Merge branch 'develop' into fuad-commits-not-interpolation

.github/actions/install-repo/action.yml

@@ -0,0 +1,44 @@
+name: Install-Repo
+
+inputs:
+  repo-name:
+    required: true
+  repo-path:
+    required: true
+  repo-ref:
+    required: true
+  options:
+    required: true
+  cache:
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+
+  - name: Check Cache
+    if: ${{ inputs.cache == 'true'}}
+    uses: actions/cache@v3
+    id: check-cache
+    with:
+      key: build-${{ inputs.repo-name }}
+      path: ${{ runner.temp }}/build-${{ inputs.repo-name }}
+
+  - name: Checkout Repo
+    uses: actions/checkout@v3
+    with:
+      repository: ${{inputs.repo-path }}
+      ref: ${{ inputs.repo-ref }}
+      path: ${{ inputs.repo-name }}
+
+  - name: Configure CMake
+    if: ${{ !steps.check-cache.outputs.cache-hit }}
+    shell: bash
+    run: cmake -S $GITHUB_WORKSPACE/${{ inputs.repo-name }} -B ${{ runner.temp }}/build-${{ inputs.repo-name }}
+      -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/build-${{ inputs.repo-name }}/install
+      ${{ inputs.options }}
+
+  - name: Build Cmake
+    if: ${{ !steps.check-cache.outputs.cache-hit }}
+    shell: bash
+    run: cmake --build ${{ runner.temp }}/build-${{ inputs.repo-name }} -j8 --target install

.github/workflows/cmake-test.yml

@@ -0,0 +1,150 @@
+name: Test-Build
+on:
+  push:
+  schedule:
+    - cron: '12 14 * * 3' 
+
+jobs:
+  test-build:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash
+
+    strategy:
+      matrix:
+        build_type: [Release]
+        memory_test: [ON, OFF]
+        compiler: [g++]
+        language: ['cpp']
+        exclude:
+          - build_type: Release
+            memory_test: ON
+          - build_type: RelWithDebInfo
+            memory_test: OFF
+
+    steps:
+
+    - name: Update packages
+      run: sudo apt-get update
+
+    - name: Install mpi
+      run: sudo apt-get install -yq mpich libmpich-dev
+
+    - uses: actions/checkout@v4
+
+    - name: build kokkos
+      uses: ./.github/actions/install-repo
+      with:
+        repo-name: 'kokkos'
+        repo-path: 'kokkos/kokkos'
+        repo-ref: '4.2.00'
+        cache: true
+        options: '-DCMAKE_CXX_COMPILER=${{ matrix.compiler }}
+                  -DKokkos_ENABLE_SERIAL=ON
+                  -DKokkos_ENABLE_OPENMP=off
+                  -DKokkos_ENABLE_CUDA=off
+                  -DKokkos_ENABLE_CUDA_LAMBDA=off
+                  -DKokkos_ENABLE_DEBUG=on'
+
+    - name: build ADIOS2
+      uses: ./.github/actions/install-repo
+      with:
+        repo-name: 'ADIOS2'
+        repo-path: 'ornladios/ADIOS2'
+        repo-ref: ''
+        cache: true
+        options: '-DADIOS2_USE_CUDA=off
+                  -DCMAKE_BUILD_TYPE=Release
+                  -DCMAKE_CXX_COMPILER=mpicxx
+                  -DCMAKE_C_COMPILER=mpicc'
+
+    - name: build perfstubs
+      uses: ./.github/actions/install-repo
+      with:
+        repo-name: 'perfstubs'
+        repo-path: 'UO-OACISS/perfstubs'
+        repo-ref: ''
+        cache: true
+        options: '-DCMAKE_BUILD_TYPE=Release
+                  -DCMAKE_CXX_COMPILER=mpicxx
+                  -DCMAKE_C_COMPILER=mpicc'
+
+    - name: build redev
+      uses: ./.github/actions/install-repo
+      with:
+        repo-name: 'redev'
+        repo-path: 'SCOREC/redev'
+        repo-ref: ''
+        cache: true
+        options: '-DCMAKE_BUILD_TYPE=Release
+                  -DCMAKE_CXX_COMPILER=mpicxx
+                  -DCMAKE_C_COMPILER=mpicc
+                  -DMPIEXEC_EXECUTABLE=`which srun`
+                  -Dperfstubs_DIR=${{ runner.temp }}/build-perfstubs
+                  -DADIOS2_ROOT=${{ runner.temp }}/build-ADIOS2/install'
+
+    - name: build omega_h
+      uses: ./.github/actions/install-repo
+      with:
+        repo-name: 'omega_h'
+        repo-path: 'SCOREC/omega_h'
+        repo-ref: ''
+        cache: true
+        options: '-DCMAKE_BUILD_TYPE=Release
+                  -DBUILD_SHARED_LIBS=off
+                  -DOmega_h_USE_Kokkos=on
+                  -DOmega_h_USE_CUDA=off
+                  -DOmega_h_USE_MPI=on
+                  -DMPIEXEC_EXECUTABLE=srun
+                  -DBUILD_TESTING=off
+                  -DCMAKE_C_COMPILER=mpicc
+                  -DCMAKE_CXX_COMPILER=mpicxx
+                  -DKokkos_PREFIX=${{ runner.temp }}/build-kokkos/install/lib/cmake'
+
+    - name: build Catch2
+      uses: ./.github/actions/install-repo
+      with:
+        repo-name: 'Catch2'
+        repo-path: 'catchorg/Catch2'
+        repo-ref: ''
+        cache: true
+        options: '-DCMAKE_BUILD_TYPE=Release
+                  -DCMAKE_CXX_COMPILER=mpicxx'
+
+    - name: checkout pcms_testcases
+      uses: actions/checkout@v3
+      with:
+        repository: jacobmerson/pcms_testcases
+        path: pcms_testcases
+
+    - name: Install fftw3
+      run: sudo apt-get install -yq fftw3 fftw3-dev pkg-config
+
+    - name: build pcms
+      uses: ./.github/actions/install-repo
+      with:
+        repo-name: 'pcms'
+        repo-path: 'SCOREC/pcms'
+        repo-ref: ''
+        cache: false
+        options: '-DCMAKE_BUILD_TYPE=Release
+                  -DCMAKE_C_COMPILER=mpicc
+                  -DCMAKE_CXX_COMPILER=mpicxx
+                  -Dredev_DIR=${{ runner.temp }}/build-redev/install/lib/cmake/redev
+                  -Dperfstubs_DIR=${{ runner.temp }}/build-perfstubs
+                  -DOmega_h_DIR=${{ runner.temp }}/build-omega_h/install/lib/cmake/Omega_h
+                  -DKokkos_DIR=${{ runner.temp }}/build-kokkos/install/lib/cmake/Kokkos
+                  -DCatch2_DIR=${{ runner.temp }}/build-Catch2/install/lib/cmake/Catch2
+                  -DPCMS_TEST_DATA_DIR=$PWD/pcms_testcases'
+
+    # - name: Install Valgrind
+    #   run: sudo apt-get install -yq valgrind
+
+    # - name: Run CTest
+    #   run: ctest --test-dir ${{ runner.temp }}/build-pcms
+
+    # - name: Print Test
+    #   if: always()
+    #   run: cat ${{ runner.temp }}/build-pcms/Testing/Temporary/LastTest.log

.github/workflows/globus-tests.yml

@@ -0,0 +1,12 @@
+name: Globus-Systems
+on:
+  schedule:
+    # Monday 8:35 UTC or 04:35 EDT
+    - cron: '35 8 * * 1'
+
+jobs:
+  perlmutter-test:
+    uses: SCOREC/github-actions/.github/workflows/globus-test.yml@main
+    secrets: inherit
+    with:
+      machine: "perlmutter"

.github/workflows/perlmutter/install.sh

@@ -0,0 +1,110 @@
+#!/bin/bash -e
+
+branch=$1
+
+cd $SCRATCH/globus-compute/pcms-test
+
+module load cray-fftw
+
+# # kokkos
+# rm build-kokkos -rf
+# # rm kokkos -rf
+# git clone -b 4.2.00 https://github.com/kokkos/kokkos.git
+# cmake -S kokkos -B build-kokkos \
+#   -DCMAKE_INSTALL_PREFIX=build-kokkos/install \
+#   -DCMAKE_BUILD_TYPE="Release" \
+#   -DCMAKE_CXX_COMPILER=$PWD/kokkos/bin/nvcc_wrapper \
+#   -DKokkos_ARCH_AMPERE80=ON \
+#   -DKokkos_ENABLE_SERIAL=ON \
+#   -DKokkos_ENABLE_OPENMP=off \
+#   -DKokkos_ENABLE_CUDA=on \
+#   -DKokkos_ENABLE_CUDA_LAMBDA=on \
+#   -DKokkos_ENABLE_CUDA_CONSTEXPR=on \
+#   -DKokkos_ENABLE_DEBUG=off
+# cmake --build build-kokkos -j 24 --target install
+
+# # ADIOS2
+# rm build-ADIOS2 -rf
+# # rm ADIOS2 -rf
+# git clone [email protected]:ornladios/ADIOS2.git
+# cmake -S ADIOS2/ -B build-ADIOS2 \
+#   -DCMAKE_INSTALL_PREFIX=build-ADIOS2/install \
+#   -DADIOS2_USE_CUDA=on \
+#   -DCMAKE_BUILD_TYPE=Release \
+#   -DCMAKE_CXX_COMPILER=CC \
+#   -DCMAKE_C_COMPILER=cc
+# cmake --build build-ADIOS2 --target install -j8
+
+# # perfstubs
+# rm build-perfstubs -rf
+# # rm perfstubs -rf
+# git clone [email protected]:UO-OACISS/perfstubs.git
+# cmake -S perfstubs -B build-perfstubs \
+#   -DCMAKE_CXX_COMPILER=CC \
+#   -DCMAKE_C_COMPILER=cc \
+#   -DCMAKE_INSTALL_PREFIX=build-perfstubs/install
+# cmake --build build-perfstubs -j2 --target install
+
+# # redev
+# rm build-redev -rf
+# # rm redev -rf
+# git clone [email protected]:SCOREC/redev.git
+# cmake -S redev -B build-redev \
+#   -DCMAKE_CXX_COMPILER=CC \
+#   -DCMAKE_C_COMPILER=cc \
+#   -DMPIEXEC_EXECUTABLE=`which srun` \
+#   -DCMAKE_BUILD_TYPE=Release \
+#   -DCMAKE_INSTALL_PREFIX=build-redev/install \
+#   -Dperfstubs_DIR=$PWD/build-perfstubs \
+#   -DADIOS2_ROOT=build-ADIOS2/install
+# cmake --build build-redev -j2 --target install
+
+# # omega_h
+# rm build-omega_h -rf
+# # rm omega_h -rf
+# git clone [email protected]:SCOREC/omega_h.git
+# cmake -S omega_h -B build-omega_h \
+#   -DCMAKE_INSTALL_PREFIX=build-omega_h/install \
+#   -DCMAKE_BUILD_TYPE=Release \
+#   -DBUILD_SHARED_LIBS=off \
+#   -DOmega_h_USE_Kokkos=ON \
+#   -DOmega_h_USE_CUDA=on \
+#   -DOmega_h_CUDA_ARCH=80 \
+#   -DOmega_h_USE_MPI=on  \
+#   -DMPIEXEC_EXECUTABLE=srun \
+#   -DBUILD_TESTING=off  \
+#   -DCMAKE_C_COMPILER=cc \
+#   -DCMAKE_CXX_COMPILER=CC \
+#   -DKokkos_PREFIX=build-kokkos/install/lib64/cmake
+# cmake --build build-omega_h -j24 --target install
+
+# # Catch2
+# rm build-Catch2 -rf
+# # rm Catch2 -rf
+# git clone https://github.com/catchorg/Catch2
+# cmake -S Catch2 -B build-Catch2 \
+#   -DCMAKE_INSTALL_PREFIX=$PWD/build-Catch2/install \
+#   -DCMAKE_CXX_COMPILER=CC
+# cmake --build build-Catch2 -j2 --target install
+
+# pcms
+rm pcms -rf
+rm build-pcms -rf
+rm pcms_testcases -rf
+
+git clone [email protected]:jacobmerson/pcms_testcases.git
+git clone https://github.com/SCOREC/pcms.git
+cd pcms && git checkout $branch && cd -
+
+cmake -S pcms -B build-pcms \
+  -DCMAKE_C_COMPILER=cc \
+  -DCMAKE_CXX_COMPILER=CC \
+  -DCMAKE_BUILD_TYPE=Release \
+  -DPCMS_TIMEOUT=0 \
+  -Dperfstubs_DIR=$PWD/build-perfstubs \
+  -Dredev_DIR=$PWD/build-redev/install/lib64/cmake/redev \
+  -DOmega_h_DIR=$PWD/build-omega_h/install/lib64/cmake/Omega_h/ \
+  -DKokkos_DIR=$PWD/build-kokkos/install/lib64/cmake/Kokkos/ \
+  -DCatch2_DIR=$PWD/build-Catch2/install/lib64/cmake/Catch2/ \
+  -DPCMS_TEST_DATA_DIR=$PWD/pcms_testcases
+cmake --build build-pcms -j8

.github/workflows/perlmutter/run.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+name=pcms
+
+cd $SCRATCH/globus-compute/$name-test
+
+module load cray-fftw
+
+cd build-$name
+salloc --time 00:20:00 --constrain=gpu --qos=interactive --nodes=1 --ntasks-per-node=40 --cpus-per-task=1 --gpus=1 --account=m4564 ctest
+cat $PWD/Testing/Temporary/LastTest.log

.github/workflows/update_doxygen_page.yml

@@ -0,0 +1,49 @@
+name: Update Doxygen Page
+
+on:
+  push:
+    branches:
+        - master
+
+jobs:
+  doxygen:
+    runs-on: ubuntu-latest
+    permissions:
+       contents: write
+
+    steps:
+
+    - name: Install Doxygen
+      run: |
+        sudo apt-add-repository universe
+        sudo apt-get update
+        sudo apt-get install doxygen
+
+    - name: Checkout Original
+      uses: actions/checkout@v4
+      with:
+        path: original
+
+    - name: Run Doxygen
+      working-directory: original
+      run: doxygen
+
+    - name: Checkout Pages
+      uses: actions/checkout@v4
+      with:
+        path: pages
+
+    - name: Set up pages directory
+      working-directory: pages
+      run: |
+        git checkout --orphan gh-pages
+        git rm -rf .
+        cp -r ../original/html/. .
+    - name: Update Github
+      working-directory: pages
+      run: |
+        git config user.name "GitHub Actions Bot"
+        git config user.email "<>"
+        git add .
+        git commit -m "Update page from action"
+        git push -f origin gh-pages