Merge branch 'devel' into glads_gl

.github/workflows/act_test.yaml

@@ -0,0 +1,162 @@
+name: act_test
+on:
+  workflow_dispatch:
+  # push:
+  #   paths-ignore:
+  #     - '**.nix'
+  #     - 'flake.lock'
+  # pull_request:
+  #   paths-ignore:
+  #     - '**.nix'
+  #     - 'flake.lock'
+
+concurrency: act_test-${{ github.ref }}
+
+jobs:
+
+  ubuntu:
+    # For available GitHub-hosted runners, see:
+    # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
+    runs-on: ${{ matrix.os }}
+
+    name: ${{ matrix.os }} (${{ matrix.compiler }} ${{ matrix.mpi }} MPI ${{ matrix.openmp }} OpenMP)
+
+    strategy:
+      # Allow other runners in the matrix to continue if some fail
+      fail-fast: false
+
+      matrix:
+        os: [ubuntu-24.04]
+        compiler: [gcc]
+        mpi: [with]
+        openmp: [with]
+        include:
+          - os: ubuntu-24.04-arm
+            compiler: gcc
+            compiler-pkgs: "g++ gcc"
+            cc: "gcc"
+            cxx: "g++"
+            mpi: with
+            openmp: without
+            openmp-cmake-flags: "-DWITH_OpenMP=OFF"
+    env:
+      CC: ${{ matrix.cc }}
+      CXX: ${{ matrix.cxx }}
+
+    steps:
+      - name: get CPU information
+        run: lscpu
+
+      - name: checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: install dependencies
+        run: |
+          sudo apt -qq update
+          sudo apt install -y ${{ matrix.compiler-pkgs }} cmake gfortran \
+            libopenblas-dev \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "libhypre-dev") \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "libopenmpi-dev libmumps-dev libparmetis-dev") \
+            $([ "${{ matrix.compiler }}" == "gcc" ] && echo "libsuitesparse-dev") \
+            $([ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ] && echo "librocalution-dev") \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "trilinos-all-dev libptscotch-dev") \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "libnetcdff-dev")
+
+      - name: configure
+        # CHOLMOD and rocALUTION require a working OpenMP package. So, disable them for clang.
+        run: |
+          # work around error in the rocALUTION CMake config file distributed by Ubuntu
+          if [ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ]; then
+            sudo sed -i '/find_dependency(HIP)/d' /usr/lib/$(dpkg-architecture -qDEB_HOST_MULTIARCH)/cmake/rocalution/rocalution-config.cmake
+          fi
+          mkdir ${GITHUB_WORKSPACE}/build
+          cd ${GITHUB_WORKSPACE}/build
+          cmake \
+            -DCMAKE_BUILD_TYPE="RelWithDebInfo" \
+            -DCMAKE_INSTALL_PREFIX="${GITHUB_WORKSPACE}/usr" \
+            -DBLA_VENDOR="OpenBLAS" \
+            ${{ matrix.openmp-cmake-flags }} \
+            -DWITH_LUA=ON \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Zoltan=OFF" || echo "-DWITH_Zoltan=OFF") \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Mumps=OFF" || echo "-DWITH_Mumps=OFF") \
+            $([ "${{ matrix.compiler }}" == "gcc" ] && echo "-DWITH_CHOLMOD=OFF" || echo "-DWITH_CHOLMOD=OFF") \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Hypre=OFF -DHYPRE_INCLUDE_DIR=/usr/include/hypre" || echo "-DWITH_Hypre=OFF") \
+            $([ "${{ matrix.compiler }}" == "gcc" ] && [ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_ROCALUTION=OFF" || echo "-DWITH_ROCALUTION=OFF") \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_ElmerIce=OFF" || echo "-DWITH_ElmerIce=OFF") \
+            -DWITH_ELMERGUI=OFF \
+            -DWITH_VTK=OFF \
+            -DWITH_OCC=OFF \
+            -DWITH_MATC=OFF \
+            -DWITH_PARAVIEW=OFF \
+            -DCREATE_PKGCONFIG_FILE=ON \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_MPI=ON -DMPI_TEST_MAXPROC=2 -DMPIEXEC_PREFLAGS=--allow-run-as-root" || echo "-DWITH_MPI=OFF") \
+            $([ "${{ matrix.mpi }}" == "with" ] && echo "-DWITH_Trilinos=OFF" || echo "-DWITH_Trilinos=OFF") \
+            ..
+
+      - name: build
+        run: |
+          cd ${GITHUB_WORKSPACE}/build
+          cmake --build . -j$(nproc)
+
+      - name: install
+        run: |
+          cd ${GITHUB_WORKSPACE}/build
+          cmake --install .
+
+      - name: check
+        id: run-ctest
+        timeout-minutes: 150
+        env:
+          CTEST_OUTPUT_ON_FAILURE: 1
+        run: |
+          cd ${GITHUB_WORKSPACE}/build
+          ctest . \
+            -LE slow \
+            -j$(nproc) \
+            --timeout 300
+
+      - name: Re-run tests
+        if: always() && (steps.run-ctest.outcome == 'failure')
+        timeout-minutes: 60
+        env:
+          CTEST_OUTPUT_ON_FAILURE: 1
+        run: |
+          cd ${GITHUB_WORKSPACE}/build
+          # get names of failed tests and strip potential "_np*" suffix
+          failed_tests=($(ctest . -N --rerun-failed | grep -E "Test\s+#.*" | awk '{print $3}' | sed -e 's/_np[0-9]*$//g'))
+          # remove duplicate test names
+          unique_failed_tests=($(echo "${failed_tests[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' '))
+          for test in "${unique_failed_tests[@]}"; do
+            # check if test is from fem or ElmerIce
+            if [ -d fem/tests/${test} ]; then
+              test_root=fem/tests
+            else
+              test_root=elmerice/Tests
+            fi
+            echo "::group::Content of ${test_root}/${test}"
+            echo ---- Files ----
+            ls -Rl ${test_root}/${test}
+            if [ -f ${test_root}/${test}/test-stderr*.log ]; then
+              err_logs=($(ls ${test_root}/${test}/test-stderr*.log))
+              for err_log in "${err_logs[@]}"; do
+                echo ---- Content of ${err_log} ----
+                cat ${err_log}
+              done
+            fi
+            if [ -f ${test_root}/${test}/test-stdout*.log ]; then
+              out_logs=($(ls ${test_root}/${test}/test-stdout*.log))
+              for out_log in "${out_logs[@]}"; do
+                echo ---- Content of ${out_log} ----
+                cat ${out_log}
+              done
+            fi
+            echo "::endgroup::"
+          done
+          echo "::group::Re-run failing tests"
+          ctest --rerun-failed --output-on-failure --timeout 180 || true
+          echo "::endgroup::"
+          echo "::group::Log from these tests"
+          [ ! -f Testing/Temporary/LastTest.log ] || cat Testing/Temporary/LastTest.log
+          echo "::endgroup::"

.github/workflows/build-macos-homebrew.yaml

@@ -18,12 +18,28 @@ jobs:
 
     runs-on: ${{ matrix.os }}
 
+    name: ${{ matrix.os }} (${{ matrix.openmp }} OpenMP)
+
     strategy:
       # Allow other runners in the matrix to continue if some fail
       fail-fast: false
 
       matrix:
-        os: [macos-14, macos-13]
+        os: [macos-14]
+        openmp: [without]
+        # Building with OpenMP causes some test failures on macOS on Apple
+        # Silicon.
+        # The affected tests currently are: H1BasisEvaluation and
+        # SD_H1BasisEvaluation.
+        # For the time being, disable building with OpenMP in CI on Apple
+        # Silicon.
+        # OpenMP is also needed as a transitional build dependency of the
+        # SuiteSparse package from Homebrew.
+        # FIXME: Consider building with OpenMP again when this (potentially
+        # upstream) issue has been fixed.
+        include:
+          - os: macos-13
+            openmp: with
 
     steps:
       - name: get CPU information
@@ -49,34 +65,40 @@ jobs:
           brew install --overwrite [email protected] [email protected]
           brew reinstall gcc
           brew install \
-            cmake libomp openblas open-mpi suitesparse \
+            cmake openblas open-mpi \
+            ${{ matrix.openmp == 'with' && 'libomp suitesparse' || '' }} \
             qwt vtk opencascade
           echo "HOMEBREW_PREFIX=$(brew --prefix)" >> $GITHUB_ENV
 
       - name: configure
         env:
-          LDFLAGS: -L${{ env.HOMEBREW_PREFIX }}/opt/libomp/lib -lomp
+          LDFLAGS: ${{ matrix.openmp == 'with' && format('-L{0}/opt/libomp/lib -lomp', env.HOMEBREW_PREFIX) || '' }}
+        # The tests `SD_H1BasisEvaluation` and `SD_LinearFormsAssembly` are
+        # failing on macos-13 (Intel CPU) at optimization level `-O3`.
+        # They are passing if ElmerFEM is built with optimization level `-O2`.
         run: |
           mkdir ${GITHUB_WORKSPACE}/build
           cd ${GITHUB_WORKSPACE}/build
           cmake \
-            -DCMAKE_BUILD_TYPE="Release" \
+            -DCMAKE_BUILD_TYPE=${{ matrix.os == 'macos-13' && 'RelWithDebInfo' || 'Release' }} \
             -DCMAKE_C_COMPILER=clang \
             -DCMAKE_CXX_COMPILER=clang++ \
             -DCMAKE_Fortran_COMPILER=gfortran \
             -DCMAKE_INSTALL_PREFIX="${GITHUB_WORKSPACE}/usr" \
             -DBLA_VENDOR="OpenBLAS" \
-            -DCMAKE_PREFIX_PATH="${HOMEBREW_PREFIX}/opt/libomp;${HOMEBREW_PREFIX}/opt/openblas;${HOMEBREW_PREFIX}/opt/qt;${HOMEBREW_PREFIX}/opt/qwt" \
-            -DWITH_OpenMP=ON \
-            -DOpenMP_C_FLAGS="-Xclang -fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include" \
-            -DOpenMP_CXX_FLAGS="-Xclang -fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include" \
-            -DOpenMP_Fortran_FLAGS="-fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include" \
+            -DCMAKE_PREFIX_PATH="$( [ "${{ matrix.openmp }}" == "with" ] && echo "${HOMEBREW_PREFIX}/opt/libomp;")${HOMEBREW_PREFIX}/opt/openblas;${HOMEBREW_PREFIX}/opt/qt;${HOMEBREW_PREFIX}/opt/qwt" \
+            ${{ matrix.openmp == 'with'
+              && '-DWITH_OpenMP=ON \
+                  -DOpenMP_C_FLAGS="-Xclang -fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include" \
+                  -DOpenMP_CXX_FLAGS="-Xclang -fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include" \
+                  -DOpenMP_Fortran_FLAGS="-fopenmp -I${HOMEBREW_PREFIX}/opt/libomp/include"'
+              || '-DWITH_OpenMP=OFF' }} \
             -DWITH_LUA=ON \
             -DWITH_MPI=ON \
             -DMPI_TEST_MAXPROC=2 \
             -DWITH_Zoltan=OFF \
             -DWITH_Mumps=OFF \
-            -DWITH_CHOLMOD=ON \
+            -DWITH_CHOLMOD=${{ matrix.openmp == 'with' && 'ON' || 'OFF' }} \
             -DWITH_ElmerIce=ON \
             -DWITH_ELMERGUI=ON \
             -DWITH_QT6=ON \
@@ -132,12 +154,18 @@ jobs:
             echo ---- Files ----
             ls -Rl ${test_root}/${test}
             if [ -f ${test_root}/${test}/test-stderr*.log ]; then
-              echo ---- Content of test-stderr*.log ----
-              cat ${test_root}/${test}/test-stderr*.log
+              err_logs=($(ls ${test_root}/${test}/test-stderr*.log))
+              for err_log in "${err_logs[@]}"; do
+                echo ---- Content of ${err_log} ----
+                cat ${err_log}
+              done
             fi
             if [ -f ${test_root}/${test}/test-stdout*.log ]; then
-              echo ---- Content of test-stdout*.log ----
-              cat ${test_root}/${test}/test-stdout*.log
+              out_logs=($(ls ${test_root}/${test}/test-stdout*.log))
+              for out_log in "${out_logs[@]}"; do
+                echo ---- Content of ${out_log} ----
+                cat ${out_log}
+              done
             fi
             echo "::endgroup::"
           done

.github/workflows/build-windows-mingw.yaml

@@ -170,12 +170,18 @@ jobs:
             echo ---- Files ----
             ls -Rl ${test_root}/${test}
             if [ -f ${test_root}/${test}/test-stderr*.log ]; then
-              echo ---- Content of test-stderr*.log ----
-              cat ${test_root}/${test}/test-stderr*.log
+              err_logs=($(ls ${test_root}/${test}/test-stderr*.log))
+              for err_log in "${err_logs[@]}"; do
+                echo ---- Content of ${err_log} ----
+                cat ${err_log}
+              done
             fi
             if [ -f ${test_root}/${test}/test-stdout*.log ]; then
-              echo ---- Content of test-stdout*.log ----
-              cat ${test_root}/${test}/test-stdout*.log
+              out_logs=($(ls ${test_root}/${test}/test-stdout*.log))
+              for out_log in "${out_logs[@]}"; do
+                echo ---- Content of ${out_log} ----
+                cat ${out_log}
+              done
             fi
             echo "::endgroup::"
           done