PyRosetta Singularity File with Anaconda and OpenMPI

singularity_pyrosetta

Bootstrap: docker
From: centos:centos7

%environment
    PATH="/opt/software/bin:$PATH"
    export PATH
    LD_LIBRARY_PATH="/opt/software/lib/openmpi:$LD_LIBRARY_PATH"
    export LD_LIBRARY_PATH

%files
    PyRosetta4.Release.python27.linux.release-175.tar.bz2 /opt

%post
    yum -y groupinstall "Development Tools"
    yum -y install wget vim zeromq

    # download and install Anaconda
    CONDA_INSTALL_PATH="/opt/software"
    wget https://repo.continuum.io/archive/Anaconda2-5.1.0-Linux-x86_64.sh
    chmod +x Anaconda2-5.1.0-Linux-x86_64.sh
    ./Anaconda2-5.1.0-Linux-x86_64.sh -b -p $CONDA_INSTALL_PATH

    # download openmpi
    wget https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.2.tar.bz2
    tar jxf openmpi-2.1.2.tar.bz2
    cd openmpi-2.1.2
    ./configure --prefix=/opt/software
    make
    make install

    # example ring
    cd examples
    /opt/software/bin/mpicc ring_c.c -o ring
    cp ring /opt/software/bin

    # marcc uses centos 6, no overlay support
    mkdir -p /scratch /work-zfs /my-apps /my-work /home-0 /home-1 /home-2 /home-3 /home-4

    # update conda
    /opt/software/bin/conda update -y -n base conda

    # install jupyter notebook
    /opt/software/bin/conda install -y jupyter
    /opt/software/bin/conda install -y numpy
    /opt/software/bin/conda install -y matplotlib
    /opt/software/bin/conda install -y scipy
    /opt/software/bin/conda install -y zeromq
    /opt/software/bin/conda install -y pyzmq
    /opt/software/bin/conda install -y ipyparallel

    # install pyrosetta
    cd /opt
    tar xf PyRosetta4.Release.python27.linux.release-175.tar.bz2
    cd /opt/PyRosetta4.Release.python27.linux.release-175/setup
    /opt/software/bin/python setup.py install

    # install mpi4py
    env MPICC=/opt/software/bin/mpicc /opt/software/bin/pip install mpi4py -t /opt/software/lib/python2.7/site-packages/

Previous OpenMPI didn't work because conda install mpi4py installs MPICH2, and we picked the same software install location at /opt/software!