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MathieuMorlighemMathieuMorlighem
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Merge branch 'main' of github.com:ISSMteam/ISSM
2 parents caad0b5 + 3cb91ea commit 0907848

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‎.github/workflows/common-workflow.yml‎

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@@ -21,6 +21,12 @@ on:
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additional_options:
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required: true
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type: string
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interface:
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required: true
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type: string
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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: ${{ github.workspace }}
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uses: actions/cache@v3
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id: cache-externalpackages
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env:
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cache-name: cache-externalpackages-${{ inputs.build_type }}
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cache-name: cache-externalpackages-${{ inputs.build_type}}
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with:
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path: |
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${{ env.ISSM_DIR }}/externalpackages/
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${{ inputs.ext_install_command }}
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- name: Get MATLAB
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if: ${{inputs.interface == 'matlab'}}
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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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cache: true
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- name: Prepare python
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if: contains( inputs.interface, 'python')
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uses: actions/setup-python@v5
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id: setup-python
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with:
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python-version: ${{ inputs.python_version }}
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- name: Install dependencies
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if: contains( inputs.interface, 'python')
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run: |
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sudo apt-get install libpython${{ inputs.python_version }}-dev
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sudo apt-get install python3-dev
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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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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 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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shell: 'bash'
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- name: Get MATLAB
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if: ${{inputs.interface == 'matlab'}}
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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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cache: true
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- name: Creating matlab_ci.m
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if: ${{inputs.interface == 'matlab'}}
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run: |
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cat > ${ISSM_DIR}/matlab_ci.m << EOF
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% Go to the test directory
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cat ${ISSM_DIR}/matlab_ci.m
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- name: Get run-matlab-command
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if: ${{inputs.interface == 'matlab'}}
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run: |
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wget -O /usr/local/bin/run-matlab-command https://ssd.mathworks.com/supportfiles/ci/run-matlab-command/v2/glnxa64/run-matlab-command
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chmod +x /usr/local/bin/run-matlab-command
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- name: Run MATLAB tests
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if: ${{inputs.interface == 'matlab'}}
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run: |
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source $ISSM_DIR/etc/environment.sh
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LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$ISSM_DIR/externalpackages/petsc/install/lib/libmpi.so:$ISSM_DIR/externalpackages/petsc/install/lib/libmpifort.so run-matlab-command "matlab_ci"
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- name: Prepare python
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if: contains( inputs.interface, 'python')
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uses: actions/setup-python@v5
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id: setup-python
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with:
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python-version: ${{ inputs.python_version }}
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- name: Install dependencies
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if: contains( inputs.interface, 'python')
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run: |
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python -m pip install --upgrade pip
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sudo apt-get update && sudo apt-get install -y python-tk python3-tk
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python -m pip install numpy scipy matplotlib nose netCDF4
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- name: Run Python tests
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if: contains( inputs.interface, 'python')
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run: |
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export PYTHONPATH="${ISSM_DIR}/src/m/dev:${PYTHONPATH}"
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export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
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export PYTHONUNBUFFERED=1
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source $ISSM_DIR/etc/environment.sh
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cd $ISSM_DIR/test/NightlyRun
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LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6:$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

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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
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build_type: basic-matlab
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interface: matlab
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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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ext_install_command: |
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cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh
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cd $ISSM_DIR/externalpackages/m1qn3 && ./install-linux.sh
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cd $ISSM_DIR/externalpackages/petsc && ./install-3.21-linux.sh
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cd $ISSM_DIR/externalpackages/petsc && ./install-3.22-linux.sh
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cd $ISSM_DIR/externalpackages/semic && ./install.sh
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test_cases: '["101:399", "401:899"]'
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additional_options: " "

‎.github/workflows/ubuntu-codipack.yml‎

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with:
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os: ubuntu-latest
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build_type: codipack
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interface: matlab
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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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ext_install_command: |
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cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh
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cd $ISSM_DIR/externalpackages/m1qn3 && ./install-linux.sh
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cd $ISSM_DIR/externalpackages/petsc && ./install-3.20-linux.sh
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cd $ISSM_DIR/externalpackages/petsc && ./install-3.22-linux.sh
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cd $ISSM_DIR/externalpackages/gsl && ./install.sh
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cd $ISSM_DIR/externalpackages/codipack && ./install.sh
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cd $ISSM_DIR/externalpackages/medipack && ./install.sh

‎.github/workflows/ubuntu-python.yml‎

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name: Ubuntu Python
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on:
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push:
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branches: [ "main" ]
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pull_request:
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branches: [ "main" ]
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env:
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ISSM_DIR: ${{ github.workspace }}
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jobs:
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build-test:
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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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interface: python
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python_version: 3.11
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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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--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-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" \
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--with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-parmetis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
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--with-triangle-dir="${ISSM_DIR}/externalpackages/triangle/install" \
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--with-semic-dir="${ISSM_DIR}/externalpackages/semic/install" \
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--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"
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ext_install_command: |
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cd $ISSM_DIR/externalpackages/triangle && ./install-linux.sh
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cd $ISSM_DIR/externalpackages/m1qn3 && ./install-linux.sh
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cd $ISSM_DIR/externalpackages/petsc && ./install-3.22-linux.sh
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cd $ISSM_DIR/externalpackages/semic && ./install.sh
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test_cases: '["range(101,400)", "range(401, 900)"]'
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additional_options: " "
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secrets: inherit
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name: build-test-ubuntu-python

‎README.md‎

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# Ice-sheet and Sea-level System Model - ISSM
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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)
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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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[![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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## Description
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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/adjoinablempi.tar.gz‎

-1.16 MB
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‎externalpackages/adjoinablempi/install-linux.sh‎

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

‎externalpackages/adjoinablempi/install-mac.sh‎

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

‎externalpackages/adjoinablempi/install-pleaides-gcc.sh‎

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

‎externalpackages/adjoinablempi/install-pleaides.sh‎

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

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