_superlu_np=${MFEM_MPI_NP}
-      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-      ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:ex11p> "-no-vis" "--superlu"
-      ${MPIEXEC_POSTFLAGS})
-  endif()
+# If STRUMPACK is enabled, add a test run that uses it.
+if (MFEM_USE_STRUMPACK)
+  add_test(NAME ex11p_strumpack_np=${MFEM_MPI_NP}
+    COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+    ${MPIEXEC_PREFLAGS}
+    $<TARGET_FILE:ex11p> "-no-vis" "--strumpack"
+    ${MPIEXEC_POSTFLAGS})
+endif()
+
+# If SuperLU_DIST is enabled, add a test run that uses it.
+if (MFEM_USE_SUPERLU)
+  add_test(NAME ex11p_superlu_np=${MFEM_MPI_NP}
+    COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+    ${MPIEXEC_PREFLAGS}
+    $<TARGET_FILE:ex11p> "-no-vis" "--superlu"
+    ${MPIEXEC_POSTFLAGS})
 endif()
 
 # Include the examples/amgx directory if AmgX is enabled

examples/amgx/CMakeLists.txt

@@ -50,32 +50,30 @@ add_mfem_examples(AMGX_EXAMPLES_SRCS ${PFX} copy_amgx_json_files test_amgx)
 # which builds the examples and runs:
 #   ctest -R amgx
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  # Example 1/1p:
-  set(EX1_TEST_OPTS)
-  set(EX1P_TEST_OPTS)
+# Command line options for the tests.
+# Example 1/1p:
+set(EX1_TEST_OPTS)
+set(EX1P_TEST_OPTS)
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${AMGX_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${AMGX_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    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}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  if (NOT (${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()

examples/caliper/CMakeLists.txt

@@ -30,22 +30,22 @@ set(PREFIX caliper_)
 add_mfem_examples(CALIPER_EXE_SRCS ${PREFIX})
 
 # Add a test for each example
-if (MFEM_ENABLE_TESTING)
-  foreach(SRC_FILE ${CALIPER_EXE_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+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()
 
-    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()
-endif()

examples/caliper/README

@@ -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.

examples/caliper/ex1.cpp

@@ -206,9 +206,9 @@ int main(int argc, char *argv[])
    cout << "Size of linear system: " << A->Height() << endl;
 
    // 11. Solve the linear system A X = B.
+   MFEM_PERF_BEGIN("Solve 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));
@@ -223,7 +223,6 @@ int main(int argc, char *argv[])
    }
    else // Jacobi preconditioning in partial assembly mode
    {
-      MFEM_PERF_SCOPE("Solve A X=B (PA)");
       if (UsesTensorBasis(fespace))
       {
          OperatorJacobiSmoother M(a, ess_tdof_list);
@@ -234,6 +233,7 @@ int main(int argc, char *argv[])
          CG(*A, B, X, 1, 400, 1e-12, 0.0);
       }
    }
+   MFEM_PERF_END("Solve A X=B");
    // 12. Recover the solution as a finite element grid function.
    a.RecoverFEMSolution(X, b, x);
 

examples/caliper/ex1p.cpp

@@ -231,29 +231,28 @@ int main(int argc, char *argv[])
    // 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_BEGIN("Solve A X = B");
+   Solver *prec = NULL;
+   if (pa)
    {
-      MFEM_PERF_SCOPE("Solve A X=B");
-      Solver *prec = NULL;
-      if (pa)
+      if (UsesTensorBasis(fespace))
       {
-         if (UsesTensorBasis(fespace))
-         {
-            prec = new OperatorJacobiSmoother(a, ess_tdof_list);
-         }
+         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;
    }
+   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;
+   MFEM_PERF_END("Solve A X = B");
    // 14. Recover the parallel grid function corresponding to X. This is the
    //     local finite element solution on each processor.
    a.RecoverFEMSolution(X, b, x);

examples/ex1.cpp

@@ -9,7 +9,6 @@
 //               ex1 -m ../data/fichera.mesh
 //               ex1 -m ../data/fichera-mixed.mesh
 //               ex1 -m ../data/toroid-wedge.mesh
-//               ex1 -m ../data/octahedron.mesh -o 1
 //               ex1 -m ../data/periodic-annulus-sector.msh
 //               ex1 -m ../data/periodic-torus-sector.msh
 //               ex1 -m ../data/square-disc-p2.vtk -o 2
@@ -120,8 +119,8 @@ int main(int argc, char *argv[])
    //    largest number that gives a final mesh with no more than 50,000
    //    elements.
    {
-      const int NE = Device::IsEnabled() ? 1e5 : 50000.;
-      const int ref_levels = (int)floor(log(NE/mesh.GetNE())/log(2.)/dim);
+      int ref_levels =
+         (int)floor(log(50000./mesh.GetNE())/log(2.)/dim);
       for (int l = 0; l < ref_levels; l++)
       {
          mesh.UniformRefinement();
@@ -171,7 +170,6 @@ int main(int argc, char *argv[])
    LinearForm b(&fespace);
    ConstantCoefficient one(1.0);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   if (Device::IsEnabled()) { b.SetAssemblyLevel(LinearAssemblyLevel::FULL); }
    b.Assemble();
 
    // 8. Define the solution vector x as a finite element grid function
@@ -185,10 +183,7 @@ int main(int argc, char *argv[])
    //    domain integrator.
    BilinearForm a(&fespace);
    if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
-   // 'Default' E2E kernel
-   //a.AddDomainIntegrator(new DiffusionIntegrator(one));
-   // Can be E2E, L2L, libCeed, etc.
-   a.AddDomainIntegrator(new MassIntegrator(one));
+   a.AddDomainIntegrator(new DiffusionIntegrator(one));
 
    // 10. Assemble the bilinear form and the corresponding linear system,
    //     applying any necessary transformations such as: eliminating boundary
@@ -201,7 +196,7 @@ int main(int argc, char *argv[])
    Vector B, X;
    a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);
 
-   //cout << "Size of linear system: " << A->Height() << endl;
+   cout << "Size of linear system: " << A->Height() << endl;
 
    // 11. Solve the linear system A X = B.
    if (!pa)
@@ -227,70 +222,10 @@ int main(int argc, char *argv[])
             ceed::AlgebraicSolver M(a, ess_tdof_list);
             PCG(*A, M, B, X, 1, 400, 1e-12, 0.0);
          }
-         /*else
+         else
          {
             OperatorJacobiSmoother M(a, ess_tdof_list);
             PCG(*A, M, B, X, 1, 400, 1e-12, 0.0);
-         }*/
-         else
-         {
-            const int myid = 0;
-            const int max_it = 50;
-            const int print_lvl = -1;
-            const double rtol = 1e-12;
-
-            CGSolver cg;
-            cg.SetRelTol(rtol);
-            cg.SetOperator(*A);
-
-            // Warm-up CG solve (in case of JIT to avoid timing it)
-            {
-               Vector Y(X);
-               cg.SetMaxIter(2);
-               cg.SetPrintLevel(-1);
-               cg.Mult(B, Y);
-               MFEM_DEVICE_SYNC;
-            }
-
-            // benchmark this problem
-            {
-               tic_toc.Clear();
-               cg.SetMaxIter(max_it);
-               cg.SetPrintLevel(print_lvl);
-               {
-                  tic_toc.Start();
-                  cg.Mult(B, X);
-                  MFEM_DEVICE_SYNC;
-                  tic_toc.Stop();
-               }
-            }
-            // Final norm check
-            const double final_norm = cg.GetFinalNorm();
-            MFEM_VERIFY(final_norm < sqrt(rtol),
-                        "FinalNorm (" << final_norm << ") Error!");
-            // Number of iteration check
-            const int num_iter = cg.GetNumIterations();
-            MFEM_VERIFY(num_iter <= max_it,
-                        "NumIterations (" << num_iter << ") Error!");
-
-            const double rt = tic_toc.RealTime();
-            const double rt_min = rt, rt_max = rt;
-            const int dofs = fespace.GetVSize();
-            const int cg_iter = cg.GetNumIterations();
-            const double mdofs_max = ((1e-6 * dofs) * cg_iter) / rt_max;
-            const double mdofs_min = ((1e-6 * dofs) * cg_iter) / rt_min;
-            if (myid == 0)
-            {
-               mfem::out << "Total CG time:    " << rt_max << " (" << rt_min << ") sec."
-                         << std::endl;
-               mfem::out << "Time per CG step: "
-                         << rt_max / cg_iter << " ("
-                         << rt_min / cg_iter << ") sec." << std::endl;
-               mfem::out << "\033[32m";
-               mfem::out << "\"DOFs/sec\" in CG: " << mdofs_max << " ("
-                         << mdofs_min << ") million.";
-               mfem::out << "\033[m" << std::endl;
-            }
          }
       }
       else

examples/ex10.cpp

@@ -149,7 +149,7 @@ void InitialDeformation(const Vector &x, Vector &y);
 
 void InitialVelocity(const Vector &x, Vector &v);
 
-void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
+void visualize(ostream &out, Mesh *mesh, GridFunction *deformed_nodes,
                GridFunction *field, const char *field_name = NULL,
                bool init_vis = false);
 
@@ -376,10 +376,10 @@ int main(int argc, char *argv[])
 }
 
 
-void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
+void visualize(ostream &out, Mesh *mesh, GridFunction *deformed_nodes,
                GridFunction *field, const char *field_name, bool init_vis)
 {
-   if (!os)
+   if (!out)
    {
       return;
    }
@@ -389,25 +389,24 @@ void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
 
    mesh->SwapNodes(nodes, owns_nodes);
 
-   os << "solution\n" << *mesh << *field;
+   out << "solution\n" << *mesh << *field;
 
    mesh->SwapNodes(nodes, owns_nodes);
 
    if (init_vis)
    {
-      os << "window_size 800 800\n";
-      os << "window_title '" << field_name << "'\n";
+      out << "window_size 800 800\n";
+      out << "window_title '" << field_name << "'\n";
       if (mesh->SpaceDimension() == 2)
       {
-         os << "view 0 0\n"; // view from top
-         os << "keys jl\n";  // turn off perspective and light
+         out << "view 0 0\n"; // view from top
+         out << "keys jl\n";  // turn off perspective and light
       }
-      os << "keys cm\n";         // show colorbar and mesh
-      // update value-range; keep mesh-extents fixed
-      os << "autoscale value\n";
-      os << "pause\n";
+      out << "keys cm\n";         // show colorbar and mesh
+      out << "autoscale value\n"; // update value-range; keep mesh-extents fixed
+      out << "pause\n";
    }
-   os << flush;
+   out << flush;
 }
 
 

examples/ex10p.cpp

@@ -154,8 +154,7 @@ void InitialDeformation(const Vector &x, Vector &y);
 
 void InitialVelocity(const Vector &x, Vector &v);
 
-void visualize(ostream &os, ParMesh *mesh,
-               ParGridFunction *deformed_nodes,
+void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
                ParGridFunction *field, const char *field_name = NULL,
                bool init_vis = false);
 
@@ -439,11 +438,10 @@ int main(int argc, char *argv[])
    return 0;
 }
 
-void visualize(ostream &os, ParMesh *mesh,
-               ParGridFunction *deformed_nodes,
+void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
                ParGridFunction *field, const char *field_name, bool init_vis)
 {
-   if (!os)
+   if (!out)
    {
       return;
    }
@@ -453,27 +451,25 @@ void visualize(ostream &os, ParMesh *mesh,
 
    mesh->SwapNodes(nodes, owns_nodes);
 
-   os << "parallel " << mesh->GetNRanks()
-      << " " << mesh->GetMyRank() << "\n";
-   os << "solution\n" << *mesh << *field;
+   out << "parallel " << mesh->GetNRanks() << " " << mesh->GetMyRank() << "\n";
+   out << "solution\n" << *mesh << *field;
 
    mesh->SwapNodes(nodes, owns_nodes);
 
    if (init_vis)
    {
-      os << "window_size 800 800\n";
-      os << "window_title '" << field_name << "'\n";
+      out << "window_size 800 800\n";
+      out << "window_title '" << field_name << "'\n";
       if (mesh->SpaceDimension() == 2)
       {
-         os << "view 0 0\n"; // view from top
-         os << "keys jl\n";  // turn off perspective and light
+         out << "view 0 0\n"; // view from top
+         out << "keys jl\n";  // turn off perspective and light
       }
-      os << "keys cm\n";         // show colorbar and mesh
-      // update value-range; keep mesh-extents fixed
-      os << "autoscale value\n";
-      os << "pause\n";
+      out << "keys cm\n";         // show colorbar and mesh
+      out << "autoscale value\n"; // update value-range; keep mesh-extents fixed
+      out << "pause\n";
    }
-   os << flush;
+   out << flush;
 }
 
 

examples/ex13p.cpp

@@ -55,7 +55,6 @@ int main(int argc, char *argv[])
    int order = 1;
    int nev = 5;
    bool visualization = 1;
-   const char *device_config = "cpu";
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
@@ -72,8 +71,6 @@ int main(int argc, char *argv[])
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                   "--no-visualization",
                   "Enable or disable GLVis visualization.");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.Parse();
    if (!args.Good())
    {
@@ -89,18 +86,13 @@ int main(int argc, char *argv[])
       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(); }
-
-   // 4. Read the (serial) mesh from the given mesh file on all processors. We
+   // 3. 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 = new Mesh(mesh_file, 1, 1);
    int dim = mesh->Dimension();
 
-   // 5. Refine the serial mesh on all processors to increase the resolution. In
+   // 4. Refine the serial mesh on all processors to increase the resolution. In
    //    this example we do 'ref_levels' of uniform refinement (2 by default, or
    //    specified on the command line with -rs).
    for (int lev = 0; lev < ser_ref_levels; lev++)
@@ -108,7 +100,7 @@ int main(int argc, char *argv[])
       mesh->UniformRefinement();
    }
 
-   // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
+   // 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
    //    this mesh further in parallel to increase the resolution (1 time by
    //    default, or specified on the command line with -rp). Once the parallel
    //    mesh is defined, the serial mesh can be deleted.
@@ -118,8 +110,9 @@ int main(int argc, char *argv[])
    {
       pmesh->UniformRefinement();
    }
+   pmesh->ReorientTetMesh();
 
-   // 7. Define a parallel finite element space on the parallel mesh. Here we
+   // 6. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Nedelec finite elements of the specified order.
    FiniteElementCollection *fec = new ND_FECollection(order, dim);
    ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
@@ -129,7 +122,7 @@ int main(int argc, char *argv[])
       cout << "Number of unknowns: " << size << endl;
    }
 
-   // 8. Set up the parallel bilinear forms a(.,.) and m(.,.) on the finite
+   // 7. Set up the parallel bilinear forms a(.,.) and m(.,.) on the finite
    //    element space. The first corresponds to the curl curl, while the second
    //    is a simple mass matrix needed on the right hand side of the
    //    generalized eigenvalue problem below. The boundary conditions are
@@ -171,7 +164,7 @@ int main(int argc, char *argv[])
    delete a;
    delete m;
 
-   // 9. Define and configure the AME eigensolver and the AMS preconditioner for
+   // 8. Define and configure the AME eigensolver and the AMS preconditioner for
    //    A to be used within the solver. Set the matrices which define the
    //    generalized eigenproblem A x = lambda M x.
    HypreAMS *ams = new HypreAMS(*A,fespace);
@@ -187,15 +180,15 @@ int main(int argc, char *argv[])
    ame->SetMassMatrix(*M);
    ame->SetOperator(*A);
 
-   // 10. Compute the eigenmodes and extract the array of eigenvalues. Define a
-   //     parallel grid function to represent each of the eigenmodes returned by
-   //     the solver.
+   // 9. Compute the eigenmodes and extract the array of eigenvalues. Define a
+   //    parallel grid function to represent each of the eigenmodes returned by
+   //    the solver.
    Array<double> eigenvalues;
    ame->Solve();
    ame->GetEigenvalues(eigenvalues);
    ParGridFunction x(fespace);
 
-   // 11. Save the refined mesh and the modes in parallel. This output can be
+   // 10. Save the refined mesh and the modes in parallel. This output can be
    //     viewed later using GLVis: "glvis -np <np> -m mesh -g mode".
    {
       ostringstream mesh_name, mode_name;
@@ -220,7 +213,7 @@ int main(int argc, char *argv[])
       }
    }
 
-   // 12. Send the solution by socket to a GLVis server.
+   // 11. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -260,7 +253,7 @@ int main(int argc, char *argv[])
       mode_sock.close();
    }
 
-   // 13. Free the used memory.
+   // 12. Free the used memory.
    delete ame;
    delete ams;
    delete M;

examples/ex14.cpp

@@ -135,8 +135,8 @@ int main(int argc, char *argv[])
    a->AddBdrFaceIntegrator(new DGDiffusionIntegrator(one, sigma, kappa));
    if (eta > 0)
    {
-      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
-      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
+      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
+      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
    }
    a->Assemble();
    a->Finalize();

examples/ex14p.cpp

@@ -199,8 +199,8 @@ int main(int argc, char *argv[])
    a->AddBdrFaceIntegrator(new DGDiffusionIntegrator(one, sigma, kappa));
    if (eta > 0)
    {
-      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
-      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(*fespace, eta));
+      a->AddInteriorFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
+      a->AddBdrFaceIntegrator(new DGDiffusionBR2Integrator(fespace, eta));
    }
    a->Assemble();
    a->Finalize();
@@ -221,7 +221,7 @@ int main(int argc, char *argv[])
    {
       HyprePCG pcg(*A);
       pcg.SetTol(1e-12);
-      pcg.SetMaxIter(500);
+      pcg.SetMaxIter(200);
       pcg.SetPrintLevel(2);
       pcg.SetPreconditioner(*amg);
       pcg.Mult(*B, *X);
@@ -232,7 +232,7 @@ int main(int argc, char *argv[])
       GMRESSolver gmres(MPI_COMM_WORLD);
       gmres.SetAbsTol(0.0);
       gmres.SetRelTol(1e-12);
-      gmres.SetMaxIter(500);
+      gmres.SetMaxIter(200);
       gmres.SetKDim(10);
       gmres.SetPrintLevel(1);
       gmres.SetOperator(*A);

examples/ex16.cpp

@@ -24,10 +24,7 @@
 //               class ConductionOperator defining C(u)), as well as their
 //               implicit time integration. Note that implementing the method
 //               ConductionOperator::ImplicitSolve is the only requirement for
-//               high-order implicit (SDIRK) time integration. In this example,
-//               the diffusion operator is linearized by evaluating with the
-//               lagged solution from the previous timestep, so there is only
-//               a linear solve.
+//               high-order implicit (SDIRK) time integration.
 //
 //               We recommend viewing examples 2, 9 and 10 before viewing this
 //               example.
@@ -329,8 +326,8 @@ ConductionOperator::ConductionOperator(FiniteElementSpace &f, double al,
 void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
 {
    // Compute:
-   //    du_dt = M^{-1}*-Ku
-   // for du_dt, where K is linearized by using u from the previous timestep
+   //    du_dt = M^{-1}*-K(u)
+   // for du_dt
    Kmat.Mult(u, z);
    z.Neg(); // z = -z
    M_solver.Mult(z, du_dt);
@@ -341,7 +338,7 @@ void ConductionOperator::ImplicitSolve(const double dt,
 {
    // Solve the equation:
    //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
-   // for du_dt, where K is linearized by using u from the previous timestep
+   // for du_dt
    if (!T)
    {
       T = Add(1.0, Mmat, dt, Kmat);

examples/ex16p.cpp

@@ -24,11 +24,8 @@
 //               class ConductionOperator defining C(u)), as well as their
 //               implicit time integration. Note that implementing the method
 //               ConductionOperator::ImplicitSolve is the only requirement for
-//               high-order implicit (SDIRK) time integration. In this example,
-//               the diffusion operator is linearized by evaluating with the
-//               lagged solution from the previous timestep, so there is only
-//               a linear solve. Optional saving with ADIOS2
-//               (adios2.readthedocs.io) is also illustrated.
+//               high-order implicit (SDIRK) time integration. Optional saving
+//               with ADIOS2 (adios2.readthedocs.io) is also illustrated.
 //
 //               We recommend viewing examples 2, 9 and 10 before viewing this
 //               example.
@@ -423,8 +420,8 @@ ConductionOperator::ConductionOperator(ParFiniteElementSpace &f, double al,
 void ConductionOperator::Mult(const Vector &u, Vector &du_dt) const
 {
    // Compute:
-   //    du_dt = M^{-1}*-Ku
-   // for du_dt, where K is linearized by using u from the previous timestep
+   //    du_dt = M^{-1}*-K(u)
+   // for du_dt
    Kmat.Mult(u, z);
    z.Neg(); // z = -z
    M_solver.Mult(z, du_dt);
@@ -435,7 +432,7 @@ void ConductionOperator::ImplicitSolve(const double dt,
 {
    // Solve the equation:
    //    du_dt = M^{-1}*[-K(u + dt*du_dt)]
-   // for du_dt, where K is linearized by using u from the previous timestep
+   // for du_dt
    if (!T)
    {
       T = Add(1.0, Mmat, dt, Kmat);

examples/ex18.hpp

@@ -32,7 +32,7 @@ private:
    mutable DenseTensor flux;
    mutable Vector z;
 
-   void GetFlux(const DenseMatrix &state_, DenseTensor &flux_) const;
+   void GetFlux(const DenseMatrix &state, DenseTensor &flux) const;
 
 public:
    FE_Evolution(FiniteElementSpace &vfes_,
@@ -256,26 +256,26 @@ inline double ComputeMaxCharSpeed(const Vector &state, const int dim)
 }
 
 // Compute the flux at solution nodes.
-void FE_Evolution::GetFlux(const DenseMatrix &x_, DenseTensor &flux_) const
+void FE_Evolution::GetFlux(const DenseMatrix &x, DenseTensor &flux) const
 {
-   const int flux_dof = flux_.SizeI();
-   const int flux_dim = flux_.SizeJ();
+   const int dof = flux.SizeI();
+   const int dim = flux.SizeJ();
 
-   for (int i = 0; i < flux_dof; i++)
+   for (int i = 0; i < dof; i++)
    {
-      for (int k = 0; k < num_equation; k++) { state(k) = x_(i, k); }
-      ComputeFlux(state, flux_dim, f);
+      for (int k = 0; k < num_equation; k++) { state(k) = x(i, k); }
+      ComputeFlux(state, dim, f);
 
-      for (int d = 0; d < flux_dim; d++)
+      for (int d = 0; d < dim; d++)
       {
          for (int k = 0; k < num_equation; k++)
          {
-            flux_(i, d, k) = f(k, d);
+            flux(i, d, k) = f(k, d);
          }
       }
 
       // Update max char speed
-      const double mcs = ComputeMaxCharSpeed(state, flux_dim);
+      const double mcs = ComputeMaxCharSpeed(state, dim);
       if (mcs > max_char_speed) { max_char_speed = mcs; }
    }
 }

examples/ex19.cpp

@@ -171,7 +171,7 @@ public:
 };
 
 // Visualization driver
-void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
+void visualize(ostream &out, Mesh *mesh, GridFunction *deformed_nodes,
                GridFunction *field, const char *field_name = NULL,
                bool init_vis = false);
 
@@ -542,10 +542,10 @@ RubberOperator::~RubberOperator()
 
 
 // Inline visualization
-void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
+void visualize(ostream &out, Mesh *mesh, GridFunction *deformed_nodes,
                GridFunction *field, const char *field_name, bool init_vis)
 {
-   if (!os)
+   if (!out)
    {
       return;
    }
@@ -555,25 +555,23 @@ void visualize(ostream &os, Mesh *mesh, GridFunction *deformed_nodes,
 
    mesh->SwapNodes(nodes, owns_nodes);
 
-   os << "solution\n" << *mesh << *field;
+   out << "solution\n" << *mesh << *field;
 
    mesh->SwapNodes(nodes, owns_nodes);
 
    if (init_vis)
    {
-      os << "window_size 800 800\n";
-      os << "window_title '" << field_name << "'\n";
+      out << "window_size 800 800\n";
+      out << "window_title '" << field_name << "'\n";
       if (mesh->SpaceDimension() == 2)
       {
-         os << "view 0 0\n"; // view from top
-         // turn off perspective and light, +anti-aliasing
-         os << "keys jlA\n";
+         out << "view 0 0\n"; // view from top
+         out << "keys jlA\n"; // turn off perspective and light, +anti-aliasing
       }
-      os << "keys cmA\n"; // show colorbar and mesh, +anti-aliasing
-      // update value-range; keep mesh-extents fixed
-      os << "autoscale value\n";
+      out << "keys cmA\n";        // show colorbar and mesh, +anti-aliasing
+      out << "autoscale value\n"; // update value-range; keep mesh-extents fixed
    }
-   os << flush;
+   out << flush;
 }
 
 void ReferenceConfiguration(const Vector &x, Vector &y)

examples/ex19p.cpp

@@ -185,8 +185,7 @@ public:
 };
 
 // Visualization driver
-void visualize(ostream &os, ParMesh *mesh,
-               ParGridFunction *deformed_nodes,
+void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
                ParGridFunction *field, const char *field_name = NULL,
                bool init_vis = false);
 
@@ -197,12 +196,6 @@ void InitialDeformation(const Vector &x, Vector &y);
 
 int main(int argc, char *argv[])
 {
-#ifdef HYPRE_USING_CUDA
-   cout << "\nAs of mfem-4.3 and hypre-2.22.0 (July 2021) this example\n"
-        << "is NOT supported with the CUDA version of hypre.\n\n";
-   return 255;
-#endif
-
    // 1. Initialize MPI
    MPI_Session mpi;
    const int myid = mpi.WorldRank();
@@ -445,19 +438,15 @@ JacobianPreconditioner::JacobianPreconditioner(Array<ParFiniteElementSpace *>
 void JacobianPreconditioner::Mult(const Vector &k, Vector &y) const
 {
    // Extract the blocks from the input and output vectors
-   Vector disp_in;
-   disp_in.MakeRef(const_cast<Vector&>(k), block_trueOffsets[0],
-                   block_trueOffsets[1]-block_trueOffsets[0]);
-   Vector pres_in;
-   pres_in.MakeRef(const_cast<Vector&>(k), block_trueOffsets[1],
-                   block_trueOffsets[2]-block_trueOffsets[1]);
+   Vector disp_in(k.GetData() + block_trueOffsets[0],
+                  block_trueOffsets[1]-block_trueOffsets[0]);
+   Vector pres_in(k.GetData() + block_trueOffsets[1],
+                  block_trueOffsets[2]-block_trueOffsets[1]);
 
-   Vector disp_out;
-   disp_out.MakeRef(y, block_trueOffsets[0],
-                    block_trueOffsets[1]-block_trueOffsets[0]);
-   Vector pres_out;
-   pres_out.MakeRef(y, block_trueOffsets[1],
-                    block_trueOffsets[2]-block_trueOffsets[1]);
+   Vector disp_out(y.GetData() + block_trueOffsets[0],
+                   block_trueOffsets[1]-block_trueOffsets[0]);
+   Vector pres_out(y.GetData() + block_trueOffsets[1],
+                   block_trueOffsets[2]-block_trueOffsets[1]);
 
    Vector temp(block_trueOffsets[1]-block_trueOffsets[0]);
    Vector temp2(block_trueOffsets[1]-block_trueOffsets[0]);
@@ -470,9 +459,6 @@ void JacobianPreconditioner::Mult(const Vector &k, Vector &y) const
    subtract(disp_in, temp, temp2);
 
    stiff_pcg->Mult(temp2, disp_out);
-
-   disp_out.SyncAliasMemory(y);
-   pres_out.SyncAliasMemory(y);
 }
 
 void JacobianPreconditioner::SetOperator(const Operator &op)
@@ -487,10 +473,7 @@ void JacobianPreconditioner::SetOperator(const Operator &op)
 
       if (!spaces[0]->GetParMesh()->Nonconforming())
       {
-#ifndef HYPRE_USING_CUDA
-         // Not available yet when hypre is built with CUDA
          stiff_prec_amg->SetElasticityOptions(spaces[0]);
-#endif
       }
 
       stiff_prec = stiff_prec_amg;
@@ -618,11 +601,10 @@ RubberOperator::~RubberOperator()
 
 
 // Inline visualization
-void visualize(ostream &os, ParMesh *mesh,
-               ParGridFunction *deformed_nodes,
+void visualize(ostream &out, ParMesh *mesh, ParGridFunction *deformed_nodes,
                ParGridFunction *field, const char *field_name, bool init_vis)
 {
-   if (!os)
+   if (!out)
    {
       return;
    }
@@ -632,27 +614,24 @@ void visualize(ostream &os, ParMesh *mesh,
 
    mesh->SwapNodes(nodes, owns_nodes);
 
-   os << "parallel " << mesh->GetNRanks() << " " << mesh->GetMyRank() <<
-      "\n";
-   os << "solution\n" << *mesh << *field;
+   out << "parallel " << mesh->GetNRanks() << " " << mesh->GetMyRank() << "\n";
+   out << "solution\n" << *mesh << *field;
 
    mesh->SwapNodes(nodes, owns_nodes);
 
    if (init_vis)
    {
-      os << "window_size 800 800\n";
-      os << "window_title '" << field_name << "'\n";
+      out << "window_size 800 800\n";
+      out << "window_title '" << field_name << "'\n";
       if (mesh->SpaceDimension() == 2)
       {
-         os << "view 0 0\n"; // view from top
-         // turn off perspective and light, +anti-aliasing
-         os << "keys jlA\n";
+         out << "view 0 0\n"; // view from top
+         out << "keys jlA\n"; // turn off perspective and light, +anti-aliasing
       }
-      os << "keys cmA\n"; // show colorbar and mesh, +anti-aliasing
-      // update value-range; keep mesh-extents fixed
-      os << "autoscale value\n";
+      out << "keys cmA\n";        // show colorbar and mesh, +anti-aliasing
+      out << "autoscale value\n"; // update value-range; keep mesh-extents fixed
    }
-   os << flush;
+   out << flush;
 }
 
 void ReferenceConfiguration(const Vector &x, Vector &y)

examples/ex1p.cpp

@@ -9,7 +9,6 @@
 //               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/octahedron.mesh -o 1
 //               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
@@ -90,8 +89,7 @@ int main(int argc, char *argv[])
    args.AddOption(&device_config, "-d", "--device",
                   "Device configuration string, see Device::Configure().");
 #ifdef MFEM_USE_CEED
-   args.AddOption(&algebraic_ceed, "-a", "--algebraic",
-                  "-no-a", "--no-algebraic",
+   args.AddOption(&algebraic_ceed, "-a", "--algebraic", "-no-a", "--no-algebraic",
                   "Use algebraic Ceed solver");
 #endif
    args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
@@ -128,7 +126,7 @@ int main(int argc, char *argv[])
    //    more than 10,000 elements.
    {
       int ref_levels =
-         (int)floor(log(1000./mesh.GetNE())/log(2.)/dim);
+         (int)floor(log(10000./mesh.GetNE())/log(2.)/dim);
       for (int l = 0; l < ref_levels; l++)
       {
          mesh.UniformRefinement();
@@ -197,22 +195,20 @@ int main(int argc, char *argv[])
    ParLinearForm b(&fespace);
    ConstantCoefficient one(1.0);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   if (Device::IsEnabled()) { b.SetAssemblyLevel(LinearAssemblyLevel::FULL); }
    b.Assemble();
 
-   // 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.
+   // 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.
+   //     corresponding to the Laplacian operator -Delta, by adding the Diffusion
+   //     domain integrator.
    ParBilinearForm a(&fespace);
    if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
-   //a.AddDomainIntegrator(new DiffusionIntegrator(one));
-   a.AddDomainIntegrator(new MassIntegrator(one));
+   a.AddDomainIntegrator(new DiffusionIntegrator(one));
 
    // 12. Assemble the parallel bilinear form and the corresponding linear
    //     system, applying any necessary transformations such as: parallel
@@ -247,67 +243,13 @@ int main(int argc, char *argv[])
    {
       prec = new HypreBoomerAMG;
    }
-
-   const int max_it = 50;
-   const int print_lvl = -1;
-   const double rtol = 1e-12;
-
    CGSolver cg(MPI_COMM_WORLD);
-   cg.SetRelTol(rtol);
-   //cg.SetMaxIter(max_it);
-   //cg.SetPrintLevel(print_lvl);
+   cg.SetRelTol(1e-12);
+   cg.SetMaxIter(2000);
+   cg.SetPrintLevel(1);
    if (prec) { cg.SetPreconditioner(*prec); }
    cg.SetOperator(*A);
-
-   // Warm-up CG solve (in case of JIT to avoid timing it)
-   {
-      Vector Y(X);
-      cg.SetMaxIter(2);
-      cg.SetPrintLevel(-1);
-      cg.Mult(B, Y);
-      MFEM_DEVICE_SYNC;
-   }
-
-   // benchmark this problem
-   {
-      tic_toc.Clear();
-      cg.SetMaxIter(max_it);
-      cg.SetPrintLevel(print_lvl);
-      {
-         tic_toc.Start();
-         cg.Mult(B, X);
-         MFEM_DEVICE_SYNC;
-         tic_toc.Stop();
-      }
-   }
-   // Final norm check
-   const double final_norm = cg.GetFinalNorm();
-   MFEM_VERIFY(final_norm < sqrt(rtol),
-               "FinalNorm (" << final_norm << ") Error!");
-   // Number of iteration check
-   const int num_iter = cg.GetNumIterations();
-   MFEM_VERIFY(num_iter <= max_it,
-               "NumIterations (" << num_iter << ") Error!");
-
-   const double rt = tic_toc.RealTime();
-   const double rt_min = rt, rt_max = rt;
-   HYPRE_BigInt dofs = fespace.GlobalTrueVSize();
-   const int cg_iter = cg.GetNumIterations();
-   const double mdofs_max = ((1e-6 * dofs) * cg_iter) / rt_max;
-   const double mdofs_min = ((1e-6 * dofs) * cg_iter) / rt_min;
-   if (myid == 0)
-   {
-      mfem::out << "Total CG time:    " << rt_max << " (" << rt_min << ") sec."
-                << std::endl;
-      mfem::out << "Time per CG step: "
-                << rt_max / cg_iter << " ("
-                << rt_min / cg_iter << ") sec." << std::endl;
-      mfem::out << "\033[32m";
-      mfem::out << "\"DOFs/sec\" in CG: " << mdofs_max << " ("
-                << mdofs_min << ") million.";
-      mfem::out << "\033[m" << std::endl;
-   }
-   //cg.Mult(B, X);
+   cg.Mult(B, X);
    delete prec;
 
    // 14. Recover the parallel grid function corresponding to X. This is the

examples/ex22.cpp

@@ -13,8 +13,6 @@
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 1
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 2
 //               ex22 -m ../data/inline-hex.mesh -o 2 -p 2 -pa
-//               ex22 -m ../data/inline-wedge.mesh -o 1
-//               ex22 -m ../data/inline-pyramid.mesh -o 1
 //               ex22 -m ../data/star.mesh -r 1 -o 2 -sigma 10.0
 //
 // Device sample runs:

examples/ex22p.cpp

@@ -13,8 +13,6 @@
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 1
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 2 -p 2
 //               mpirun -np 4 ex22p -m ../data/inline-hex.mesh -o 1 -p 2 -pa
-//               mpirun -np 4 ex22p -m ../data/inline-wedge.mesh -o 1
-//               mpirun -np 4 ex22p -m ../data/inline-pyramid.mesh -o 1
 //               mpirun -np 4 ex22p -m ../data/star.mesh -o 2 -sigma 10.0
 //
 // Device sample runs:

examples/ex24.cpp

@@ -113,6 +113,7 @@ int main(int argc, char *argv[])
          mesh->UniformRefinement();
       }
    }
+   mesh->ReorientTetMesh();
 
    // 5. Define a finite element space on the mesh. Here we use Nedelec or
    //    Raviart-Thomas finite elements of the specified order.

examples/ex24p.cpp

@@ -141,6 +141,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use Nedelec or Raviart-Thomas finite elements of the specified order.

examples/ex25.cpp

@@ -92,7 +92,7 @@ class PMLDiagMatrixCoefficient : public VectorCoefficient
 {
 private:
    CartesianPML * pml = nullptr;
-   void (*Function)(const Vector &, CartesianPML *, Vector &);
+   void (*Function)(const Vector &, CartesianPML * , Vector &);
 public:
    PMLDiagMatrixCoefficient(int dim, void(*F)(const Vector &, CartesianPML *,
                                               Vector &),
@@ -277,8 +277,10 @@ int main(int argc, char *argv[])
       mesh->UniformRefinement();
    }
 
-   // 6. Set element attributes in order to distinguish elements in the
-   //    PML region
+   // 6. Reorient mesh in case of a tet mesh
+   mesh->ReorientTetMesh();
+
+   // Set element attributes in order to distinguish elements in the PML region
    pml->SetAttributes(mesh);
 
    // 7. Define a finite element space on the mesh. Here we use the Nedelec

examples/ex25p.cpp

@@ -92,7 +92,7 @@ class PMLDiagMatrixCoefficient : public VectorCoefficient
 {
 private:
    CartesianPML * pml = nullptr;
-   void (*Function)(const Vector &, CartesianPML *, Vector &);
+   void (*Function)(const Vector &, CartesianPML * , Vector &);
 public:
    PMLDiagMatrixCoefficient(int dim, void(*F)(const Vector &, CartesianPML *,
                                               Vector &),
@@ -316,6 +316,9 @@ int main(int argc, char *argv[])
       }
    }
 
+   // 7a. Reorient mesh in case of a tet mesh
+   pmesh->ReorientTetMesh();
+
    // 8. Set element attributes in order to distinguish elements in the PML
    pml->SetAttributes(pmesh);
 

examples/ex27.cpp

@@ -75,7 +75,7 @@ Mesh * GenerateSerialMesh(int ref);
 // alpha*n.Grad(sol) + beta*sol - gamma over the same boundary.
 double IntegrateBC(const GridFunction &sol, const Array<int> &bdr_marker,
                    double alpha, double beta, double gamma,
-                   double &error);
+                   double &err);
 
 int main(int argc, char *argv[])
 {
@@ -295,33 +295,43 @@ int main(int argc, char *argv[])
    //     element solution.
    a.RecoverFEMSolution(X, b, u);
 
-   // 13. Compute the various boundary integrals.
+   // 13. Build a mass matrix to help solve for n.Grad(u) where 'n' is a surface
+   //     normal.
+   BilinearForm m(&fespace);
+   m.AddDomainIntegrator(new MassIntegrator);
+   m.Assemble();
+
+   ess_tdof_list.SetSize(0);
+   OperatorPtr M;
+   m.FormSystemMatrix(ess_tdof_list, M);
+
+   // 14. Compute the various boundary integrals.
    mfem::out << endl
              << "Verifying boundary conditions" << endl
              << "=============================" << endl;
    {
       // Integrate the solution on the Dirichlet boundary and compare to the
       // expected value.
-      double error, avg = IntegrateBC(u, dbc_bdr, 0.0, 1.0, dbc_val, error);
+      double err, avg = IntegrateBC(u, dbc_bdr, 0.0, 1.0, dbc_val, err);
 
       bool hom_dbc = (dbc_val == 0.0);
-      error /=  hom_dbc ? 1.0 : fabs(dbc_val);
+      err /=  hom_dbc ? 1.0 : fabs(dbc_val);
       mfem::out << "Average of solution on Gamma_dbc:\t"
                 << avg << ", \t"
                 << (hom_dbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
    {
       // Integrate n.Grad(u) on the inhomogeneous Neumann boundary and compare
       // to the expected value.
-      double error, avg = IntegrateBC(u, nbc_bdr, 1.0, 0.0, nbc_val, error);
+      double err, avg = IntegrateBC(u, nbc_bdr, 1.0, 0.0, nbc_val, err);
 
       bool hom_nbc = (nbc_val == 0.0);
-      error /=  hom_nbc ? 1.0 : fabs(nbc_val);
+      err /=  hom_nbc ? 1.0 : fabs(nbc_val);
       mfem::out << "Average of n.Grad(u) on Gamma_nbc:\t"
                 << avg << ", \t"
                 << (hom_nbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
    {
       // Integrate n.Grad(u) on the homogeneous Neumann boundary and compare to
@@ -330,29 +340,28 @@ int main(int argc, char *argv[])
       nbc0_bdr = 0;
       nbc0_bdr[3] = 1;
 
-      double error, avg = IntegrateBC(u, nbc0_bdr, 1.0, 0.0, 0.0, error);
+      double err, avg = IntegrateBC(u, nbc0_bdr, 1.0, 0.0, 0.0, err);
 
       bool hom_nbc = true;
       mfem::out << "Average of n.Grad(u) on Gamma_nbc0:\t"
                 << avg << ", \t"
                 << (hom_nbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
    {
       // Integrate n.Grad(u) + a * u on the Robin boundary and compare to the
       // expected value.
-      double error;
-      double avg = IntegrateBC(u, rbc_bdr, 1.0, rbc_a_val, rbc_b_val, error);
+      double err, avg = IntegrateBC(u, rbc_bdr, 1.0, rbc_a_val, rbc_b_val, err);
 
       bool hom_rbc = (rbc_b_val == 0.0);
-      error /=  hom_rbc ? 1.0 : fabs(rbc_b_val);
+      err /=  hom_rbc ? 1.0 : fabs(rbc_b_val);
       mfem::out << "Average of n.Grad(u)+a*u on Gamma_rbc:\t"
                 << avg << ", \t"
                 << (hom_rbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
 
-   // 14. Save the refined mesh and the solution. This output can be viewed
+   // 15. Save the refined mesh and the solution. This output can be viewed
    //     later using GLVis: "glvis -m refined.mesh -g sol.gf".
    {
       ofstream mesh_ofs("refined.mesh");
@@ -363,7 +372,7 @@ int main(int argc, char *argv[])
       u.Save(sol_ofs);
    }
 
-   // 15. Send the solution by socket to a GLVis server.
+   // 16. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       string title_str = h1 ? "H1" : "DG";
@@ -376,7 +385,7 @@ int main(int argc, char *argv[])
                << " keys 'mmc'" << flush;
    }
 
-   // 16. Free the used memory.
+   // 17. Free the used memory.
    delete fec;
    delete mesh;
 
@@ -638,11 +647,11 @@ Mesh * GenerateSerialMesh(int ref)
 
 double IntegrateBC(const GridFunction &x, const Array<int> &bdr,
                    double alpha, double beta, double gamma,
-                   double &error)
+                   double &err)
 {
    double nrm = 0.0;
    double avg = 0.0;
-   error = 0.0;
+   err = 0.0;
 
    const bool a_is_zero = alpha == 0.0;
    const bool b_is_zero = beta == 0.0;
@@ -706,20 +715,20 @@ double IntegrateBC(const GridFunction &x, const Array<int> &bdr,
 
          // Integrate |alpha * n.Grad(x) + beta * x - gamma|^2
          val -= gamma;
-         error += (val*val) * ip.weight * face_weight;
+         err += (val*val) * ip.weight * face_weight;
       }
    }
 
    // Normalize by the length of the boundary
    if (std::abs(nrm) > 0.0)
    {
-      error /= nrm;
+      err /= nrm;
       avg /= nrm;
    }
 
    // Compute l2 norm of the error in the boundary condition (negative
-   // quadrature weights may produce negative 'error')
-   error = (error >= 0.0) ? sqrt(error) : -sqrt(-error);
+   // quadrature weights may produce negative 'err')
+   err = (err >= 0.0) ? sqrt(err) : -sqrt(-err);
 
    // Return the average value of alpha * n.Grad(x) + beta * x
    return avg;

examples/ex27p.cpp

@@ -75,7 +75,7 @@ Mesh * GenerateSerialMesh(int ref);
 // alpha*n.Grad(sol) + beta*sol - gamma over the same boundary.
 double IntegrateBC(const ParGridFunction &sol, const Array<int> &bdr_marker,
                    double alpha, double beta, double gamma,
-                   double &error);
+                   double &err);
 
 int main(int argc, char *argv[])
 {
@@ -314,33 +314,43 @@ int main(int argc, char *argv[])
    //     local finite element solution on each processor.
    a.RecoverFEMSolution(X, b, u);
 
-   // 14. Compute the various boundary integrals.
+   // 14. Build a mass matrix to help solve for n.Grad(u) where 'n' is a surface
+   //     normal.
+   ParBilinearForm m(&fespace);
+   m.AddDomainIntegrator(new MassIntegrator);
+   m.Assemble();
+
+   ess_tdof_list.SetSize(0);
+   OperatorPtr M;
+   m.FormSystemMatrix(ess_tdof_list, M);
+
+   // 15. Compute the various boundary integrals.
    mfem::out << endl
              << "Verifying boundary conditions" << endl
              << "=============================" << endl;
    {
       // Integrate the solution on the Dirichlet boundary and compare to the
       // expected value.
-      double error, avg = IntegrateBC(u, dbc_bdr, 0.0, 1.0, dbc_val, error);
+      double err, avg = IntegrateBC(u, dbc_bdr, 0.0, 1.0, dbc_val, err);
 
       bool hom_dbc = (dbc_val == 0.0);
-      error /=  hom_dbc ? 1.0 : fabs(dbc_val);
+      err /=  hom_dbc ? 1.0 : fabs(dbc_val);
       mfem::out << "Average of solution on Gamma_dbc:\t"
                 << avg << ", \t"
                 << (hom_dbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
    {
       // Integrate n.Grad(u) on the inhomogeneous Neumann boundary and compare
       // to the expected value.
-      double error, avg = IntegrateBC(u, nbc_bdr, 1.0, 0.0, nbc_val, error);
+      double err, avg = IntegrateBC(u, nbc_bdr, 1.0, 0.0, nbc_val, err);
 
       bool hom_nbc = (nbc_val == 0.0);
-      error /=  hom_nbc ? 1.0 : fabs(nbc_val);
+      err /=  hom_nbc ? 1.0 : fabs(nbc_val);
       mfem::out << "Average of n.Grad(u) on Gamma_nbc:\t"
                 << avg << ", \t"
                 << (hom_nbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
    {
       // Integrate n.Grad(u) on the homogeneous Neumann boundary and compare to
@@ -349,29 +359,28 @@ int main(int argc, char *argv[])
       nbc0_bdr = 0;
       nbc0_bdr[3] = 1;
 
-      double error, avg = IntegrateBC(u, nbc0_bdr, 1.0, 0.0, 0.0, error);
+      double err, avg = IntegrateBC(u, nbc0_bdr, 1.0, 0.0, 0.0, err);
 
       bool hom_nbc = true;
       mfem::out << "Average of n.Grad(u) on Gamma_nbc0:\t"
                 << avg << ", \t"
                 << (hom_nbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
    {
       // Integrate n.Grad(u) + a * u on the Robin boundary and compare to the
       // expected value.
-      double error, avg = IntegrateBC(u, rbc_bdr, 1.0, rbc_a_val, rbc_b_val,
-                                      error);
+      double err, avg = IntegrateBC(u, rbc_bdr, 1.0, rbc_a_val, rbc_b_val, err);
 
       bool hom_rbc = (rbc_b_val == 0.0);
-      error /=  hom_rbc ? 1.0 : fabs(rbc_b_val);
+      err /=  hom_rbc ? 1.0 : fabs(rbc_b_val);
       mfem::out << "Average of n.Grad(u)+a*u on Gamma_rbc:\t"
                 << avg << ", \t"
                 << (hom_rbc ? "absolute" : "relative")
-                << " error " << error << endl;
+                << " error " << err << endl;
    }
 
-   // 15. Save the refined mesh and the solution in parallel. This output can be
+   // 16. Save the refined mesh and the solution in parallel. This output can be
    //     viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
    {
       ostringstream mesh_name, sol_name;
@@ -387,7 +396,7 @@ int main(int argc, char *argv[])
       u.Save(sol_ofs);
    }
 
-   // 16. Send the solution by socket to a GLVis server.
+   // 17. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       string title_str = h1 ? "H1" : "DG";
@@ -402,7 +411,7 @@ int main(int argc, char *argv[])
                << " keys 'mmc'" << flush;
    }
 
-   // 17. Free the used memory.
+   // 18. Free the used memory.
    delete fec;
 
    return 0;
@@ -668,11 +677,11 @@ double IntegrateBC(const ParGridFunction &x, const Array<int> &bdr,
    double loc_vals[3];
    double &nrm = loc_vals[0];
    double &avg = loc_vals[1];
-   double &error = loc_vals[2];
+   double &err = loc_vals[2];
 
    nrm = 0.0;
    avg = 0.0;
-   error = 0.0;
+   err = 0.0;
 
    const bool a_is_zero = alpha == 0.0;
    const bool b_is_zero = beta == 0.0;
@@ -736,7 +745,7 @@ double IntegrateBC(const ParGridFunction &x, const Array<int> &bdr,
 
          // Integrate |alpha * n.Grad(x) + beta * x - gamma|^2
          val -= gamma;
-         error += (val*val) * ip.weight * face_weight;
+         err += (val*val) * ip.weight * face_weight;
       }
    }
 
@@ -755,7 +764,7 @@ double IntegrateBC(const ParGridFunction &x, const Array<int> &bdr,
    }
 
    // Compute l2 norm of the error in the boundary condition (negative
-   // quadrature weights may produce negative 'error')
+   // quadrature weights may produce negative 'err')
    glb_err = (glb_err >= 0.0) ? sqrt(glb_err) : -sqrt(-glb_err);
 
    // Return the average value of alpha * n.Grad(x) + beta * x

examples/ex28p.cpp

@@ -81,12 +81,6 @@ Mesh * build_trapezoid_mesh(double offset)
 
 int main(int argc, char *argv[])
 {
-#ifdef HYPRE_USING_CUDA
-   cout << "\nAs of mfem-4.3 and hypre-2.22.0 (July 2021) this example\n"
-        << "is NOT supported with the CUDA version of hypre.\n\n";
-   return 255;
-#endif
-
    // 1. Initialize MPI.
    int num_procs, myid;
    MPI_Init(&argc, &argv);
@@ -366,7 +360,6 @@ int main(int argc, char *argv[])
    }
    delete pmesh;
 
-   // HYPRE_Finalize();
    MPI_Finalize();
 
    return 0;

examples/ex29.cpp

@@ -167,9 +167,9 @@ int main(int argc, char *argv[])
 
    // 13. Compute error in the solution and its flux
    FunctionCoefficient uCoef(uExact);
-   double error = x.ComputeL2Error(uCoef);
+   double err = x.ComputeL2Error(uCoef);
 
-   cout << "|u - u_h|_2 = " << error << endl;
+   cout << "|u - u_h|_2 = " << err << endl;
 
    FiniteElementSpace flux_fespace(mesh, &fec, 3);
    GridFunction flux(&flux_fespace);

examples/ex29p.cpp

@@ -197,9 +197,9 @@ int main(int argc, char *argv[])
 
    // 15. Compute error in the solution and its flux
    FunctionCoefficient uCoef(uExact);
-   double error = x.ComputeL2Error(uCoef);
+   double err = x.ComputeL2Error(uCoef);
 
-   if (myid == 0) { cout << "|u - u_h|_2 = " << error << endl; }
+   if (myid == 0) { cout << "|u - u_h|_2 = " << err << endl; }
 
    ParFiniteElementSpace flux_fespace(&pmesh, &fec, 3);
    ParGridFunction flux(&flux_fespace);

examples/ex2p.cpp

@@ -61,7 +61,6 @@ int main(int argc, char *argv[])
    bool visualization = 1;
    bool amg_elast = 0;
    bool reorder_space = false;
-   const char *device_config = "cpu";
 
    OptionsParser args(argc, argv);
    args.AddOption(&mesh_file, "-m", "--mesh",
@@ -79,8 +78,6 @@ int main(int argc, char *argv[])
                   "Enable or disable GLVis visualization.");
    args.AddOption(&reorder_space, "-nodes", "--by-nodes", "-vdim", "--by-vdim",
                   "Use byNODES ordering of vector space instead of byVDIM");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.Parse();
    if (!args.Good())
    {
@@ -96,12 +93,7 @@ int main(int argc, char *argv[])
       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(); }
-
-   // 4. Read the (serial) mesh from the given mesh file on all processors.  We
+   // 3. 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 = new Mesh(mesh_file, 1, 1);
@@ -117,14 +109,14 @@ int main(int argc, char *argv[])
       return 3;
    }
 
-   // 5. Select the order of the finite element discretization space. For NURBS
+   // 4. Select the order of the finite element discretization space. For NURBS
    //    meshes, we increase the order by degree elevation.
    if (mesh->NURBSext)
    {
       mesh->DegreeElevate(order, order);
    }
 
-   // 6. Refine the serial mesh on all processors to increase the resolution. In
+   // 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 1,000 elements.
@@ -137,7 +129,7 @@ int main(int argc, char *argv[])
       }
    }
 
-   // 7. Define a parallel mesh by a partitioning of the serial mesh. Refine
+   // 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 = new ParMesh(MPI_COMM_WORLD, *mesh);
@@ -150,7 +142,7 @@ int main(int argc, char *argv[])
       }
    }
 
-   // 8. Define a parallel finite element space on the parallel mesh. Here we
+   // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use vector finite elements, i.e. dim copies of a scalar finite element
    //    space. We use the ordering by vector dimension (the last argument of
    //    the FiniteElementSpace constructor) which is expected in the systems
@@ -183,7 +175,7 @@ int main(int argc, char *argv[])
            << "Assembling: " << flush;
    }
 
-   // 9. Determine the list of true (i.e. parallel conforming) essential
+   // 8. Determine the list of true (i.e. parallel conforming) essential
    //    boundary dofs. In this example, the boundary conditions are defined by
    //    marking only boundary attribute 1 from the mesh as essential and
    //    converting it to a list of true dofs.
@@ -192,14 +184,14 @@ int main(int argc, char *argv[])
    ess_bdr[0] = 1;
    fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
 
-   // 10. Set up the parallel linear form b(.) which corresponds to the
-   //     right-hand side of the FEM linear system. In this case, b_i equals the
-   //     boundary integral of f*phi_i where f represents a "pull down" force on
-   //     the Neumann part of the boundary and phi_i are the basis functions in
-   //     the finite element fespace. The force is defined by the object f, which
-   //     is a vector of Coefficient objects. The fact that f is non-zero on
-   //     boundary attribute 2 is indicated by the use of piece-wise constants
-   //     coefficient for its last component.
+   // 9. Set up the parallel linear form b(.) which corresponds to the
+   //    right-hand side of the FEM linear system. In this case, b_i equals the
+   //    boundary integral of f*phi_i where f represents a "pull down" force on
+   //    the Neumann part of the boundary and phi_i are the basis functions in
+   //    the finite element fespace. The force is defined by the object f, which
+   //    is a vector of Coefficient objects. The fact that f is non-zero on
+   //    boundary attribute 2 is indicated by the use of piece-wise constants
+   //    coefficient for its last component.
    VectorArrayCoefficient f(dim);
    for (int i = 0; i < dim-1; i++)
    {
@@ -220,13 +212,13 @@ int main(int argc, char *argv[])
    }
    b->Assemble();
 
-   // 11. Define the solution vector x as a parallel finite element grid
+   // 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;
 
-   // 12. Set up the parallel bilinear form a(.,.) on the finite element space
+   // 11. Set up the parallel bilinear form a(.,.) on the finite element space
    //     corresponding to the linear elasticity integrator with piece-wise
    //     constants coefficient lambda and mu.
    Vector lambda(pmesh->attributes.Max());
@@ -241,7 +233,7 @@ int main(int argc, char *argv[])
    ParBilinearForm *a = new ParBilinearForm(fespace);
    a->AddDomainIntegrator(new ElasticityIntegrator(lambda_func, mu_func));
 
-   // 13. Assemble the parallel bilinear form and the corresponding linear
+   // 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.
@@ -258,7 +250,7 @@ int main(int argc, char *argv[])
       cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
    }
 
-   // 14. Define and apply a parallel PCG solver for A X = B with the BoomerAMG
+   // 13. Define and apply a parallel PCG solver for A X = B with the BoomerAMG
    //     preconditioner from hypre.
    HypreBoomerAMG *amg = new HypreBoomerAMG(A);
    if (amg_elast && !a->StaticCondensationIsEnabled())
@@ -276,11 +268,11 @@ int main(int argc, char *argv[])
    pcg->SetPreconditioner(*amg);
    pcg->Mult(B, X);
 
-   // 15. Recover the parallel grid function corresponding to X. This is the
+   // 14. Recover the parallel grid function corresponding to X. This is the
    //     local finite element solution on each processor.
    a->RecoverFEMSolution(X, *b, x);
 
-   // 16. For non-NURBS meshes, make the mesh curved based on the finite element
+   // 15. For non-NURBS meshes, make the mesh curved based on the finite element
    //     space. This means that we define the mesh elements through a fespace
    //     based transformation of the reference element.  This allows us to save
    //     the displaced mesh as a curved mesh when using high-order finite
@@ -292,7 +284,7 @@ int main(int argc, char *argv[])
       pmesh->SetNodalFESpace(fespace);
    }
 
-   // 17. Save in parallel the displaced mesh and the inverted solution (which
+   // 16. Save in parallel the displaced mesh and the inverted solution (which
    //     gives the backward displacements to the original grid). This output
    //     can be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
    {
@@ -313,7 +305,7 @@ int main(int argc, char *argv[])
       x.Save(sol_ofs);
    }
 
-   // 18. Send the above data by socket to a GLVis server.  Use the "n" and "b"
+   // 17. Send the above data by socket to a GLVis server.  Use the "n" and "b"
    //     keys in GLVis to visualize the displacements.
    if (visualization)
    {
@@ -325,7 +317,7 @@ int main(int argc, char *argv[])
       sol_sock << "solution\n" << *pmesh << x << flush;
    }
 
-   // 19. Free the used memory.
+   // 18. Free the used memory.
    delete pcg;
    delete amg;
    delete a;

examples/ex3.cpp

@@ -16,8 +16,6 @@
 //               ex3 -m ../data/beam-hex-nurbs.mesh
 //               ex3 -m ../data/amr-hex.mesh
 //               ex3 -m ../data/fichera-amr.mesh
-//               ex3 -m ../data/ref-prism.mesh -o 1
-//               ex3 -m ../data/octahedron.mesh -o 1
 //               ex3 -m ../data/star-surf.mesh -o 1
 //               ex3 -m ../data/mobius-strip.mesh -f 0.1
 //               ex3 -m ../data/klein-bottle.mesh -f 0.1
@@ -115,6 +113,7 @@ int main(int argc, char *argv[])
          mesh->UniformRefinement();
       }
    }
+   mesh->ReorientTetMesh();
 
    // 5. Define a finite element space on the mesh. Here we use the Nedelec
    //    finite elements of the specified order.

examples/ex30.cpp

@@ -1,195 +0,0 @@
-//                            MFEM Example 30
-//
-// Compile with: make ex30
-//
-// Sample runs:  ex30 -m ../data/square-disc.mesh -o 1
-//               ex30 -m ../data/square-disc.mesh -o 2
-//               ex30 -m ../data/square-disc.mesh -o 2 -me 1e3
-//               ex30 -m ../data/square-disc-nurbs.mesh -o 2
-//               ex30 -m ../data/star.mesh -o 2 -eo 4
-//               ex30 -m ../data/fichera.mesh -o 2 -me 1e4
-//               ex30 -m ../data/disc-nurbs.mesh -o 2
-//               ex30 -m ../data/ball-nurbs.mesh -o 2 -eo 3 -e 1e-2 -me 1e4
-//               ex30 -m ../data/star-surf.mesh -o 2
-//               ex30 -m ../data/square-disc-surf.mesh -o 2
-//               ex30 -m ../data/amr-quad.mesh -l 2
-//
-// Description:  This is an example of adaptive mesh refinement preprocessing
-//               which lowers the data oscillation [1] to a user-defined
-//               relative threshold. There is no PDE being solved.
-//
-//               MFEM's capability to work with both conforming and
-//               nonconforming meshes is demonstrated in example 6. In some
-//               problems, the material data or loading data is not sufficiently
-//               resolved on the initial mesh. This missing fine scale data
-//               reduces the accuracy of the solution as well as the accuracy
-//               of some local error estimators. By preprocessing the mesh
-//               before solving the PDE, many issues can be avoided.
-//
-//               [1] Morin, P., Nochetto, R. H., & Siebert, K. G. (2000).
-//                   Data oscillation and convergence of adaptive FEM. SIAM
-//                   Journal on Numerical Analysis, 38(2), 466-488.
-//
-//               [2] Mitchell, W. F. (2013). A collection of 2D elliptic
-//                   problems for testing adaptive grid refinement algorithms.
-//                   Applied mathematics and computation, 220, 350-364.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Piecewise-affine function which is sometimes mesh-conforming
-double affine_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   if (x < 0.0)
-   {
-      return 1.0 + x + y;
-   }
-   else
-   {
-      return 1.0;
-   }
-}
-
-// Piecewise-constant function which is never mesh-conforming
-double jump_function(const Vector &p)
-{
-   if (p.Normlp(2.0) > 0.4 && p.Normlp(2.0) < 0.6) { return 1.0; }
-   return 5.0;
-}
-
-// Singular function derived from the Laplacian of the "steep wavefront"
-// problem in [2].
-double singular_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   double alpha = 1000.0;
-   double xc = 0.75, yc = 0.5;
-   double r0 = 0.7;
-   double r = sqrt(pow(x - xc,2.0) + pow(y - yc,2.0));
-   double num = - ( alpha - pow(alpha,3) * (pow(r,2) - pow(r0,2)) );
-   double denom = pow(r * ( pow(alpha,2) * pow(r0,2) + pow(alpha,2) * pow(r,2) \
-                            - 2 * pow(alpha,2) * r0 * r + 1.0 ),2);
-   denom = max(denom,1e-8);
-   return num / denom;
-}
-
-int main(int argc, char *argv[])
-{
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/star.mesh";
-   int order = 1;
-   int nc_limit = 1;
-   int max_elems = 1e5;
-   double double_max_elems = double(max_elems);
-   bool visualization = true;
-   double osc_threshold = 1e-3;
-   int enriched_order = 5;
-
-   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(&nc_limit, "-l", "--nc-limit",
-                  "Maximum level of hanging nodes.");
-   args.AddOption(&double_max_elems, "-me", "--max-elems",
-                  "Stop after reaching this many elements.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&osc_threshold, "-e", "--error",
-                  "relative data oscillation threshold.");
-   args.AddOption(&enriched_order, "-eo", "--enriched_order",
-                  "Enriched quadrature order.");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      args.PrintUsage(cout);
-      return 1;
-   }
-   args.PrintOptions(cout);
-
-   max_elems = int(double_max_elems);
-   Mesh mesh(mesh_file, 1, 1);
-
-   // 2. 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);
-   }
-
-   // 3. Define functions and refiner.
-   FunctionCoefficient affine_coeff(affine_function);
-   FunctionCoefficient jump_coeff(jump_function);
-   FunctionCoefficient singular_coeff(singular_function);
-   CoefficientRefiner coeffrefiner(affine_coeff, order);
-
-   // 4. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-   if (visualization)
-   {
-      sol_sock.open(vishost, visport);
-   }
-
-   // 5. Define custom integration rule (optional).
-   const IntegrationRule *irs[Geometry::NumGeom];
-   int order_quad = 2*order + enriched_order;
-   for (int i = 0; i < Geometry::NumGeom; ++i)
-   {
-      irs[i] = &(IntRules.Get(i, order_quad));
-   }
-
-   // 6. Apply custom refiner settings.
-   coeffrefiner.SetIntRule(irs);
-   coeffrefiner.SetMaxElements(max_elems);
-   coeffrefiner.SetThreshold(osc_threshold);
-   coeffrefiner.SetNCLimit(nc_limit);
-   coeffrefiner.PrintWarnings();
-
-   // 7. Preprocess mesh to control osc (piecewise-affine function).
-   //    This is mostly just a verification check. The oscillation should
-   //    be zero if the function is mesh-conforming and order > 0.
-   coeffrefiner.PreprocessMesh(mesh);
-
-   mfem::out  << "\n";
-   mfem::out << "Function 0 (affine) \n";
-   mfem::out << "Number of Elements " << mesh.GetNE() << "\n";
-   mfem::out << "Osc error " << coeffrefiner.GetOsc() << "\n";
-
-   // 8. Preprocess mesh to control osc (jump function).
-   coeffrefiner.ResetCoefficient(jump_coeff);
-   coeffrefiner.PreprocessMesh(mesh);
-
-   mfem::out  << "\n";
-   mfem::out << "Function 1 (discontinuous) \n";
-   mfem::out << "Number of Elements " << mesh.GetNE() << "\n";
-   mfem::out << "Osc error " << coeffrefiner.GetOsc() << "\n";
-
-   // 9. Preprocess mesh to control osc (singular function).
-   coeffrefiner.ResetCoefficient(singular_coeff);
-   coeffrefiner.PreprocessMesh(mesh);
-
-   mfem::out  << "\n";
-   mfem::out << "Function 2 (singular) \n";
-   mfem::out << "Number of Elements " << mesh.GetNE() << "\n";
-   mfem::out << "Osc error " << coeffrefiner.GetOsc() << "\n";
-
-   sol_sock.precision(8);
-   sol_sock << "mesh\n" << mesh << flush;
-
-   return 0;
-}

examples/ex30p.cpp

@@ -1,241 +0,0 @@
-//                        MFEM Example 30 - Parallel Version
-//
-// Compile with: make ex30p
-//
-// Sample runs:  mpirun -np 4 ex30p -m ../data/square-disc.mesh -o 1
-//               mpirun -np 4 ex30p -m ../data/square-disc.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/square-disc.mesh -o 2 -me 1e3
-//               mpirun -np 4 ex30p -m ../data/square-disc-nurbs.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/star.mesh -o 2 -eo 4
-//               mpirun -np 4 oscp -m ../data/fichera.mesh -o 2 -me 1e4
-//               mpirun -np 4 ex30p -m ../data/disc-nurbs.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/ball-nurbs.mesh -o 2 -eo 3 -e 1e-2
-//               mpirun -np 4 ex30p -m ../data/star-surf.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/square-disc-surf.mesh -o 2
-//               mpirun -np 4 ex30p -m ../data/amr-quad.mesh -l 2
-//
-// Description:  This is an example of adaptive mesh refinement preprocessing
-//               which lowers the data oscillation [1] to a user-defined
-//               relative threshold. There is no PDE being solved.
-//
-//               MFEM's capability to work with both conforming and
-//               nonconforming meshes is demonstrated in example 6. In some
-//               problems, the material data or loading data is not sufficiently
-//               resolved on the initial mesh. This missing fine scale data
-//               reduces the accuracy of the solution as well as the accuracy
-//               of some local error estimators. By preprocessing the mesh
-//               before solving the PDE, many issues can be avoided.
-//
-//               [1] Morin, P., Nochetto, R. H., & Siebert, K. G. (2000).
-//                   Data oscillation and convergence of adaptive FEM. SIAM
-//                   Journal on Numerical Analysis, 38(2), 466-488.
-//
-//               [2] Mitchell, W. F. (2013). A collection of 2D elliptic
-//                   problems for testing adaptive grid refinement algorithms.
-//                   Applied mathematics and computation, 220, 350-364.
-
-#include "mfem.hpp"
-#include <fstream>
-#include <iostream>
-
-using namespace std;
-using namespace mfem;
-
-// Piecewise-affine function which is sometimes mesh-conforming
-double affine_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   if (x < 0.0)
-   {
-      return 1.0 + x + y;
-   }
-   else
-   {
-      return 1.0;
-   }
-}
-
-// Piecewise-constant function which is never mesh-conforming
-double jump_function(const Vector &p)
-{
-   if (p.Normlp(2.0) > 0.4 && p.Normlp(2.0) < 0.6) { return 1.0; }
-   return 5.0;
-}
-
-// Singular function derived from the Laplacian of the "steep wavefront"
-// problem in [2].
-double singular_function(const Vector &p)
-{
-   double x = p(0), y = p(1);
-   double alpha = 1000.0;
-   double xc = 0.75, yc = 0.5;
-   double r0 = 0.7;
-   double r = sqrt(pow(x - xc,2.0) + pow(y - yc,2.0));
-   double num = - ( alpha - pow(alpha,3) * (pow(r,2) - pow(r0,2)) );
-   double denom = pow(r * ( pow(alpha,2) * pow(r0,2) + pow(alpha,2) * pow(r,2) \
-                            - 2 * pow(alpha,2) * r0 * r + 1.0 ),2);
-   denom = max(denom,1e-8);
-   return num / denom;
-}
-
-int main(int argc, char *argv[])
-{
-   // 0. 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);
-
-   // 1. Parse command-line options.
-   const char *mesh_file = "../data/star.mesh";
-   int order = 1;
-   int nc_limit = 1;
-   int max_elems = 1e5;
-   double double_max_elems = double(max_elems);
-   bool visualization = true;
-   bool nc_simplices = true;
-   double osc_threshold = 1e-3;
-   int enriched_order = 5;
-
-   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(&nc_limit, "-l", "--nc-limit",
-                  "Maximum level of hanging nodes.");
-   args.AddOption(&double_max_elems, "-me", "--max-elems",
-                  "Stop after reaching this many elements.");
-   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
-                  "--no-visualization",
-                  "Enable or disable GLVis visualization.");
-   args.AddOption(&osc_threshold, "-e", "--error",
-                  "relative data oscillation threshold.");
-   args.AddOption(&enriched_order, "-eo", "--enriched_order",
-                  "Enriched quadrature order.");
-   args.AddOption(&nc_simplices, "-ns", "--nonconforming-simplices",
-                  "-cs", "--conforming-simplices",
-                  "For simplicial meshes, enable/disable nonconforming"
-                  " refinement");
-
-   args.Parse();
-   if (!args.Good())
-   {
-      if (myid == 0)
-      {
-         args.PrintUsage(cout);
-      }
-      MPI_Finalize();
-      return 1;
-   }
-   if (myid == 0)
-   {
-      args.PrintOptions(cout);
-   }
-
-   max_elems = int(double_max_elems);
-   Mesh mesh(mesh_file, 1, 1);
-
-   // 2. 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);
-   }
-
-   // 3. Make sure the mesh is in the non-conforming mode to enable local
-   //    refinement of quadrilaterals/hexahedra. Simplices can be refined
-   //    either in conforming or in non-conforming mode. The conforming
-   //    mode however does not support dynamic partitioning.
-   mesh.EnsureNCMesh(nc_simplices);
-
-   // 4. Define a parallel mesh by partitioning the serial mesh.
-   //    Once the parallel mesh is defined, the serial mesh can be deleted.
-   ParMesh pmesh(MPI_COMM_WORLD, mesh);
-   mesh.Clear();
-
-   // 5. Define functions and refiner.
-   FunctionCoefficient affine_coeff(affine_function);
-   FunctionCoefficient jump_coeff(jump_function);
-   FunctionCoefficient singular_coeff(singular_function);
-   CoefficientRefiner coeffrefiner(affine_coeff,order);
-
-   // 6. Connect to GLVis.
-   char vishost[] = "localhost";
-   int  visport   = 19916;
-   socketstream sol_sock;
-   if (visualization)
-   {
-      sol_sock.open(vishost, visport);
-   }
-
-   // 7. Define custom integration rule (optional).
-   const IntegrationRule *irs[Geometry::NumGeom];
-   int order_quad = 2*order + enriched_order;
-   for (int i=0; i < Geometry::NumGeom; ++i)
-   {
-      irs[i] = &(IntRules.Get(i, order_quad));
-   }
-
-   // 8. Apply custom refiner settings.
-   coeffrefiner.SetIntRule(irs);
-   coeffrefiner.SetMaxElements(max_elems);
-   coeffrefiner.SetThreshold(osc_threshold);
-   coeffrefiner.SetNCLimit(nc_limit);
-   coeffrefiner.PrintWarnings();
-
-   // 9. Preprocess mesh to control osc (piecewise-affine function).
-   //    This is mostly just a verification check. The oscillation should
-   //    be zero if the function is mesh-conforming and order > 0.
-   coeffrefiner.PreprocessMesh(pmesh);
-
-   int globalNE = pmesh.GetGlobalNE();
-   double osc = coeffrefiner.GetOsc();
-   if (myid == 0)
-   {
-      mfem::out  << "\n";
-      mfem::out << "Function 0 (affine) \n";
-      mfem::out << "Number of Elements " << globalNE << "\n";
-      mfem::out << "Osc error " << osc << "\n";
-   }
-
-   // 10. Preprocess mesh to control osc (jump function).
-   coeffrefiner.ResetCoefficient(jump_coeff);
-   coeffrefiner.PreprocessMesh(pmesh);
-
-   globalNE = pmesh.GetGlobalNE();
-   osc = coeffrefiner.GetOsc();
-   if (myid == 0)
-   {
-      mfem::out  << "\n";
-      mfem::out << "Function 1 (discontinuous) \n";
-      mfem::out << "Number of Elements " << globalNE << "\n";
-      mfem::out << "Osc error " << osc << "\n";
-   }
-
-   // 11. Preprocess mesh to control osc (singular function).
-   coeffrefiner.ResetCoefficient(singular_coeff);
-   coeffrefiner.PreprocessMesh(pmesh);
-
-   globalNE = pmesh.GetGlobalNE();
-   osc = coeffrefiner.GetOsc();
-   if (myid == 0)
-   {
-      mfem::out  << "\n";
-      mfem::out << "Function 2 (singular) \n";
-      mfem::out << "Number of Elements " << globalNE << "\n";
-      mfem::out << "Osc error " << osc << "\n";
-   }
-
-   sol_sock.precision(8);
-   sol_sock << "parallel " << num_procs << " " << myid << "\n";
-   sol_sock << "mesh\n" << pmesh << flush;
-
-   MPI_Finalize();
-   return 0;
-}

examples/ex3p.cpp

@@ -16,8 +16,6 @@
 //               mpirun -np 4 ex3p -m ../data/beam-hex-nurbs.mesh
 //               mpirun -np 4 ex3p -m ../data/amr-quad.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/amr-hex.mesh
-//               mpirun -np 4 ex3p -m ../data/ref-prism.mesh -o 1
-//               mpirun -np 4 ex3p -m ../data/octahedron.mesh -o 1
 //               mpirun -np 4 ex3p -m ../data/star-surf.mesh -o 2
 //               mpirun -np 4 ex3p -m ../data/mobius-strip.mesh -o 2 -f 0.1
 //               mpirun -np 4 ex3p -m ../data/klein-bottle.mesh -o 2 -f 0.1
@@ -105,7 +103,6 @@ int main(int argc, char *argv[])
       {
          args.PrintUsage(cout);
       }
-      // HYPRE_Finalize();
       MPI_Finalize();
       return 1;
    }
@@ -141,7 +138,9 @@ int main(int argc, char *argv[])
 
    // 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.
+   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
+   //    meshes need to be reoriented before we can define high-order Nedelec
+   //    spaces on them.
    ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
    {
@@ -151,6 +150,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Nedelec finite elements of the specified order.
@@ -255,10 +255,10 @@ int main(int argc, char *argv[])
 
    // 15. Compute and print the L^2 norm of the error.
    {
-      double error = x.ComputeL2Error(E);
+      double err = x.ComputeL2Error(E);
       if (myid == 0)
       {
-         cout << "\n|| E_h - E ||_{L^2} = " << error << '\n' << endl;
+         cout << "\n|| E_h - E ||_{L^2} = " << err << '\n' << endl;
       }
    }
 

examples/ex4.cpp

@@ -19,8 +19,6 @@
 //               ex4 -m ../data/amr-hex.mesh
 //               ex4 -m ../data/amr-hex.mesh -o 2 -hb
 //               ex4 -m ../data/fichera-amr.mesh -o 2 -sc
-//               ex4 -m ../data/ref-prism.mesh -o 1
-//               ex4 -m ../data/octahedron.mesh -o 1
 //               ex4 -m ../data/star-surf.mesh -o 1
 //
 // Device sample runs:

examples/ex4p.cpp

@@ -19,8 +19,6 @@
 //               mpirun -np 3 ex4p -m ../data/amr-quad.mesh -o 2 -hb
 //               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -o 2 -sc
 //               mpirun -np 4 ex4p -m ../data/amr-hex.mesh -o 2 -hb
-//               mpirun -np 4 ex4p -m ../data/ref-prism.mesh -o 1
-//               mpirun -np 4 ex4p -m ../data/octahedron.mesh -o 1
 //               mpirun -np 4 ex4p -m ../data/star-surf.mesh -o 3 -hb
 //
 // Device sample runs:
@@ -137,7 +135,9 @@ int main(int argc, char *argv[])
 
    // 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.
+   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
+   //    meshes need to be reoriented before we can define high-order Nedelec
+   //    spaces on them (this is needed in the ADS solver below).
    ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
    {
@@ -147,6 +147,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 7. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Raviart-Thomas finite elements of the specified order.
@@ -256,10 +257,10 @@ int main(int argc, char *argv[])
 
    // 15. Compute and print the L^2 norm of the error.
    {
-      double error = x.ComputeL2Error(F);
+      double err = x.ComputeL2Error(F);
       if (myid == 0)
       {
-         cout << "\n|| F_h - F ||_{L^2} = " << error << '\n' << endl;
+         cout << "\n|| F_h - F ||_{L^2} = " << err << '\n' << endl;
       }
    }
 

examples/ex5.cpp

@@ -197,7 +197,6 @@ int main(int argc, char *argv[])
       SparseMatrix &M(mVarf->SpMat());
       SparseMatrix &B(bVarf->SpMat());
       B *= -1.;
-      if (Device::IsEnabled()) { B.BuildTranspose(); }
       Bt = new TransposeOperator(&B);
 
       darcyOp.SetBlock(0,0, &M);
@@ -241,7 +240,6 @@ int main(int argc, char *argv[])
    {
       SparseMatrix &M(mVarf->SpMat());
       M.GetDiag(Md);
-      Md.HostReadWrite();
 
       SparseMatrix &B(bVarf->SpMat());
       MinvBt = Transpose(B);
@@ -289,18 +287,12 @@ int main(int argc, char *argv[])
    chrono.Stop();
 
    if (solver.GetConverged())
-   {
       std::cout << "MINRES converged in " << solver.GetNumIterations()
-                << " iterations with a residual norm of "
-                << solver.GetFinalNorm() << ".\n";
-   }
+                << " iterations with a residual norm of " << solver.GetFinalNorm() << ".\n";
    else
-   {
       std::cout << "MINRES did not converge in " << solver.GetNumIterations()
-                << " iterations. Residual norm is " << solver.GetFinalNorm()
-                << ".\n";
-   }
-   std::cout << "MINRES solver took " << chrono.RealTime() << "s.\n";
+                << " iterations. Residual norm is " << solver.GetFinalNorm() << ".\n";
+   std::cout << "MINRES solver took " << chrono.RealTime() << "s. \n";
 
    // 12. Create the grid functions u and p. Compute the L2 error norms.
    GridFunction u, p;

examples/ex6.cpp

@@ -125,7 +125,6 @@ int main(int argc, char *argv[])
    BilinearFormIntegrator *integ = new DiffusionIntegrator(one);
    a.AddDomainIntegrator(integ);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   if (Device::IsEnabled()) { b.SetAssemblyLevel(LinearAssemblyLevel::FULL); }
 
    // 7. The solution vector x and the associated finite element grid function
    //    will be maintained over the AMR iterations. We initialize it to zero.

examples/ex6p.cpp

@@ -202,7 +202,6 @@ int main(int argc, char *argv[])
    BilinearFormIntegrator *integ = new DiffusionIntegrator(one);
    a.AddDomainIntegrator(integ);
    b.AddDomainIntegrator(new DomainLFIntegrator(one));
-   if (Device::IsEnabled()) { b.SetAssemblyLevel(LinearAssemblyLevel::FULL); }
 
    // 12. The solution vector x and the associated finite element grid function
    //     will be maintained over the AMR iterations. We initialize it to zero.

examples/ex7p.cpp

@@ -47,7 +47,6 @@ int main(int argc, char *argv[])
    int order = 2;
    bool always_snap = false;
    bool visualization = 1;
-   const char *device_config = "cpu";
 
    OptionsParser args(argc, argv);
    args.AddOption(&elem_type, "-e", "--elem",
@@ -66,8 +65,6 @@ int main(int argc, char *argv[])
                   "--snap-at-the-end",
                   "If true, snap nodes to the sphere initially and after each refinement "
                   "otherwise, snap only after the last refinement");
-   args.AddOption(&device_config, "-d", "--device",
-                  "Device configuration string, see Device::Configure().");
    args.Parse();
    if (!args.Good())
    {
@@ -83,12 +80,7 @@ int main(int argc, char *argv[])
       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(); }
-
-   // 4. Generate an initial high-order (surface) mesh on the unit sphere. The
+   // 3. Generate an initial high-order (surface) mesh on the unit sphere. The
    //    Mesh object represents a 2D mesh in 3 spatial dimensions. We first add
    //    the elements and the vertices of the mesh, and then make it high-order
    //    by specifying a finite element space for its nodes.
@@ -154,7 +146,7 @@ int main(int argc, char *argv[])
    FiniteElementSpace nodal_fes(mesh, &fec, mesh->SpaceDimension());
    mesh->SetNodalFESpace(&nodal_fes);
 
-   // 5. Refine the mesh while snapping nodes to the sphere. Number of parallel
+   // 4. Refine the mesh while snapping nodes to the sphere. Number of parallel
    //    refinements is fixed to 2.
    for (int l = 0; l <= ref_levels; l++)
    {
@@ -226,7 +218,7 @@ int main(int argc, char *argv[])
       SnapNodes(*pmesh);
    }
 
-   // 6. Define a finite element space on the mesh. Here we use isoparametric
+   // 5. Define a finite element space on the mesh. Here we use isoparametric
    //    finite elements -- the same as the mesh nodes.
    ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, &fec);
    HYPRE_BigInt size = fespace->GlobalTrueVSize();
@@ -235,7 +227,7 @@ int main(int argc, char *argv[])
       cout << "Number of unknowns: " << size << endl;
    }
 
-   // 7. Set up the linear form b(.) which corresponds to the right-hand side of
+   // 6. 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.
    ParLinearForm *b = new ParLinearForm(fespace);
@@ -245,27 +237,27 @@ int main(int argc, char *argv[])
    b->AddDomainIntegrator(new DomainLFIntegrator(rhs_coef));
    b->Assemble();
 
-   // 8. Define the solution vector x as a finite element grid function
+   // 7. Define the solution vector x as a finite element grid function
    //    corresponding to fespace. Initialize x with initial guess of zero.
    ParGridFunction x(fespace);
    x = 0.0;
 
-   // 9. Set up the bilinear form a(.,.) on the finite element space
+   // 8. Set up the bilinear form a(.,.) on the finite element space
    //    corresponding to the Laplacian operator -Delta, by adding the Diffusion
    //    and Mass domain integrators.
    ParBilinearForm *a = new ParBilinearForm(fespace);
    a->AddDomainIntegrator(new DiffusionIntegrator(one));
    a->AddDomainIntegrator(new MassIntegrator(one));
 
-   // 10. Assemble the parallel linear system, applying any transformations
-   //     such as: parallel assembly, applying conforming constraints, etc.
+   // 9. Assemble the parallel linear system, applying any transformations
+   //    such as: parallel assembly, applying conforming constraints, etc.
    a->Assemble();
    HypreParMatrix A;
    Vector B, X;
    Array<int> empty_tdof_list;
    a->FormLinearSystem(empty_tdof_list, x, *b, A, X, B);
 
-   // 11. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
+   // 10. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
    //     preconditioner from hypre. Extract the parallel grid function x
    //     corresponding to the finite element approximation X. This is the local
    //     solution on each processor.
@@ -281,14 +273,14 @@ int main(int argc, char *argv[])
    delete a;
    delete b;
 
-   // 12. Compute and print the L^2 norm of the error.
-   double error = x.ComputeL2Error(sol_coef);
+   // 11. Compute and print the L^2 norm of the error.
+   double err = x.ComputeL2Error(sol_coef);
    if (myid == 0)
    {
-      cout << "\nL2 norm of error: " << error << endl;
+      cout << "\nL2 norm of error: " << err << endl;
    }
 
-   // 13. Save the refined mesh and the solution. This output can be viewed
+   // 12. Save the refined mesh and the solution. This output can be viewed
    //     later using GLVis: "glvis -np <np> -m sphere_refined -g sol".
    {
       ostringstream mesh_name, sol_name;
@@ -304,7 +296,7 @@ int main(int argc, char *argv[])
       x.Save(sol_ofs);
    }
 
-   // 14. Send the solution by socket to a GLVis server.
+   // 13. Send the solution by socket to a GLVis server.
    if (visualization)
    {
       char vishost[] = "localhost";
@@ -315,7 +307,7 @@ int main(int argc, char *argv[])
       sol_sock << "solution\n" << *pmesh << x << flush;
    }
 
-   // 15. Free the used memory.
+   // 14. Free the used memory.
    delete pcg;
    delete amg;
    delete fespace;

examples/ex8p.cpp

@@ -106,6 +106,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 6. Define the trial, interfacial (trace) and test DPG spaces:
    //    - The trial space, x0_space, contains the non-interfacial unknowns and

examples/ginkgo/CMakeLists.txt

@@ -31,31 +31,29 @@ add_mfem_examples(GINKGO_EXAMPLES_SRCS ${PFX} "" test_ginkgo)
 # which builds the examples and runs:
 #   ctest -R ginkgo
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  set(EX1_COMMON_OPTS ex1 -m ../data/star.mesh --use_gko_solver)
-  set(EX1_TEST_OPTS ${EX9_COMMON_OPTS})
+# Command line options for the tests.
+set(EX1_COMMON_OPTS ex1 -m ../data/star.mesh --use_gko_solver)
+set(EX1_TEST_OPTS ${EX9_COMMON_OPTS})
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${GINKGO_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${GINKGO_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    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=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/hiop/CMakeLists.txt

@@ -33,33 +33,31 @@ add_mfem_examples(HIOP_EXAMPLES_SRCS ${PFX} "" test_hiop)
 # which builds the examples and runs:
 #   ctest -R hiop
 
-if (MFEM_ENABLE_TESTING)
-  # Command line options for the tests.
-  # Example 9:
-  set(EX9_COMMON_OPTS -m ../../data/periodic-segment.mesh -p 0 -dt 0.005)
-  set(EX9_TEST_OPTS ${EX9_COMMON_OPTS}  -r  2 )
-  set(EX9P_TEST_OPTS ${EX9_COMMON_OPTS})
+# Command line options for the tests.
+# Example 9:
+set(EX9_COMMON_OPTS -m ../../data/periodic-segment.mesh -p 0 -dt 0.005)
+set(EX9_TEST_OPTS ${EX9_COMMON_OPTS}  -r  2 )
+set(EX9P_TEST_OPTS ${EX9_COMMON_OPTS})
 
-  # Add the tests: one test per source file.
-  foreach(SRC_FILE ${HIOP_EXAMPLES_SRCS})
-    get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
-    string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
-    string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
-    set(TEST_NAME ${PFX}${TEST_NAME})
+# Add the tests: one test per source file.
+foreach(SRC_FILE ${HIOP_EXAMPLES_SRCS})
+  get_filename_component(SRC_FILENAME ${SRC_FILE} NAME)
+  string(REPLACE ".cpp" "" TEST_NAME ${SRC_FILENAME})
+  string(TOUPPER ${TEST_NAME} UP_TEST_NAME)
+  set(TEST_NAME ${PFX}${TEST_NAME})
 
-    set(THIS_TEST_OPTIONS "-no-vis")
-    list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
-    # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
+  set(THIS_TEST_OPTIONS "-no-vis")
+  list(APPEND THIS_TEST_OPTIONS ${${UP_TEST_NAME}_TEST_OPTS})
+  # message(STATUS "Test ${TEST_NAME} options: ${THIS_TEST_OPTIONS}")
 
-    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=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
-endif()
+  if (NOT (${TEST_NAME} MATCHES ".*p$"))
+    add_test(NAME ${TEST_NAME}_ser
+      COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
+  else()
+    add_test(NAME ${TEST_NAME}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 4
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${THIS_TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/jupyter/README.md

@@ -1,31 +0,0 @@
-# Jupyter Notebooks using xeus-cling
-
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mfem/mfem/master?filepath=examples%2Fjupyter%2Fex.ipynb)
-
-[xeus-cling](https://github.com/jupyter-xeus/xeus-cling) is a C++ Jupyter Kernel based on [cling](https://github.com/root-project/cling),
-which can be used to create interactive C++ MFEM and GLVis notebooks.
-
-Click on the `binder` button above for an interactive example.
-
-## Installing Locally
-
-In order to run notebooks locally you will need `xeus-cling` along with `mfem` and `xglvis`. We recommend you use
-[miniconda](https://docs.conda.io/en/latest/miniconda.html) or, if you already have it installed,
-[conda](https://docs.conda.io/projects/conda/en/latest/).
-
-1. Follow the install steps on https://github.com/jupyter-xeus/xeus-cling to install the C++ kernels
-2. Build and install a _shared_ version of mfem
-    * for example: `make serial SHARED=YES`
-3. Install [pyglvis](https://github.com/glvis/pyglvis)
-    * for the widget frontend
-4. Get [xeus-glvis](https://github.com/glvis/xeus-glvis) and `cp` the header to `{PREFIX}/glvis/xglvis.hpp`
-    * (this could be improved)
-
-## Running Locally
-
-Once you've installed Jupyter, the C++ Kernel, mfem, and glvis start the notebook server (`jupyter-notebook`)
-and open an existing example or a new `C++ 1x` kernel.
-
-You will _always_ need to `#pragma cling load("mfem")` and you may need to point the `cling` runtime at your
-mfem and/or glvis installs, do this with the
-`#pragma cling` [statements](https://xeus-cling.readthedocs.io/en/latest/build_options.html#using-third-party-libraries).

examples/jupyter/ex.ipynb

@@ -1,155 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "owned-extraction",
-   "metadata": {},
-   "source": [
-    "## Load the MFEM library\n",
-    "\n",
-    "Any non-default libraries must be loaded before you can `#include` files that use them. For more info see the [xeus-cling help](https://xeus-cling.readthedocs.io/en/latest/build_options.html)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "waiting-portrait",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#pragma cling load(\"mfem\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "foreign-recycling",
-   "metadata": {},
-   "source": [
-    "## MFEM Example 1"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "public-white",
-   "metadata": {},
-   "source": [
-    "This is the simplest MFEM example and a good starting point for new users. The example demonstrates the use of MFEM to define and solve an $H^1$ finite element discretization of the Laplace problem\n",
-    "\n",
-    "$$\n",
-    "-\\Delta u = 1\n",
-    "$$\n",
-    "\n",
-    "with homogeneous Dirichlet boundary conditions $u=0$.\n",
-    "\n",
-    "The example illustrates the use of the basic MFEM classes for defining the mesh, finite element space, as well as linear and bilinear forms corresponding to the left-hand side and right-hand side of the discrete linear system.\n",
-    "\n",
-    "Compare with MFEM's [ex1.cpp](https://github.com/mfem/mfem/blob/master/examples/ex1.cpp) and PyMFEM's [ex1.py](https://github.com/mfem/PyMFEM/blob/master/examples/ex1.py)."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "protective-darkness",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#include <fstream>\n",
-    "#include <iostream>\n",
-    "#include <sstream>\n",
-    "\n",
-    "#include <mfem.hpp>\n",
-    "#include <glvis/xglvis.hpp>"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "falling-monkey",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "using namespace std;\n",
-    "using namespace mfem;\n",
-    "\n",
-    "Mesh mesh = Mesh::MakeCartesian2D(5, 5, Element::TRIANGLE);\n",
-    "mesh.UniformRefinement();\n",
-    "\n",
-    "H1_FECollection fec(2, mesh.Dimension());\n",
-    "\n",
-    "FiniteElementSpace fespace(&mesh, &fec);\n",
-    "cout << \"Number of finite element unknowns: \" << fespace.GetTrueVSize() << endl;\n",
-    "\n",
-    "Array<int> ess_tdof_list;\n",
-    "if (mesh.bdr_attributes.Size())\n",
-    "{\n",
-    "  Array<int> ess_bdr(mesh.bdr_attributes.Max());\n",
-    "  ess_bdr = 1;\n",
-    "  fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list);\n",
-    "}\n",
-    "\n",
-    "LinearForm b(&fespace);\n",
-    "ConstantCoefficient one(1.0);\n",
-    "b.AddDomainIntegrator(new DomainLFIntegrator(one));\n",
-    "b.Assemble();\n",
-    "\n",
-    "GridFunction x(&fespace);\n",
-    "x = 0.0;\n",
-    "\n",
-    "BilinearForm a(&fespace);\n",
-    "a.AddDomainIntegrator(new DiffusionIntegrator(one));\n",
-    "a.Assemble();\n",
-    "\n",
-    "OperatorPtr A;\n",
-    "Vector B, X;\n",
-    "a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);\n",
-    "\n",
-    "cout << \"Size of linear system: \" << A->Height() << endl;\n",
-    "\n",
-    "GSSmoother M((SparseMatrix&)(*A));\n",
-    "PCG(*A, M, B, X, 1, 200, 1e-12, 0.0);\n",
-    "a.RecoverFEMSolution(X, b, x);"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "hawaiian-republican",
-   "metadata": {},
-   "source": [
-    "## GLVis Visualization\n",
-    "\n",
-    "For now we save the computational mesh and finite element solution in a string and pass that to the glvis widget, see https://github.com/glvis/xeus-glvis for the widget backend and https://github.com/GLVis/pyglvis/tree/master/js for the widget frontend."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ordinary-equation",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "std::stringstream ss;\n",
-    "ss << \"solution\\n\" << mesh << x << flush;\n",
-    "\n",
-    "auto glv = glvis::glvis();\n",
-    "glv.plot(ss.str() + \"keys Rjml\"); // the `+ \"keys ....\"' is optional\n",
-    "glv"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "C++14",
-   "language": "C++14",
-   "name": "xcpp14"
-  },
-  "language_info": {
-   "codemirror_mode": "text/x-c++src",
-   "file_extension": ".cpp",
-   "mimetype": "text/x-c++src",
-   "name": "c++",
-   "version": "14"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

examples/makefile

@@ -22,13 +22,10 @@ MFEM_LIB_FILE = mfem_is_not_built
 -include $(CONFIG_MK)
 
 SEQ_EXAMPLES = ex0 ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9 ex10 ex14 ex15 ex16 \
-  ex17 ex18 ex19 ex20 ex21 ex22 ex23 ex24 ex25 ex26 ex27 ex28 ex29 ex30
+  ex17 ex18 ex19 ex20 ex21 ex22 ex23 ex24 ex25 ex26 ex27 ex28 ex29
 PAR_EXAMPLES = ex0p ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex8p ex9p ex10p ex11p \
   ex12p ex13p ex14p ex15p ex16p ex17p ex18p ex19p ex20p ex21p ex22p ex24p \
-  ex25p ex26p ex27p ex28p ex29p ex30p
-SEQ_DEVICE_EXAMPLES = ex1 ex3 ex4 ex5 ex6 ex9 ex22 ex24 ex25 ex26
-PAR_DEVICE_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex22p \
-  ex24p ex25p ex26p
+  ex25p ex26p ex27p ex28p ex29p
 
 ifeq ($(MFEM_USE_MPI),NO)
    EXAMPLES = $(SEQ_EXAMPLES)
@@ -102,14 +99,6 @@ RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) $(MFEM_MPI_NP)
 	@$(call mfem-test,$<, $(RUN_MPI), Parallel example)
 %-test-seq: %
 	@$(call mfem-test,$<,, Serial example)
-%-test-par-cuda: %
-	@$(call mfem-test,$<, $(RUN_MPI), Parallel CUDA example,-d cuda)
-%-test-seq-cuda: %
-	@$(call mfem-test,$<,, Serial CUDA example,-d cuda)
-%-test-par-hip: %
-	@$(call mfem-test,$<, $(RUN_MPI), Parallel HIP example,-d hip)
-%-test-seq-hip: %
-	@$(call mfem-test,$<,, Serial HIP example,-d hip)
 
 # Testing: Specific execution options
 ex0-test-seq: ex0

examples/petsc/CMakeLists.txt

@@ -94,32 +94,30 @@ if (MFEM_USE_SLEPC)
 endif()
 
 # Add the tests: one test per command-line-variable.
-if (MFEM_ENABLE_TESTING)
-  set(TEST_OPTIONS_VARS
-      EX1_ARGS_W EX1_ARGS_P EX2_ARGS EX3_ARGS EX4_ARGS EX4_HYB_ARGS
-      EX5_BDDC_LB_ARGS EX5_BDDC_GB_ARGS EX5_FSPL_ARGS EX6_ARGS EX6_NONOVL_ARGS
-      EX9_E_ARGS EX9_ES_ARGS EX9_IS_ARGS EX10_ARGS)
-  if (MFEM_USE_SLEPC)
-      list(APPEND TEST_OPTIONS_VARS EX11_ARGS_SINV EX11_ARGS_LOBPCG EX11_ARGS_GD)
-  endif()
-
-  foreach(TEST_OPTIONS_VAR ${TEST_OPTIONS_VARS})
-    string(REGEX REPLACE "^(.+)_ARGS" "\\1" TEST_NAME_UC ${TEST_OPTIONS_VAR})
-    string(REGEX REPLACE "^([^_]+)" "\\1P" TEST_NAME_UC ${TEST_NAME_UC})
-    string(TOLOWER ${TEST_NAME_UC} TEST_NAME_FULL)
-    string(REGEX REPLACE "^([^_]+).*" "\\1" TEST_NAME ${TEST_NAME_FULL})
-    set(TEST_NAME_FULL ${PFX}${TEST_NAME_FULL})
-    set(TEST_NAME ${PFX}${TEST_NAME})
-    set(TEST_OPTIONS "-no-vis" ${${TEST_OPTIONS_VAR}})
-    # message(STATUS "${TEST_NAME_FULL} --> ${TEST_NAME} ${TEST_OPTIONS}")
-
-    # All PETSC tests are parallel.
-    if (MFEM_USE_MPI)
-      add_test(NAME ${TEST_NAME_FULL}_np=4
-        COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
-        ${MPIEXEC_PREFLAGS}
-        $<TARGET_FILE:${TEST_NAME}> ${TEST_OPTIONS}
-        ${MPIEXEC_POSTFLAGS})
-    endif()
-  endforeach()
+set(TEST_OPTIONS_VARS
+    EX1_ARGS_W EX1_ARGS_P EX2_ARGS EX3_ARGS EX4_ARGS EX4_HYB_ARGS
+    EX5_BDDC_LB_ARGS EX5_BDDC_GB_ARGS EX5_FSPL_ARGS EX6_ARGS EX6_NONOVL_ARGS
+    EX9_E_ARGS EX9_ES_ARGS EX9_IS_ARGS EX10_ARGS)
+if (MFEM_USE_SLEPC)
+    list(APPEND TEST_OPTIONS_VARS EX11_ARGS_SINV EX11_ARGS_LOBPCG EX11_ARGS_GD)
 endif()
+
+foreach(TEST_OPTIONS_VAR ${TEST_OPTIONS_VARS})
+  string(REGEX REPLACE "^(.+)_ARGS" "\\1" TEST_NAME_UC ${TEST_OPTIONS_VAR})
+  string(REGEX REPLACE "^([^_]+)" "\\1P" TEST_NAME_UC ${TEST_NAME_UC})
+  string(TOLOWER ${TEST_NAME_UC} TEST_NAME_FULL)
+  string(REGEX REPLACE "^([^_]+).*" "\\1" TEST_NAME ${TEST_NAME_FULL})
+  set(TEST_NAME_FULL ${PFX}${TEST_NAME_FULL})
+  set(TEST_NAME ${PFX}${TEST_NAME})
+  set(TEST_OPTIONS "-no-vis" ${${TEST_OPTIONS_VAR}})
+  # message(STATUS "${TEST_NAME_FULL} --> ${TEST_NAME} ${TEST_OPTIONS}")
+
+  # All PETSC tests are parallel.
+  if (MFEM_USE_MPI)
+    add_test(NAME ${TEST_NAME_FULL}_np=4
+      COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:${TEST_NAME}> ${TEST_OPTIONS}
+      ${MPIEXEC_POSTFLAGS})
+  endif()
+endforeach()

examples/petsc/ex3p.cpp

@@ -121,7 +121,9 @@ int main(int argc, char *argv[])
 
    // 5. 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.
+   //    parallel mesh is defined, the serial mesh can be deleted. Tetrahedral
+   //    meshes need to be reoriented before we can define high-order Nedelec
+   //    spaces on them.
    ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
    delete mesh;
    {
@@ -131,6 +133,7 @@ int main(int argc, char *argv[])
          pmesh->UniformRefinement();
       }
    }
+   pmesh->ReorientTetMesh();
 
    // 6. Define a parallel finite element space on the parallel mesh. Here we
    //    use the Nedelec finite elements of the specified order.