Attempt at compiling the Ice Sheet System Model (ISSM) on docker (Python 3 interface, hopefully). Also using conda to install some packages.

Dockerfile

FROM jupyter/minimal-notebook

USER root
RUN apt -qq update && apt install -y --no-install-recommends \
    git-svn \
    python-dev \
    python3-dev \
    && rm -rf /var/lib/apt/lists/*

USER $NB_UID

# Use git svn to clone the ISSM svn trunk repository from revision 24493 (24 Dec 2019)
RUN echo 'anon' | git svn clone --username anon -r 24493 https://issm.ess.uci.edu/svn/issm/issm/trunk

# Install various conda dependencies
RUN conda install \
    automake \
    blas=*=*mkl \
    cmake \
    fortran-compiler \
    lapack \
    libtool \
    matplotlib \
    mpich-mpicxx \
    nose \
    numpy \
    petsc \
    scipy \
    triangle \
    && conda clean --all --yes

# Change to interactive bash shell, so that `conda activate` works
SHELL ["/bin/bash", "-ic"]
RUN conda init --verbose

# Install dependencies shipped with ISSM
ENV ISSM_DIR ${HOME}/trunk
#RUN unset F90 && \
#    cd $ISSM_DIR/externalpackages/mpich && \
#    ./install-3.0-linux64.sh
#RUN . $ISSM_DIR/etc/environment.sh && \
#    cd $ISSM_DIR/externalpackages/petsc && \
#    ./install-3.11-linux64.sh
RUN . $ISSM_DIR/etc/environment.sh && \
    cd $ISSM_DIR/externalpackages/m1qn3 && \
    ./install.sh
RUN . $ISSM_DIR/etc/environment.sh && \
    cd $ISSM_DIR/externalpackages/triangle && \
    ./install-linux64.sh

# Compile ISSM
RUN cd $ISSM_DIR && \
    . $ISSM_DIR/etc/environment.sh && \
    autoreconf -ivf

RUN cd $ISSM_DIR && \
    ./configure \
    --prefix="$ISSM_DIR" \
    --disable-static \
    --with-numthreads=8 \
    --with-python-dir="$CONDA_DIR" \
    --with-python-numpy-dir="$CONDA_DIR/lib/python3.7/site-packages/numpy" \
    #--with-fortran-lib="-L$CONDA_DIR/lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0 -lgfortran" \
    --with-mpi-include="$CONDA_DIR/lib/include" \
    --with-mpi-libflags="-L$CONDA_DIR/lib -lmpi -lmpicxx -lmpifort" \
    #--with-blas-lapack-dir="$CONDA_DIR/lib" \
    --with-metis-dir="$CONDA_DIR/lib" \
    --with-scalapack-dir="$CONDA_DIR/lib" \
    --with-mumps-dir="$CONDA_DIR/lib" \
    --with-petsc-dir="$CONDA_DIR" \
    --with-triangle-dir="$CONDA_DIR/include" \
    --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install"

ENV LD_LIBRARY_PATH ${CONDA_DIR}/lib
RUN cd $ISSM_DIR && \
    make --jobs=8 && \
    make install

Development of this code moved to https://github.com/weiji14/pyissm.