reorganize CI, add linux-codipack build+test

.github/workflows/c-cpp.yml

@@ -11,6 +11,10 @@ env:
 jobs:
   build:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        ad_type: ['', 'codipack']
     steps:
       - run: echo "The job was automatically triggered by a ${{ github.event_name }} event."
       - run: echo "This job is now running on a ${{ runner.os }} server hosted by GitHub!"
@@ -35,14 +39,23 @@ jobs:
           cd $ISSM_DIR/externalpackages/m1qn3    && ./install-linux.sh
           cd $ISSM_DIR/externalpackages/petsc    && ./install-3.21-linux.sh
 
+      - name: Install Codipack
+        if: ${{ matrix.ad_type == 'codipack'}}
+        run: |
+          source $ISSM_DIR/etc/environment.sh
+          cd $ISSM_DIR/externalpackages/gsl      && ./install.sh
+          cd $ISSM_DIR/externalpackages/codipack && ./install.sh
+          cd $ISSM_DIR/externalpackages/medipack && ./install.sh
+
       - name: Get MATLAB
         id:   setup-matlab
         uses: matlab-actions/setup-matlab@v2
         with:
           release: R2023b
           cache: true
 
-      - name: Reconfigure ISSM
+      - name: Reconfigure ISSM without AD
+        if: ${{ matrix.ad_type == ''}}
         run: |
           source $ISSM_DIR/etc/environment.sh
           autoreconf -ivf
@@ -63,18 +76,48 @@ jobs:
           --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
           --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
           --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
-
+
+      - name: Reconfigure ISSM without Codipack
+        if: ${{ matrix.ad_type == 'codipack'}}
+        run: |
+          source $ISSM_DIR/etc/environment.sh
+          autoreconf -ivf
+          ./configure --prefix=${ISSM_DIR} \
+          --enable-tape-alloc \
+          --enable-development \
+          --enable-debugging \
+          --with-numthreads=4 \
+          --without-kriging \
+          --without-kml \
+          --without-Sealevelchange \
+          --without-Love \
+          --with-matlab-dir=${{ steps.setup-matlab.outputs.matlabroot }} \
+          --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \
+          --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \
+          --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
+          --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
+          --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
+          --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
+          --with-medipack-dir="${ISSM_DIR}/externalpackages/medipack/install" \
+          --with-codipack-dir="${ISSM_DIR}/externalpackages/codipack/install" 
+
       - name: Compile ISSM
         run: make -j16 install
 
       - name: Compress ISSM artifact
-        run: tar -cvf ISSM_artifact.tar -C ${{ env.ISSM_DIR }}/ .
+        run: tar -cvf ISSM_artifact-${{ matrix.ad_type}}.tar -C ${{ env.ISSM_DIR }}/ .
 
       - name: Upload ISSM artifact
         uses: actions/upload-artifact@v4
         with:
-          name: ISSM-${{ runner.os }}
-          path: ISSM_artifact.tar
+          name: ISSM-${{ runner.os }}-${{ matrix.ad_type}}
+          path: ISSM_artifact-${{ matrix.ad_type}}.tar
           compression-level: 1
 
   test:
@@ -83,18 +126,22 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        test-cases: ["101:110", "201:210", "301:310"]
+        ad_type: ['', 'codipack']
+        test-cases: ['101:110, "201:210', '301:310']
+        include:
+          - ad_type: 'codipack'
+            test-cases: '3015,3119,3480,3201:3206'
+
     steps:
       - name: Download ISSM artifact
         uses: actions/download-artifact@v4
         with:
-          name: ISSM-${{ runner.os }}
+          name: ISSM-${{ runner.os }}-${{ matrix.ad_type}}
           path: ${{ env.ISSM_DIR }}
 
       - name: uncompress ISSM artifact
         run: |
-          tar -xvf ISSM_artifact.tar
-          rm ISSM_artifact.tar
+          tar -xvf ISSM_artifact-${{ matrix.ad_type}}.tar
           source $ISSM_DIR/etc/environment.sh
         working-directory: ${{ env.ISSM_DIR }}
         shell: 'bash'
@@ -117,7 +164,7 @@ jobs:
           devpath;
 
           % Run tests
-          runme('exclude',[IdFromString('Dakota')],'id',${{matrix.test-cases}},'quitonerror',1);
+          runme('exclude',[IdFromString('Dakota')],'id',[${{matrix.test-cases}}],'quitonerror',1);
           quit(0);
           EOF
           cat ${ISSM_DIR}/matlab_ci.m

.github/workflows/common-workflow.yml

@@ -0,0 +1,196 @@
+name: Common CI
+
+on:
+  workflow_call:
+    inputs:
+      os:
+        required: true
+        type: string
+      build_type: 
+        required: true
+        type: string
+env:
+  ISSM_DIR: ${{ github.workspace }}
+
+jobs:
+  build:
+    name: build-ISSM-${{ inputs.os }}-${{ inputs.build_type}}
+    runs-on: ${{ inputs.os }}
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+
+      - name: Cache externalpackages
+        uses: actions/cache@v3
+        id: cache-externalpackages
+        env:
+          cache-name: cache-externalpackages-${{ inputs.build_type }}
+        with:
+          path: |
+            ${{ env.ISSM_DIR }}/externalpackages/
+            !${{ env.ISSM_DIR }}/externalpackages/petsc/src/
+          key: ${{ runner.os }}-build-${{ env.cache-name }}
+
+      - name: Install External packages
+        if: ${{ ( inputs.build_type == 'basic') && (steps.cache-externalpackages.outputs.cache-hit != 'true') }}
+        run: |
+          cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh
+          cd $ISSM_DIR/externalpackages/m1qn3    && ./install-linux.sh
+          cd $ISSM_DIR/externalpackages/petsc    && ./install-3.21-linux.sh
+          cd $ISSM_DIR/externalpackages/semic    && ./install.sh
+
+      - name: Install External packages for AD
+        if: ${{ ( inputs.build_type == 'codipack') && (steps.cache-externalpackages.outputs.cache-hit != 'true') }}
+        run: |
+          cd $ISSM_DIR/externalpackages/triangle   && ./install-linux.sh
+          cd $ISSM_DIR/externalpackages/m1qn3      && ./install-linux.sh
+          cd $ISSM_DIR/externalpackages/petsc      && ./install-3.20-linux.sh
+          cd $ISSM_DIR/externalpackages/gsl        && ./install.sh
+          cd $ISSM_DIR/externalpackages/codipack   && ./install.sh
+          cd $ISSM_DIR/externalpackages/medipack   && ./install.sh
+
+      - name: Get MATLAB
+        id:   setup-matlab
+        uses: matlab-actions/setup-matlab@v2
+        with:
+          release: R2023b
+          cache: true
+
+      - name: Reconfigure ISSM without AD
+        if: ${{ inputs.build_type == 'basic'}}
+        run: |
+          source $ISSM_DIR/etc/environment.sh
+          autoreconf -ivf
+          ./configure --prefix=${ISSM_DIR} \
+          --disable-static \
+          --enable-development \
+          --enable-debugging \
+          --with-numthreads=4 \
+          --with-matlab-dir=${{ steps.setup-matlab.outputs.matlabroot }} \
+          --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \
+          --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \
+          --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
+          --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
+          --with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \
+          --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
+
+      - name: Reconfigure ISSM with Codipack
+        if: ${{ inputs.build_type == 'codipack'}}
+        run: |
+          source $ISSM_DIR/etc/environment.sh
+          autoreconf -ivf
+          ./configure --prefix=${ISSM_DIR} \
+          --enable-tape-alloc \
+          --enable-development \
+          --enable-debugging \
+          --with-numthreads=4 \
+          --without-kriging \
+          --without-kml \
+          --without-Sealevelchange \
+          --without-Love \
+          --with-matlab-dir=${{ steps.setup-matlab.outputs.matlabroot }} \
+          --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \
+          --with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \
+          --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
+          --with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+          --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
+          --with-gsl-dir="${ISSM_DIR}/externalpackages/gsl/install" \
+          --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
+          --with-medipack-dir="${ISSM_DIR}/externalpackages/medipack/install" \
+          --with-codipack-dir="${ISSM_DIR}/externalpackages/codipack/install" 
+
+      - name: Compile ISSM
+        run: make -j4 install
+
+      - name: Compress ISSM artifact
+        run: tar --exclude='./externalpackages/petsc/src' -cvf ISSM_artifact-${{ inputs.build_type}}.tar -C ${{ env.ISSM_DIR }}/ .
+
+      - name: Upload ISSM artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ISSM-${{ runner.os }}-${{ inputs.build_type}}
+          path: ISSM_artifact-${{ inputs.build_type}}.tar
+          compression-level: 1          
+  test:
+    runs-on: ${{ inputs.os }}
+    needs: build
+    strategy:
+      fail-fast: false
+      matrix:
+        test-cases: 
+          - '101:399'
+          - '401:899'
+          - '3015, 3119, 3480, 3201:3206'
+        build-type:
+          -  ${{ inputs.build_type }}
+        additional: 
+          - " "
+          - "'benchmark','all',"
+        exclude:
+          - build-type: 'basic'
+            additional: "'benchmark','all',"
+          - build-type: 'basic'
+            test-cases: '3015, 3119, 3480, 3201:3206'
+          - build-type: 'codipack'
+            additional: " "
+          - build-type: 'codipack'
+            test-cases: '101:399'
+          - build-type: 'codipack'
+            test-cases: '401:899'
+
+    steps:
+      - name: Download ISSM artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: ISSM-${{ runner.os }}-${{ inputs.build_type}}
+          path: ${{ env.ISSM_DIR }}
+
+      - name: uncompress ISSM artifact
+        run: |
+          tar -xvf ISSM_artifact-${{ inputs.build_type}}.tar
+          source $ISSM_DIR/etc/environment.sh
+        working-directory: ${{ env.ISSM_DIR }}
+        shell: 'bash'
+
+      - name: Get MATLAB
+        id:   setup-matlab
+        uses: matlab-actions/setup-matlab@v2
+        with:
+          release: R2023b
+          cache: true
+
+      - name: Creating matlab_ci.m
+        run: |
+          cat > ${ISSM_DIR}/matlab_ci.m << EOF
+          % Go to the test directory
+          cd $ISSM_DIR/test/NightlyRun/
+
+          % Add ISSM tools to path
+          addpath('${ISSM_DIR}/src/m/dev');
+          devpath;
+
+          % Run tests
+          runme('exclude',[IdFromString('Dakota')],${{matrix.additional}} 'id',[${{matrix.test-cases}}],'quitonerror',1);
+          quit(0);
+          EOF
+          cat ${ISSM_DIR}/matlab_ci.m
+
+      - name: Get run-matlab-command
+        run: |
+          wget -O /usr/local/bin/run-matlab-command https://ssd.mathworks.com/supportfiles/ci/run-matlab-command/v2/glnxa64/run-matlab-command
+          chmod +x /usr/local/bin/run-matlab-command
+
+      - name: Run MATLAB tests
+        run: |
+          source $ISSM_DIR/etc/environment.sh
+          LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so run-matlab-command "matlab_ci"

.github/workflows/main-ci.yml

@@ -0,0 +1,23 @@
+name: Main Workflow 
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+env:
+  ISSM_DIR: ${{ github.workspace }}
+
+jobs:
+  build-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        build_type: ['basic', 'codipack']
+    uses: ./.github/workflows/common-workflow.yml 
+    with:
+      os: ${{ matrix.os }}
+      build_type: ${{ matrix.build_type }}
+    secrets: inherit
+    name: build-test-${{ matrix.os }}-${{ matrix.build_type }}