Merge branch 'main' of github.com:ISSMteam/ISSM

.github/workflows/common-workflow.yml

@@ -21,6 +21,12 @@ on:
       additional_options:
         required: true
         type: string
+      interface:
+        required: true
+        type: string
+      python_version:
+        required: false
+        type: string
 env:
   ISSM_DIR: ${{ github.workspace }}
 
@@ -38,7 +44,7 @@ jobs:
         uses: actions/cache@v3
         id: cache-externalpackages
         env:
-          cache-name: cache-externalpackages-${{ inputs.build_type }}
+          cache-name: cache-externalpackages-${{ inputs.build_type}}
         with:
           path: |
             ${{ env.ISSM_DIR }}/externalpackages/
@@ -51,15 +57,34 @@ jobs:
           ${{ inputs.ext_install_command }}
 
       - name: Get MATLAB
+        if: ${{inputs.interface == 'matlab'}}
         id:   setup-matlab
         uses: matlab-actions/setup-matlab@v2
         with:
           release: R2023b
           cache: true
 
+      - name: Prepare python
+        if: contains( inputs.interface, 'python')
+        uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: ${{ inputs.python_version }}
+
+      - name: Install dependencies
+        if: contains( inputs.interface, 'python')
+        run: |
+          sudo apt-get install libpython${{ inputs.python_version }}-dev
+          sudo apt-get install python3-dev
+          python -m pip install --upgrade pip
+          sudo apt-get update && sudo apt-get install -y python-tk python3-tk
+          python -m pip install numpy scipy matplotlib nose
+
       - name: build ISSM
         run: |
           export MATLAB_ROOT=${{ steps.setup-matlab.outputs.matlabroot }}
+          export PYTHON_ROOT=${{ env.pythonLocation }}
+          export NUMPY_ROOT=${{ env.LD_LIBRARY_PATH }}/python3.11/site-packages/numpy
           ${{ inputs.build_command}}
 
       - name: Compile ISSM
@@ -99,13 +124,15 @@ jobs:
         shell: 'bash'
 
       - name: Get MATLAB
+        if: ${{inputs.interface == 'matlab'}}
         id:   setup-matlab
         uses: matlab-actions/setup-matlab@v2
         with:
           release: R2023b
           cache: true
 
       - name: Creating matlab_ci.m
+        if: ${{inputs.interface == 'matlab'}}
         run: |
           cat > ${ISSM_DIR}/matlab_ci.m << EOF
           % Go to the test directory
@@ -122,11 +149,37 @@ jobs:
           cat ${ISSM_DIR}/matlab_ci.m
           
       - name: Get run-matlab-command
+        if: ${{inputs.interface == 'matlab'}}
         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
+        if: ${{inputs.interface == 'matlab'}}
         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"
+  
+      - name: Prepare python
+        if: contains( inputs.interface, 'python')
+        uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: ${{ inputs.python_version }}
+
+      - name: Install dependencies
+        if: contains( inputs.interface, 'python')
+        run: |
+          python -m pip install --upgrade pip
+          sudo apt-get update && sudo apt-get install -y python-tk python3-tk
+          python -m pip install numpy scipy matplotlib nose netCDF4
+
+      - name: Run Python tests
+        if: contains( inputs.interface, 'python')
+        run: |
+          export PYTHONPATH="${ISSM_DIR}/src/m/dev:${PYTHONPATH}"
+          export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
+          export PYTHONUNBUFFERED=1
+          source $ISSM_DIR/etc/environment.sh
+          cd $ISSM_DIR/test/NightlyRun
+          LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so ./runme.py --output=nightly --rank=1 --numprocs=1 --id {{matrix.test_cases}} --exclude Dakota 234 418 420

.github/workflows/ubuntu-basic.yml

@@ -13,7 +13,8 @@ jobs:
     uses: ./.github/workflows/common-workflow.yml 
     with:
       os: ubuntu-latest
-      build_type: basic
+      build_type: basic-matlab
+      interface: matlab
       build_command: |
         source $ISSM_DIR/etc/environment.sh
         autoreconf -ivf
@@ -38,7 +39,7 @@ jobs:
       ext_install_command: |
         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/petsc    && ./install-3.22-linux.sh
         cd $ISSM_DIR/externalpackages/semic    && ./install.sh
       test_cases: '["101:399", "401:899"]'
       additional_options: " "

.github/workflows/ubuntu-codipack.yml

@@ -14,6 +14,7 @@ jobs:
     with:
       os: ubuntu-latest
       build_type: codipack
+      interface: matlab
       build_command: |
         source $ISSM_DIR/etc/environment.sh
         autoreconf -ivf
@@ -43,7 +44,7 @@ jobs:
       ext_install_command: |
         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/petsc      && ./install-3.22-linux.sh
         cd $ISSM_DIR/externalpackages/gsl        && ./install.sh
         cd $ISSM_DIR/externalpackages/codipack   && ./install.sh
         cd $ISSM_DIR/externalpackages/medipack   && ./install.sh

.github/workflows/ubuntu-python.yml

@@ -0,0 +1,50 @@
+name: Ubuntu Python 
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+env:
+  ISSM_DIR: ${{ github.workspace }}
+
+jobs:
+  build-test:
+    uses: ./.github/workflows/common-workflow.yml 
+    with:
+      os: ubuntu-latest
+      build_type: basic-python-3.11
+      interface: python
+      python_version: 3.11
+      build_command: |
+        source $ISSM_DIR/etc/environment.sh
+        autoreconf -ivf
+        ./configure --prefix=${ISSM_DIR} \
+        --disable-static \
+        --enable-development \
+        --enable-debugging \
+        --with-numthreads=4 \
+        --with-python-version=3.11 \
+        --with-python-dir=$PYTHON_ROOT \
+        --with-python-numpy-dir=$NUMPY_ROOT \
+        --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"
+      ext_install_command: |
+        cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh
+        cd $ISSM_DIR/externalpackages/m1qn3    && ./install-linux.sh
+        cd $ISSM_DIR/externalpackages/petsc    && ./install-3.22-linux.sh
+        cd $ISSM_DIR/externalpackages/semic    && ./install.sh
+      test_cases: '["range(101,400)", "range(401, 900)"]'
+      additional_options: " "
+    secrets: inherit
+    name: build-test-ubuntu-python

README.md

@@ -1,6 +1,7 @@
 # Ice-sheet and Sea-level System Model - ISSM
 [![Ubuntu Basic](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-basic.yml/badge.svg)](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-basic.yml)
 [![Ubuntu CodiPack](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-codipack.yml/badge.svg)](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-codipack.yml)
+[![Ubuntu Python](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-python.yml/badge.svg)](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-python.yml)
 
 ## Description
 ISSM is a large-scale thermo-mechanical 2D/3D parallelized multi-purpose finite-element software dedicated to ice sheet and sea-level modeling.

externalpackages/adjoinablempi/install-linux.sh

@@ -6,7 +6,7 @@ set -eu
 rm -rf install src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
 
 # Unpack source
 tar -zxvf adjoinablempi.tar.gz

externalpackages/adjoinablempi/install-mac.sh

@@ -11,7 +11,7 @@ export CFLAGS=-Wno-error=implicit-function-declaration
 rm -rf install src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
 
 # Unpack source
 tar -zxvf adjoinablempi.tar.gz

externalpackages/adjoinablempi/install-pleaides-gcc.sh

@@ -6,7 +6,7 @@ set -eu
 rm -rf install src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
 
 # Unpack source
 tar -zxf adjoinablempi.tar.gz

externalpackages/adjoinablempi/install-pleaides.sh

@@ -6,7 +6,7 @@ set -eu
 rm -rf install src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi.tar.gz' 'adjoinablempi.tar.gz'
 
 # Unpack source
 tar -zxf adjoinablempi.tar.gz

externalpackages/dakota/install-6.2-discover.sh

@@ -14,7 +14,7 @@ rm -rf install
 mkdir src build install 
 
 #Download from ISSM server
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz'
 
 #Untar 
 tar -zxvf dakota-6.2-public-src.tar.gz

externalpackages/dakota/install-6.2-ghub-workspace_10.sh

@@ -32,7 +32,7 @@ rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 
 # Download source
-#${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
 # Unpack source
 tar -zxvf dakota-${VER}-public-src.tar.gz

externalpackages/dakota/install-6.2-linux-static.sh

@@ -33,7 +33,7 @@ rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 
 # Download source
-#${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
 # Unpack source
 tar -zxvf dakota-${VER}-public-src.tar.gz

externalpackages/dakota/install-6.2-linux.sh

@@ -30,7 +30,7 @@ rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 
 # Download source
-#${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
 # Unpack source
 tar -zxvf dakota-${VER}-public-src.tar.gz

externalpackages/dakota/install-6.2-lonestar.sh

@@ -14,7 +14,7 @@ rm -rf install
 mkdir src build install 
 
 #Download from ISSM server
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz'
 
 #Untar 
 tar -zxvf dakota-6.2-public-src.tar.gz

externalpackages/dakota/install-6.2-mac-static.sh

@@ -34,7 +34,7 @@ rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 
 # Download source
-#${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
 # Unpack source
 tar -zxvf dakota-${VER}-public-src.tar.gz

externalpackages/dakota/install-6.2-mac.sh

@@ -31,7 +31,7 @@ rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 
 # Download source
-#${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
 # Unpack source
 tar -zxvf dakota-${VER}-public-src.tar.gz

externalpackages/dakota/install-6.2-pleiades.sh

@@ -22,7 +22,7 @@ rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 
 # Download source
-#${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
 # Unpack source
 tar -zxvf dakota-${VER}-public-src.tar.gz

externalpackages/dakota/install-6.2-pleiades_toss4.sh

@@ -22,7 +22,7 @@ rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
 
 # Download source
-#${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
+${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
 # Unpack source
 tar -zxvf dakota-${VER}-public-src.tar.gz

externalpackages/dakota/install-6.2-stallo.sh

@@ -14,7 +14,7 @@ rm -rf install
 mkdir src build install 
 
 #Download from ISSM server
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz'
 
 #Untar 
 tar -zxvf dakota-6.2-public-src.tar.gz

externalpackages/m1qn3/install-linux.sh

@@ -12,7 +12,7 @@ rm -rf ${PREFIX} src
 mkdir -p ${PREFIX} src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m1qn3-${VER}-distrib.tgz" "m1qn3-${VER}-distrib.tgz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m1qn3-${VER}-distrib.tgz" "m1qn3-${VER}-distrib.tgz"
 
 # Unpack source
 tar -xzf m1qn3-${VER}-distrib.tgz

externalpackages/m1qn3/install-mac.sh

@@ -13,7 +13,7 @@ rm -rf ${PREFIX} src
 mkdir -p ${PREFIX} src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m1qn3-${VER}-distrib.tgz" "m1qn3-${VER}-distrib.tgz"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m1qn3-${VER}-distrib.tgz" "m1qn3-${VER}-distrib.tgz"
 
 # Unpack source
 tar -xzf m1qn3-${VER}-distrib.tgz

externalpackages/triangle/install-linux.sh

@@ -11,7 +11,7 @@ rm -rf ${PREFIX}
 mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/triangle.zip" "triangle.zip"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/triangle.zip" "triangle.zip"
 
 # Unpack source
 unzip triangle.zip -d src

externalpackages/triangle/install-mac.sh

@@ -11,7 +11,7 @@ rm -rf ${PREFIX}
 mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src
 
 # Download source
-#$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/triangle.zip" "triangle.zip"
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/triangle.zip" "triangle.zip"
 
 # Unpack source
 unzip triangle.zip -d src

src/c/modules/SurfaceMassBalancex/run_semic_transient.f90

@@ -134,6 +134,8 @@ subroutine run_semic_transient(nx, ntime, nloop, sf_in, rf_in, swd_in, lwd_in, w
       surface%par%alb_scheme = "denby"
    else if (alb_scheme == 3) then
       surface%par%alb_scheme = "isba"
+   else if (alb_scheme == 4) then
+      surface%par%alb_scheme = "alex"
    else
       print*, "ERROR: current albedo scheme is not available."
       call exit(1)