From 909790be86c0ff767fd6e96dad20688c2d9f13c9 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 15:47:18 -0400
Subject: [PATCH 01/26] add codipack in CI

---
 .github/workflows/c-cpp.yml | 61 +++++++++++++++++++++++++++++++------
 1 file changed, 51 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 86b87941e..144ce932f 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.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!"
@@ -35,6 +39,13 @@ 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/codipack && ./install.sh
+          cd $ISSM_DIR/externalpackages/medipack && ./install.sh
+          
       - name: Get MATLAB
         id:   setup-matlab
         uses: matlab-actions/setup-matlab@v2
@@ -42,7 +53,8 @@ jobs:
           release: R2023b
           cache: true
           
-      - name: Reconfigure ISSM
+      - name: Reconfigure ISSM without AD
+        if: ${{ matrix.ad_type == ''}}
         run: |
           source $ISSM_DIR/etc/environment.sh
           autoreconf -ivf
@@ -63,18 +75,43 @@ jobs:
           --with-mumps-dir="${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} \
+          --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-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 -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 +120,22 @@ 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 +158,7 @@ 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

From 093a11eb9dfe11a999ab5c8814058417b83da783 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 16:10:56 -0400
Subject: [PATCH 02/26] try to fix codipack configure

---
 .github/workflows/c-cpp.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 144ce932f..6c4901fe2 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -82,10 +82,14 @@ jobs:
           source $ISSM_DIR/etc/environment.sh
           autoreconf -ivf
           ./configure --prefix=${ISSM_DIR} \
-          --disable-static \
+          --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" \

From 884b5f01fa6e224b8cfdfaa5e78144d78f1fa45a Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 16:33:39 -0400
Subject: [PATCH 03/26] add gsl

---
 .github/workflows/c-cpp.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml
index 6c4901fe2..ffe1aa6f0 100644
--- a/.github/workflows/c-cpp.yml
+++ b/.github/workflows/c-cpp.yml
@@ -43,6 +43,7 @@ jobs:
         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
           
@@ -102,6 +103,7 @@ jobs:
           --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
           --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
           --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
+          --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
           --with-medipack-dir="${ISSM_DIR}/externalpackages/medipack/install" \
           --with-codipack-dir="${ISSM_DIR}/externalpackages/codipack/install" 
           

From 728380439a53722fbfb0a65b6bf6cb5bda035c85 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 16:59:03 -0400
Subject: [PATCH 04/26] seperate basic and codipack

---
 .github/workflows/common-workflow.yml | 178 ++++++++++++++++++++++++++
 .github/workflows/main-ci.yml         |  20 +++
 2 files changed, 198 insertions(+)
 create mode 100644 .github/workflows/common-workflow.yml
 create mode 100644 .github/workflows/main-ci.yml

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
new file mode 100644
index 000000000..a0e31e413
--- /dev/null
+++ b/.github/workflows/common-workflow.yml
@@ -0,0 +1,178 @@
+name: Common CI
+
+on:
+  workflow_call:
+    inputs:
+      build_type: 
+        required: true
+        type: string
+env:
+  ISSM_DIR: ${{ github.workspace }}
+  
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    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!"
+      - run: echo "The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
+
+      - name: Check out repository code
+        uses: actions/checkout@v4
+        
+      - name: Cache externalpackages
+        uses: actions/cache@v3
+        id: cache-externalpackages
+        env:
+          cache-name: cache-triangle-m1qn3-petsc
+        with:
+          path: ${{ env.ISSM_DIR }}/externalpackages/
+          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
+          
+      - name: Install External packages
+        if: 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
+          
+      - name: Install Codipack
+        if: ${{ inputs.build_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 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-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
+          
+      - name: Reconfigure ISSM without 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${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
+          --with-petsc-dir="${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-${{ 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: ubuntu-latest
+    needs: build
+    strategy:
+      fail-fast: false
+      matrix:
+        - test-cases: ['101:110', '201:210', '301:310']
+          if: $${{ inputs.build_type == 'basic'}}
+        - test-cases: ['3015', '3119', '3480', '3201:3206']
+          if: $${{ inputs.build_type == 'codipack'}}
+
+    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')],'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"
+
+      - run: echo "This job's status is ${{ job.status }}."
diff --git a/.github/workflows/main-ci.yml b/.github/workflows/main-ci.yml
new file mode 100644
index 000000000..fca08e5c8
--- /dev/null
+++ b/.github/workflows/main-ci.yml
@@ -0,0 +1,20 @@
+name: Main Workflow 
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+env:
+  ISSM_DIR: ${{ github.workspace }}
+
+jobs:
+  build-type-matrix:
+    strategy:
+      fail-fast: false
+      matrix:
+        build_type: ['basic', 'codipack']
+    uses: ./.github/workflows/common-workflow.yml 
+    with:
+      version: ${{ matrix.build_type }}
+    secrets: inherit

From 0ce30b97600eaff4bdae6008dcf7d35bd2256458 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 17:06:17 -0400
Subject: [PATCH 05/26] Update common-workflow.yml

---
 .github/workflows/common-workflow.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index a0e31e413..997793cf8 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -123,11 +123,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        - test-cases: ['101:110', '201:210', '301:310']
-          if: $${{ inputs.build_type == 'basic'}}
-        - test-cases: ['3015', '3119', '3480', '3201:3206']
-          if: $${{ inputs.build_type == 'codipack'}}
-
+        test-cases: ['101:110', '201:210', '301:310']
+        include:
+          - test-cases: $${{ inputs.build_type == 'codipack' && ['3015', '3119', '3480', '3201:3206'] }}
+          
     steps:
       - name: Download ISSM artifact
         uses: actions/download-artifact@v4

From 92c4d5e3dc21c450b2b4a67563682f234f5f972f Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 17:10:34 -0400
Subject: [PATCH 06/26] only include ad tests for ccdipack

---
 .github/workflows/common-workflow.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 997793cf8..40b20146e 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -123,9 +123,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        test-cases: ['101:110', '201:210', '301:310']
+        test-cases: 
+          - '101:110'
+          - '201:210'
+          - '301:310'
         include:
-          - test-cases: $${{ inputs.build_type == 'codipack' && ['3015', '3119', '3480', '3201:3206'] }}
+          - test-cases: $${{ inputs.build_type == 'codipack' && '3015, 3119, 3480' }}
+          - test-cases: $${{ inputs.build_type == 'codipack' && '3201:3206' }}
           
     steps:
       - name: Download ISSM artifact

From e2e12b5d6b67480a0aac1728a3fcdc80f8be5443 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 17:12:28 -0400
Subject: [PATCH 07/26] fix bug in main-ci

---
 .github/workflows/main-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main-ci.yml b/.github/workflows/main-ci.yml
index fca08e5c8..13cc7e75b 100644
--- a/.github/workflows/main-ci.yml
+++ b/.github/workflows/main-ci.yml
@@ -16,5 +16,5 @@ jobs:
         build_type: ['basic', 'codipack']
     uses: ./.github/workflows/common-workflow.yml 
     with:
-      version: ${{ matrix.build_type }}
+      build_type: ${{ matrix.build_type }}
     secrets: inherit

From 0bde9523f45b97271dbc7a8c7ec0530893819a48 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 18:08:58 -0400
Subject: [PATCH 08/26] set different names for different runs

---
 .github/workflows/common-workflow.yml | 39 ++++++++++++++++++---------
 .github/workflows/main-ci.yml         |  5 +++-
 2 files changed, 30 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 40b20146e..6e9b68c08 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -3,6 +3,8 @@ name: Common CI
 on:
   workflow_call:
     inputs:
+      os:
+        required: true
       build_type: 
         required: true
         type: string
@@ -11,12 +13,9 @@ env:
   
 jobs:
   build:
-    runs-on: ubuntu-latest
+    name: build-ISSM-${{ inputs.os }}-${{ inputs.build_type}}
+    runs-on: ${{ inputs.os }}
     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!"
-      - run: echo "The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
-
       - name: Check out repository code
         uses: actions/checkout@v4
         
@@ -118,19 +117,32 @@ jobs:
           compression-level: 1
 
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ inputs.os }}
     needs: build
     strategy:
       fail-fast: false
       matrix:
         test-cases: 
-          - '101:110'
-          - '201:210'
-          - '301:310'
+          - '101:199'
+          - '201:299'
+          - '301:399'
+          - '401:499'
+          - '501:599'
+          - '601:699'
+          - '701:799'
+          - '801:899'
+        build-type:
+          -  ${{ inputs.build_type }}
+        additional: 
+          - ' '
         include:
-          - test-cases: $${{ inputs.build_type == 'codipack' && '3015, 3119, 3480' }}
-          - test-cases: $${{ inputs.build_type == 'codipack' && '3201:3206' }}
-          
+          - build-type: 'codipack'
+            additional: "'benchmark','all',"
+          - build-type: 'codipack'
+            test-cases: '3015, 3119, 3480'
+          - build-type: 'codipack'
+            test-cases: '3201:3206'
+            
     steps:
       - name: Download ISSM artifact
         uses: actions/download-artifact@v4
@@ -163,7 +175,7 @@ jobs:
           devpath;
 
           % Run tests
-          runme('exclude',[IdFromString('Dakota')],'id',[${{matrix.test-cases}}],'quitonerror',1);
+          runme('exclude',[IdFromString('Dakota')],${{matrix.additional}} 'id',[${{matrix.test-cases}}],'quitonerror',1);
           quit(0);
           EOF
           cat ${ISSM_DIR}/matlab_ci.m
@@ -179,3 +191,4 @@ jobs:
           LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so run-matlab-command "matlab_ci"
 
       - run: echo "This job's status is ${{ job.status }}."
+
diff --git a/.github/workflows/main-ci.yml b/.github/workflows/main-ci.yml
index 13cc7e75b..490c8459d 100644
--- a/.github/workflows/main-ci.yml
+++ b/.github/workflows/main-ci.yml
@@ -9,12 +9,15 @@ env:
   ISSM_DIR: ${{ github.workspace }}
 
 jobs:
-  build-type-matrix:
+  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 }}

From bb088f18d9cf8cdcf2dd8ea28fc6aeefe79ba74f Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 18:11:46 -0400
Subject: [PATCH 09/26] add type of input.os

---
 .github/workflows/common-workflow.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 6e9b68c08..e3ee5b4ae 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -5,6 +5,7 @@ on:
     inputs:
       os:
         required: true
+        type: string
       build_type: 
         required: true
         type: string

From 1df6ca53bf7146cc86e88572f2a5c2aff13389cc Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 18:48:09 -0400
Subject: [PATCH 10/26] try to cache src/c

---
 .github/workflows/common-workflow.yml | 31 ++++++++++++++++-----------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index e3ee5b4ae..447cec175 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -27,7 +27,16 @@ jobs:
           cache-name: cache-triangle-m1qn3-petsc
         with:
           path: ${{ env.ISSM_DIR }}/externalpackages/
-          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
+          key: ${{ runner.os }}-build-${{ env.cache-name }} 
+          
+      - name: Cache src/c
+        uses: actions/cache@v3
+        id: cache-src-c
+        env:
+          cache-name: cache-src-c
+        with:
+          path: ${{ env.ISSM_DIR }}/src/c/
+          key: ${{ runner.os }}-build-${{ env.cache-name }} 
           
       - name: Install External packages
         if: steps.cache-externalpackages.outputs.cache-hit != 'true'
@@ -132,18 +141,17 @@ jobs:
           - '601:699'
           - '701:799'
           - '801:899'
-        build-type:
+          - '3015, 3119, 3480, 3201:3206'
+        build_type:
           -  ${{ inputs.build_type }}
         additional: 
-          - ' '
-        include:
-          - build-type: 'codipack'
+          - " "
+          - "'benchmark','all',"
+        exclude:
+          - build-type: 'basic'
             additional: "'benchmark','all',"
-          - build-type: 'codipack'
-            test-cases: '3015, 3119, 3480'
-          - build-type: 'codipack'
-            test-cases: '3201:3206'
-            
+          - build-type: 'basic'
+            test-cases: '3015, 3119, 3480, 3201:3206'
     steps:
       - name: Download ISSM artifact
         uses: actions/download-artifact@v4
@@ -190,6 +198,3 @@ jobs:
         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"
-
-      - run: echo "This job's status is ${{ job.status }}."
-

From 63ba0424a2dfff355f9c034632a344c94d33178a Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 19:15:39 -0400
Subject: [PATCH 11/26] fix error in the test job

---
 .github/workflows/common-workflow.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 447cec175..2ad34b336 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -142,7 +142,7 @@ jobs:
           - '701:799'
           - '801:899'
           - '3015, 3119, 3480, 3201:3206'
-        build_type:
+        build-type:
           -  ${{ inputs.build_type }}
         additional: 
           - " "

From e253f840f7e7b892527309c8e130e02639efdb70 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 19:23:19 -0400
Subject: [PATCH 12/26] remove cache src/c

---
 .github/workflows/common-workflow.yml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 2ad34b336..143eb30b2 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -29,15 +29,6 @@ jobs:
           path: ${{ env.ISSM_DIR }}/externalpackages/
           key: ${{ runner.os }}-build-${{ env.cache-name }} 
           
-      - name: Cache src/c
-        uses: actions/cache@v3
-        id: cache-src-c
-        env:
-          cache-name: cache-src-c
-        with:
-          path: ${{ env.ISSM_DIR }}/src/c/
-          key: ${{ runner.os }}-build-${{ env.cache-name }} 
-          
       - name: Install External packages
         if: steps.cache-externalpackages.outputs.cache-hit != 'true'
         run: |

From 69212ab73b16b03ff89a8de3a504f77b4e2e9fc0 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 19:42:23 -0400
Subject: [PATCH 13/26] try petsc-3.20 for ad

---
 .github/workflows/common-workflow.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 143eb30b2..dcac9356c 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -22,7 +22,7 @@ jobs:
         
       - name: Cache externalpackages
         uses: actions/cache@v3
-        id: cache-externalpackages
+        id: cache-externalpackages-${{ inputs.build_type }}
         env:
           cache-name: cache-triangle-m1qn3-petsc
         with:
@@ -30,17 +30,19 @@ jobs:
           key: ${{ runner.os }}-build-${{ env.cache-name }} 
           
       - name: Install External packages
-        if: steps.cache-externalpackages.outputs.cache-hit != 'true'
+        if: steps.cache-externalpackages-basic.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
           
-      - name: Install Codipack
-        if: ${{ inputs.build_type == 'codipack'}}
+      - name: Install External packages for AD
+        if: steps.cache-externalpackages-codipack.outputs.cache-hit != 'true'
         run: |
           source $ISSM_DIR/etc/environment.sh
-          cd $ISSM_DIR/externalpackages/gsl      && ./install.sh
+          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/codipack && ./install.sh
           cd $ISSM_DIR/externalpackages/medipack && ./install.sh
           

From b7973ce830db53ed0e11b8dccd23fa984da7f299 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 19:56:33 -0400
Subject: [PATCH 14/26] try to use env to set the id of cache

---
 .github/workflows/common-workflow.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index dcac9356c..e1258c076 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -11,6 +11,7 @@ on:
         type: string
 env:
   ISSM_DIR: ${{ github.workspace }}
+  build_type: ${{ inputs.build_type }}
   
 jobs:
   build:
@@ -22,12 +23,12 @@ jobs:
         
       - name: Cache externalpackages
         uses: actions/cache@v3
-        id: cache-externalpackages-${{ inputs.build_type }}
+        id: cache-externalpackages-${{ env.build_type }}
         env:
-          cache-name: cache-triangle-m1qn3-petsc
+          cache-name: cache-externalpackages-${{ env.build_type }}
         with:
           path: ${{ env.ISSM_DIR }}/externalpackages/
-          key: ${{ runner.os }}-build-${{ env.cache-name }} 
+          key: ${{ runner.os }}-build-${{ env.cache-name }}
           
       - name: Install External packages
         if: steps.cache-externalpackages-basic.outputs.cache-hit != 'true'

From 1e054743746f685e4b81262e937a037a10490126 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 20:08:15 -0400
Subject: [PATCH 15/26] try github.env

---
 .github/workflows/common-workflow.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index e1258c076..be25c80e7 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -11,7 +11,6 @@ on:
         type: string
 env:
   ISSM_DIR: ${{ github.workspace }}
-  build_type: ${{ inputs.build_type }}
   
 jobs:
   build:
@@ -20,12 +19,15 @@ jobs:
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
-        
+      - name: Set build type
+        run: |
+          echo "build_type=${{inputs.build_type }}" >> "$GITHUB_ENV"
+          
       - name: Cache externalpackages
         uses: actions/cache@v3
-        id: cache-externalpackages-${{ env.build_type }}
+        id: cache-externalpackages-${{ github.env.build_type }}
         env:
-          cache-name: cache-externalpackages-${{ env.build_type }}
+          cache-name: cache-externalpackages-${{ github.env.build_type }}
         with:
           path: ${{ env.ISSM_DIR }}/externalpackages/
           key: ${{ runner.os }}-build-${{ env.cache-name }}

From 18ac8451751216465d4ef6af6ac54cae3398ac31 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 20:13:15 -0400
Subject: [PATCH 16/26] try to fix bugs when using inputs in cache id

---
 .github/workflows/common-workflow.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index be25c80e7..94e9e9339 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -19,28 +19,25 @@ jobs:
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
-      - name: Set build type
-        run: |
-          echo "build_type=${{inputs.build_type }}" >> "$GITHUB_ENV"
           
       - name: Cache externalpackages
         uses: actions/cache@v3
-        id: cache-externalpackages-${{ github.env.build_type }}
+        id: cache-externalpackages
         env:
-          cache-name: cache-externalpackages-${{ github.env.build_type }}
+          cache-name: cache-externalpackages-${{ inputs.build_type }}
         with:
           path: ${{ env.ISSM_DIR }}/externalpackages/
           key: ${{ runner.os }}-build-${{ env.cache-name }}
           
       - name: Install External packages
-        if: steps.cache-externalpackages-basic.outputs.cache-hit != 'true'
+        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
           
       - name: Install External packages for AD
-        if: steps.cache-externalpackages-codipack.outputs.cache-hit != 'true'
+        if: ${{ inputs.build_type }} == 'codipack' && steps.cache-externalpackages.outputs.cache-hit != 'true'
         run: |
           source $ISSM_DIR/etc/environment.sh
           cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh

From 1f4a9f4202ed2215994aec5d9031986578cd2ebe Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 20:35:03 -0400
Subject: [PATCH 17/26] fix bug in the if condition

---
 .github/workflows/common-workflow.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 94e9e9339..c322571d9 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -30,16 +30,15 @@ jobs:
           key: ${{ runner.os }}-build-${{ env.cache-name }}
           
       - name: Install External packages
-        if: ${{ inputs.build_type }} == 'basic' && steps.cache-externalpackages.outputs.cache-hit != 'true'
+        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
           
       - name: Install External packages for AD
-        if: ${{ inputs.build_type }} == 'codipack' && steps.cache-externalpackages.outputs.cache-hit != 'true'
+        if: ${{ ( inputs.build_type == 'codipack') && (steps.cache-externalpackages.outputs.cache-hit != 'true') }}
         run: |
-          source $ISSM_DIR/etc/environment.sh
           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

From fae90a5aa295acd3c40971f52def7bdd90133055 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 21:00:21 -0400
Subject: [PATCH 18/26] fix codipack

---
 .github/workflows/common-workflow.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index c322571d9..6a41173e8 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -42,6 +42,7 @@ jobs:
           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
           

From 66e4f82a89b9cc177b062e2963495eeee8e4e3cf Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Sun, 21 Jul 2024 21:26:28 -0400
Subject: [PATCH 19/26] try ad again

---
 .github/workflows/common-workflow.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 6a41173e8..6b3b16d7c 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -39,12 +39,14 @@ jobs:
       - 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
+          cd $ISSM_DIR/externalpackages/autotools  && ./install-linux.sh
+          cd $ISSM_DIR/externalpackages/cmake      && ./install.sh
+          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
@@ -76,7 +78,7 @@ jobs:
           --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
           --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
           
-      - name: Reconfigure ISSM without Codipack
+      - name: Reconfigure ISSM with Codipack
         if: ${{ inputs.build_type == 'codipack'}}
         run: |
           source $ISSM_DIR/etc/environment.sh

From b35a1143c5d4abdc1675f9528d3b28adb95e02a7 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Mon, 22 Jul 2024 08:30:28 -0400
Subject: [PATCH 20/26] remove with-petsc in codipack

---
 .github/workflows/common-workflow.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 6b3b16d7c..97b3aabeb 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -39,8 +39,6 @@ jobs:
       - name: Install External packages for AD
         if: ${{ ( inputs.build_type == 'codipack') && (steps.cache-externalpackages.outputs.cache-hit != 'true') }}
         run: |
-          cd $ISSM_DIR/externalpackages/autotools  && ./install-linux.sh
-          cd $ISSM_DIR/externalpackages/cmake      && ./install.sh
           cd $ISSM_DIR/externalpackages/triangle   && ./install-linux.sh
           cd $ISSM_DIR/externalpackages/m1qn3      && ./install-linux.sh
           cd $ISSM_DIR/externalpackages/petsc      && ./install-3.20-linux.sh
@@ -96,7 +94,6 @@ jobs:
           --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \
           --with-mpi-include="${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" \

From 4671a46a9734cf69fa2160dd19d0de4d0d5c8378 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Mon, 22 Jul 2024 09:36:53 -0400
Subject: [PATCH 21/26] reduce matrix size for tests

---
 .github/workflows/common-workflow.yml | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 97b3aabeb..b2cfd077e 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -106,7 +106,7 @@ jobs:
           --with-codipack-dir="${ISSM_DIR}/externalpackages/codipack/install" 
           
       - name: Compile ISSM
-        run: make -j16 install
+        run: make -j8 install
 
       - name: Compress ISSM artifact
         run: tar -cvf ISSM_artifact-${{ inputs.build_type}}.tar -C ${{ env.ISSM_DIR }}/ .
@@ -125,14 +125,8 @@ jobs:
       fail-fast: false
       matrix:
         test-cases: 
-          - '101:199'
-          - '201:299'
-          - '301:399'
-          - '401:499'
-          - '501:599'
-          - '601:699'
-          - '701:799'
-          - '801:899'
+          - '101:499'
+          - '501:899'
           - '3015, 3119, 3480, 3201:3206'
         build-type:
           -  ${{ inputs.build_type }}
@@ -142,6 +136,8 @@ jobs:
         exclude:
           - build-type: 'basic'
             additional: "'benchmark','all',"
+          - build-type: 'codipack'
+            additional: " "
           - build-type: 'basic'
             test-cases: '3015, 3119, 3480, 3201:3206'
     steps:

From 5ccd274e2d10270711e0174b6f46afc8c41de093 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Mon, 22 Jul 2024 11:42:25 -0400
Subject: [PATCH 22/26] check spaces

---
 .github/workflows/common-workflow.yml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index b2cfd077e..bc1759824 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -35,6 +35,7 @@ jobs:
           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: ${{ ( inputs.build_type == 'codipack') && (steps.cache-externalpackages.outputs.cache-hit != 'true') }}
@@ -117,7 +118,11 @@ jobs:
           name: ISSM-${{ runner.os }}-${{ inputs.build_type}}
           path: ISSM_artifact-${{ inputs.build_type}}.tar
           compression-level: 1
-
+          
+      - name: check free space
+        run: |
+          echo "Free space:"
+          df -h
   test:
     runs-on: ${{ inputs.os }}
     needs: build
@@ -147,6 +152,11 @@ jobs:
           name: ISSM-${{ runner.os }}-${{ inputs.build_type}}
           path: ${{ env.ISSM_DIR }}
       
+      - name: check free space
+        run: |
+          echo "Free space:"
+          df -h
+      
       - name: uncompress ISSM artifact
         run: |
           tar -xvf ISSM_artifact-${{ inputs.build_type}}.tar

From 3f44b86ae2b877aae923aca67a74391ca2b00cfc Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Mon, 22 Jul 2024 12:48:38 -0400
Subject: [PATCH 23/26] turn off codipack tests

---
 .github/workflows/common-workflow.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index bc1759824..da1dd7a57 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -118,11 +118,12 @@ jobs:
           name: ISSM-${{ runner.os }}-${{ inputs.build_type}}
           path: ISSM_artifact-${{ inputs.build_type}}.tar
           compression-level: 1
-          
+      
       - name: check free space
         run: |
           echo "Free space:"
-          df -h
+          du -sh ${{ env.ISSM_DIR }}/*
+          
   test:
     runs-on: ${{ inputs.os }}
     needs: build
@@ -145,6 +146,7 @@ jobs:
             additional: " "
           - build-type: 'basic'
             test-cases: '3015, 3119, 3480, 3201:3206'
+          - build-type: 'codipack'
     steps:
       - name: Download ISSM artifact
         uses: actions/download-artifact@v4
@@ -152,11 +154,6 @@ jobs:
           name: ISSM-${{ runner.os }}-${{ inputs.build_type}}
           path: ${{ env.ISSM_DIR }}
       
-      - name: check free space
-        run: |
-          echo "Free space:"
-          df -h
-      
       - name: uncompress ISSM artifact
         run: |
           tar -xvf ISSM_artifact-${{ inputs.build_type}}.tar

From 38f993e2a8cefeab175d9928d0ef36e6e13bc0a0 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Mon, 22 Jul 2024 13:17:11 -0400
Subject: [PATCH 24/26] do not compress petsc/src/ to decrease the size of the
 artifact

---
 .github/workflows/common-workflow.yml | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index da1dd7a57..4bb9a0cc2 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -26,7 +26,9 @@ jobs:
         env:
           cache-name: cache-externalpackages-${{ inputs.build_type }}
         with:
-          path: ${{ env.ISSM_DIR }}/externalpackages/
+          path: |
+            ${{ env.ISSM_DIR }}/externalpackages/
+            ! ${{ env.ISSM_DIR }}/externalpackages/petsc/src/
           key: ${{ runner.os }}-build-${{ env.cache-name }}
           
       - name: Install External packages
@@ -43,7 +45,6 @@ jobs:
           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
           
@@ -75,6 +76,7 @@ jobs:
           --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
@@ -102,28 +104,21 @@ jobs:
           --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
           --with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
           --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
-          --with-gsl-dir=${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 -j8 install
+        run: make -j4 install
 
       - name: Compress ISSM artifact
-        run: tar -cvf ISSM_artifact-${{ inputs.build_type}}.tar -C ${{ env.ISSM_DIR }}/ .
+        run: tar --exclude='${{ env.ISSM_DIR }}/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
-      
-      - name: check free space
-        run: |
-          echo "Free space:"
-          du -sh ${{ env.ISSM_DIR }}/*
-          
+          compression-level: 1          
   test:
     runs-on: ${{ inputs.os }}
     needs: build
@@ -146,7 +141,6 @@ jobs:
             additional: " "
           - build-type: 'basic'
             test-cases: '3015, 3119, 3480, 3201:3206'
-          - build-type: 'codipack'
     steps:
       - name: Download ISSM artifact
         uses: actions/download-artifact@v4

From 29dbe16eab25d7651b7537e6a89b5e3aaf3df722 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Mon, 22 Jul 2024 13:45:25 -0400
Subject: [PATCH 25/26] try to exclude petsc/src

---
 .github/workflows/common-workflow.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 4bb9a0cc2..90322a4f9 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -28,7 +28,7 @@ jobs:
         with:
           path: |
             ${{ env.ISSM_DIR }}/externalpackages/
-            ! ${{ env.ISSM_DIR }}/externalpackages/petsc/src/
+            !${{ env.ISSM_DIR }}/externalpackages/petsc/src/
           key: ${{ runner.os }}-build-${{ env.cache-name }}
           
       - name: Install External packages
@@ -111,7 +111,7 @@ jobs:
         run: make -j4 install
 
       - name: Compress ISSM artifact
-        run: tar --exclude='${{ env.ISSM_DIR }}/externalpackages/petsc/src/' -cvf ISSM_artifact-${{ inputs.build_type}}.tar -C ${{ env.ISSM_DIR }}/ .
+        run: tar --exclude='./externalpackages/petsc/src' -cvf ISSM_artifact-${{ inputs.build_type}}.tar -C ${{ env.ISSM_DIR }}/ .
         
       - name: Upload ISSM artifact
         uses: actions/upload-artifact@v4
@@ -126,8 +126,8 @@ jobs:
       fail-fast: false
       matrix:
         test-cases: 
-          - '101:499'
-          - '501:899'
+          - '101:399'
+          - '401:899'
           - '3015, 3119, 3480, 3201:3206'
         build-type:
           -  ${{ inputs.build_type }}

From 8bb700f3bd45f24493c6e52b44ea4cd11d33c056 Mon Sep 17 00:00:00 2001
From: Cheng Gong <enigne@gmail.com>
Date: Mon, 22 Jul 2024 14:22:49 -0400
Subject: [PATCH 26/26] add gsl to codipack version

---
 .github/workflows/common-workflow.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/common-workflow.yml b/.github/workflows/common-workflow.yml
index 90322a4f9..239a9036f 100644
--- a/.github/workflows/common-workflow.yml
+++ b/.github/workflows/common-workflow.yml
@@ -45,6 +45,7 @@ jobs:
           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
           
@@ -103,6 +104,7 @@ jobs:
           --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" 
@@ -137,10 +139,15 @@ jobs:
         exclude:
           - build-type: 'basic'
             additional: "'benchmark','all',"
-          - build-type: 'codipack'
-            additional: " "
           - 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