pysimm/Dockerfile at stable · SmithLabMIT/pysimm · GitHub

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FROM debian:buster as build

ARG PACKAGES="class2 extra-molecule kspace manybody misc molecule qeq rigid user-misc"
ARG BIN_DIR="/usr/local/bin"

RUN apt-get update && \
    apt-get install -y make git g++ libopenmpi-dev openmpi-bin curl

RUN git clone -b stable_3Mar2020 --single-branch https://github.com/lammps/lammps.git && \
    cd lammps/src && \
    for PACKAGE in $PACKAGES; do make yes-$PACKAGE; done && \
    make -j2 mpi && \
    cp lmp_mpi $BIN_DIR


RUN cd /usr/local/lib && \
    git clone -b v1.2.5 https://github.com/MaginnGroup/Cassandra.git && \
    cd Cassandra/Src/ && \
    make clean && make -f Makefile.gfortran.openMP && \
    cp cassandra_gfortran_openMP.exe $BIN_DIR/cs_gfort_omp.exe && \
    cd ../../ && rm -rf Cassandra


RUN cd /usr/local/lib && \
    git clone https://github.com/SarkisovGroup/PoreBlazer.git && \
    cd PoreBlazer/src/ && \
    make -f Makefile_gfort && \
    cp poreblazer.exe $BIN_DIR && \
    cd ../../ && \
    rm -rf PoreBlazer


RUN TB_NAME=zeopp.v0p3.tar.gz && DIR_NAME=zeopp.v0p3 && \
    cd /usr/local/lib && \
    curl http://www.zeoplusplus.org/zeo++-0.3.tar.gz --output $TB_NAME && \
    tar -xf $TB_NAME && \
    rm $TB_NAME && mv zeo++-0.3 $DIR_NAME && \
    cd $DIR_NAME/voro++/src && make && \
    cd ../.. && make && \
    cp network $BIN_DIR && \
    rm -rf $DIR_NAME

FROM python:3.8-slim

COPY --from=build /usr/local/bin/* /usr/local/bin/

RUN apt-get update && \
    apt-get install -y libopenmpi-dev openmpi-bin vim mc

COPY . /usr/local/pysimm

RUN python -m pip install --upgrade pip && \
    pip install -r /usr/local/pysimm/requirements.txt && \
    pip install -e /usr/local/pysimm && \
    pip install jupyterlab matplotlib nglview

ENV LAMMPS_EXEC="lmp_mpi"
ENV CASSANDRA_EXEC="cs_gfort_omp.exe"
ENV ZEOpp_EXEC="network"

# Add Tini. Tini operates as a process subreaper for jupyter. This prevents kernel crashes.
ENV TINI_VERSION v0.6.0
ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini
ENTRYPOINT ["/usr/bin/tini", "--"]

CMD ["jupyter-lab", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]