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‎.github/workflows/common-workflow.yml‎

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@@ -27,6 +27,7 @@ on:
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python_version:
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required: false
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type: string
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env:
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ISSM_DIR: ${{ github.workspace }}
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@@ -37,6 +38,47 @@ jobs:
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outputs:
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test_matrix: ${{ steps.createTestMatrix.outputs.test_output }}
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steps:
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- name: Free disk space
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run: |
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# Source: https://dev.to/mathio/squeezing-disk-space-from-github-actions-runners-an-engineers-guide-3pjg#6-how-to-automate-cleanup-in-your-ci
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#
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# Remove Java (JDKs)
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#sudo rm -rf /usr/lib/jvm
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# Remove .NET SDKs
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sudo rm -rf /usr/share/dotnet
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# Remove Swift toolchain
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sudo rm -rf /usr/share/swift
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# Remove Haskell (GHC)
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sudo rm -rf /usr/local/.ghcup
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# Remove Julia
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sudo rm -rf /usr/local/julia*
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# Remove Android SDKs
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sudo rm -rf /usr/local/lib/android
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# Remove Chromium (optional if not using for browser tests)
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sudo rm -rf /usr/local/share/chromium
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# Remove Microsoft/Edge and Google Chrome builds
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sudo rm -rf /opt/microsoft /opt/google
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# Remove Azure CLI
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sudo rm -rf /opt/az
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# Remove PowerShell
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sudo rm -rf /usr/local/share/powershell
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# Remove CodeQL and other toolcaches
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sudo rm -rf /opt/hostedtoolcache
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docker system prune -af || true
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docker builder prune -af || true
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df -h
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- name: Check out copy of repository
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uses: actions/checkout@v4
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@@ -61,7 +103,7 @@ jobs:
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id: setup-matlab
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uses: matlab-actions/setup-matlab@v2
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with:
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release: R2023b
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release: latest
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cache: true
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- name: Prepare Python
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- name: Install Python dependencies
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if: contains(inputs.interface, 'python')
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run: |
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sudo apt-get install libpython${{ inputs.python_version }}-dev
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sudo apt-get install python3-dev
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sudo apt update
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sudo apt install libpython${{ inputs.python_version }}-dev
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sudo apt install python3-dev
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python -m pip install --upgrade pip
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sudo apt-get update && sudo apt-get install -y python-tk python3-tk
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sudo apt install -y python3-tk
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python -m pip install numpy scipy matplotlib nose
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- name: Build ISSM
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run: |
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export CC=${{ env.ISSM_DIR }}/externalpackages/petsc/install/bin/mpicc
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export CXX=${{ env.ISSM_DIR }}/externalpackages/petsc/install/bin/mpicxx
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export FC=${{ env.ISSM_DIR }}/externalpackages/petsc/install/bin/mpifort
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export F77=$FC
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export F90=$FC
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export MATLAB_ROOT=${{ steps.setup-matlab.outputs.matlabroot }}
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export PYTHON_ROOT=${{ env.pythonLocation }}
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export NUMPY_ROOT=${{ env.LD_LIBRARY_PATH }}/python3.11/site-packages/numpy
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${{ inputs.build_command }}
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- name: Compile ISSM
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if: contains( inputs.interface, 'python')
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run: |
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python -m pip install --upgrade pip
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sudo apt-get update && sudo apt-get install -y python-tk python3-tk
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sudo apt update && sudo apt install -y python3-tk
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python -m pip install numpy scipy matplotlib nose netCDF4
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- name: Run Python tests

‎.github/workflows/ubuntu-basic.yml‎

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on:
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push:
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branches: [ "main" ]
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paths:
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- ".github/workflows/common-workflow.yml"
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- ".github/workflows/ubuntu-basic.yml"
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- "etc/**"
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- "externalpackages/**"
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- "m4/**"
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- "src/**"
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- "test/**"
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- "Makefile.am"
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- "configure.ac"
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pull_request:
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branches: [ "main" ]
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paths:
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- ".github/workflows/common-workflow.yml"
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- ".github/workflows/ubuntu-basic.yml"
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- "etc/**"
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- "externalpackages/**"
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- "m4/**"
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- "src/**"
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- "test/**"
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- "Makefile.am"
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- "configure.ac"
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env:
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ISSM_DIR: ${{ github.workspace }}
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‎.github/workflows/ubuntu-codipack.yml‎

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on:
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push:
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branches: [ "main" ]
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paths:
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- ".github/workflows/common-workflow.yml"
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- ".github/workflows/ubuntu-codipack.yml"
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- "etc/**"
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- "externalpackages/**"
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- "m4/**"
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- "src/**"
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- "test/**"
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- "Makefile.am"
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- "configure.ac"
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pull_request:
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branches: [ "main" ]
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paths:
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- ".github/workflows/common-workflow.yml"
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- ".github/workflows/ubuntu-codipack.yml"
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- "etc/**"
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- "externalpackages/**"
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- "m4/**"
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- "src/**"
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- "test/**"
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- "Makefile.am"
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- "configure.ac"
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env:
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ISSM_DIR: ${{ github.workspace }}
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‎.github/workflows/ubuntu-python.yml‎

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@@ -3,8 +3,29 @@ name: Ubuntu Python
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on:
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push:
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branches: [ "main" ]
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paths:
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- ".github/workflows/common-workflow.yml"
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- ".github/workflows/ubuntu-python.yml"
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- "etc/**"
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- "externalpackages/**"
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- "m4/**"
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- "src/**"
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- "test/**"
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- "Makefile.am"
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- "configure.ac"
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pull_request:
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branches: [ "main" ]
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paths:
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- ".github/workflows/common-workflow.yml"
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- ".github/workflows/ubuntu-basic.yml"
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- "etc/**"
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- "externalpackages/**"
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- "m4/**"
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- "src/**"
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- "test/**"
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- "Makefile.am"
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- "configure.ac"
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env:
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ISSM_DIR: ${{ github.workspace }}
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uses: ./.github/workflows/common-workflow.yml
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with:
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os: ubuntu-latest
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build_type: basic-python-3.11
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build_type: basic-python
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interface: python
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python_version: 3.11
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python_version: 3.12
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build_command: |
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source $ISSM_DIR/etc/environment.sh
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autoreconf -ivf
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./configure --prefix=${ISSM_DIR} \
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ls ${ISSM_DIR}/externalpackages/petsc/install/bin/
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which mpicxx
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./configure \
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--prefix=${ISSM_DIR} \
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--disable-static \
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--enable-development \
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--enable-debugging \
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--with-numthreads=4 \
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--with-python-version=3.11 \
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--with-python-dir=$PYTHON_ROOT \
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--with-python-numpy-dir=$NUMPY_ROOT \
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--with-python=${PYTHON_ROOT}/bin/python3 \
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--with-fortran-lib="-L/usr/lib/x86_64-linux-gnu -lgfortran" \
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--with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \
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--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \

‎.gitignore‎

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#==================
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*.a
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*.al
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*.js
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*.la
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*.lo
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*.mexa64
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*.pyo
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*.so
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*.so.[0-9]*
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*.wasm
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__pycache__
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bin/
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lib/
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externalpackages/*/*.gz
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externalpackages/*/*.tgz
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externalpackages/chaco/chaco*guide.pdf
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externalpackages/export_fig/.ignore
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externalpackages/vim/addons/vim/.netrwhist
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# Jenkins #
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#==========

‎Makefile.am‎

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EXTRA_DIST = reconf scripts test m4 examples etc doc packages
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EXTRA_DIST = examples scripts execution etc test
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SUBDIRS = src
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ACLOCAL_AMFLAGS = -I m4

‎README.md‎

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# Ice-sheet and Sea-level System Model - ISSM
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[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
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[![Ubuntu Basic](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-basic.yml/badge.svg)](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-basic.yml)
3-
[![Ubuntu CodiPack](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-codipack.yml/badge.svg)](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-codipack.yml)
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[![Ubuntu Python](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-python.yml/badge.svg)](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-python.yml)
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[![Ubuntu CodiPack](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-codipack.yml/badge.svg)](https://github.com/ISSMteam/ISSM/actions/workflows/ubuntu-codipack.yml)
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## Description
78
ISSM is a large-scale thermo-mechanical 2D/3D parallelized multi-purpose finite-element software dedicated to ice sheet and sea-level modeling.
89

10+
## Documentation
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<a href="https://issmteam.github.io/ISSM-Documentation" target="_blank">Just The Docs</a>
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## Contact
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- Forum: https://issm.ess.uci.edu/forum
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- GitHub: https://github.com/ISSMteam/ISSM
12-
- Website: https://issm.jpl.nasa.gov
14+
- Bug Reporting: Please direct compile and run time bug reports strictly related to ISSM's core code or API's to the 'Issues' page.
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- Questions: Please direct all other questions (e.g. model setup, configuration/compiling on a particular platform, compute cluster configuration) to the 'Discussions' page.
16+
- Website: https://issm.jpl.nasa.gov (will be decommissioned soon)
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## Checking Out a Copy of the Repository
1519
Navigate to the parent directory where you want the ISSM repository to be located. If you plan to make contributions to the code base, we recommend that you check out a copy via SSH with,
@@ -28,31 +32,25 @@ Note that checkout via HTTPS does not require credentials, but does not allow co
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## Committing Changes to the Repository
2933
A good basic workflow for committing changes to the repository is,
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1. Stash your local changes
32-
```
35+
```bash
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#1. Stash your local changes
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git stash
34-
```
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36-
2. Update your local branch
37-
```
39+
#2. Update your local branch
3840
git pull
39-
```
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41-
3. Merge your local changes
42-
```
42+
#3. Merge your local changes
4343
git stash apply
44-
```
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46-
4. Add, commit, and push your changes
47-
```
45+
#4. Add, commit, and push your changes
4846
git add [file]
4947
git commit [-m "descriptive commit message"]
5048
git push
5149
```
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53-
5. If you have forked the ISSM repository, consider making sure that your commit passes CI workflows before submitting a pull request.
51+
If you have forked the ISSM repository, consider making sure that your commit passes CI workflows before submitting a pull request.
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55-
6. Submit a pull request via GitHub so that project admins can review your changes and merge them into the main branch.
53+
Submit a pull request via GitHub so that project admins can review your changes and merge them into the main branch.
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If you find yourself making a lot of commits and pull requests, consider asking us to add you to the 'ISSM Contributors' group, which will allow you to make commits directly to the repository.
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‎configure.ac‎

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#Initializing configure
3-
AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.24],[https://issm.ess.uci.edu/forum/],[issm],[http://issm.jpl.nasa.gov])
3+
AC_INIT([Ice-sheet and Sea-level System Model (ISSM)],[4.24],[https://github.com/ISSMteam/ISSM/],[issm],[https://issmteam.github.io/ISSM-Documentation/])
44
AC_CONFIG_AUX_DIR([./aux-config]) # Put config files in aux-config
55
AC_CONFIG_MACRO_DIR([m4]) # m4 macros are located in m4
66
m4_include([m4/issm_options.m4])
@@ -14,11 +14,11 @@ AC_MSG_NOTICE(==================================================================
1414
AC_CANONICAL_TARGET
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1616
#Compilers
17-
AC_PROG_CC([icc cl icl gcc])
18-
AC_PROG_CPP
19-
AC_PROG_CXX([icpc cl icl g++])
20-
AC_PROG_F77([ifort g77 gfortran])
21-
AC_PROG_FC([ifort gfortran])
17+
AC_PROG_CC( [mpicc icc cl icl gcc]) # C compiler
18+
AC_PROG_CPP # C preprocessor (after CC)
19+
AC_PROG_CXX([mpicxx mpic++ icpc cl icl g++]) # C++ compiler
20+
AC_PROG_F77([mpifort ifort g77 gfortran]) # Fortran 77 compiler
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AC_PROG_FC( [mpifort ifort gfortran]) # Fortran compiler
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#AUTOMAKE
2424
AM_INIT_AUTOMAKE([foreign]) # Initialize automake and declare foreign (don't need a ChangeLog, INSTALL, etc)
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2929
#Libtool
3030
LT_INIT([win32-dll])
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#Run issm_options.m4
32+
# ---------------------------------------------------------------------
33+
# Run ISSM’s usual option-detection macro collection
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# ---------------------------------------------------------------------
3335
ISSM_OPTIONS
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#List all Makefiles
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# ---------------------------------------------------------------------
38+
# Output files
39+
# ---------------------------------------------------------------------
3640
AC_CONFIG_FILES([
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Makefile
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src/Makefile
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src/c/Makefile
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src/wrappers/Makefile
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src/wrappers/python/Makefile
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src/wrappers/matlab/Makefile
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src/wrappers/javascript/Makefile
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src/m/Makefile
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Makefile
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src/Makefile
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src/c/Makefile
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src/m/Makefile
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src/wrappers/Makefile
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src/wrappers/python/Makefile
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src/wrappers/matlab/Makefile
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src/wrappers/javascript/Makefile
4549
])
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#End of configure.ac
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AC_OUTPUT

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