Dockerfile for GROMACS. Compile with nvidia-docker

Dockerfile

###############################################################################
# Ubuntu 16.04, CUDA 9.0, OpenMPI, and GROMACS.
#
# Requirements:
# * gromacs directory in build directory with source for GROMACS.
#
# Build with:
# sudo nvidia-docker build -t gromacs . \
#   --build-arg GROMACS_VERSION=gromacs_version \
#   --build-arg JOBS=16
#
# The build args are optional. To get the versions consistent with GROMACS
# in general, use e.g. 2018 for the main realease, and 2018.4 for the
# fourth patch release.
#
# Run with:
# sudo nvidia-docker run -it gromacs
#
# Test with:
# sudo nvidia-docker run -it -v /path/to/gromacs/scripts:/scripts gromacs \
#   /scripts/validate_gromacs.sh
###############################################################################
ARG GROMACS_VERSION=2018.4
ARG JOBS=16

###############################################################################
# Build stage
###############################################################################
FROM nvidia/cuda:9.0-devel-ubuntu16.04 as builder

# install required packages
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    cmake \
    curl \
    libopenmpi-dev \
    openmpi-bin \
    openmpi-common \
    python \
  && rm -rf /var/lib/apt/lists/*
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/openmpi/lib

# Install fftw-3.3.8 with more optimizations than the default packages
# It is not critical to run the tests here, since our experience is that the
# Gromacs unit tests will catch fftw build errors too.
RUN curl -o fftw-3.3.8.tar.gz http://www.fftw.org/fftw-3.3.8.tar.gz \
  && tar -xzvf fftw-3.3.8.tar.gz && cd fftw-3.3.8 \
  && ./configure --disable-double --enable-float --enable-sse2 --enable-avx --enable-avx2 --enable-avx512 --enable-shared --disable-static \
  && make -j ${JOBS} \
  && make install

# build GROMACS and run unit tests
# To cater to different architectures, we build for all of them
# and install in different bin/lib directories.

RUN mkdir -p /gromacs /gromacs-src
COPY gromacs /gromacs-src

# You can change the architecture list here to add more SIMD types,
# but make sure to always include SSE2 as a fall-back.
RUN for ARCH in SSE2 AVX_256 AVX2_256 AVX_512; do \
     mkdir -p /gromacs-build.${ARCH} && cd /gromacs-build.${ARCH} \
  && CC=gcc CXX=g++ cmake /gromacs-src \
    -DGMX_OPENMP=ON \
    -DGMX_GPU=ON \
    -DGMX_MPI=OFF \
    -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
    -DCMAKE_INSTALL_PREFIX=/gromacs \
    -DREGRESSIONTEST_DOWNLOAD=ON \
    -DGMX_USE_NVML=OFF \
#    -DMPIEXEC_PREFLAGS=--allow-run-as-root \
    -DGMX_SIMD=${ARCH} \
    -DCMAKE_INSTALL_BINDIR=bin.${ARCH} \
    -DCMAKE_INSTALL_LIBDIR=lib.${ARCH} \
  && make -j ${JOBS} \
  && make install; done

# Run tests (optional)
# We avoid running tests for AVX_512, since that hardware might not be available
RUN for ARCH in SSE2 AVX_256 AVX2_256; do \
    cd /gromacs-build.${ARCH} && make -j ${JOBS} check; done

#
# Build the program to identify number of AVX512 FMA units
# This will only be executed on AVX-512-capable hosts. If there
# are dual AVX-512 FMA units, it will be faster to use AVX-512 SIMD, but if
# there's only a single one we prefer AVX2_256 SIMD instead.
#
RUN cd /gromacs-build.AVX_512 \
  && g++ -O3 -mavx512f -std=c++11 \
    -DGMX_IDENTIFY_AVX512_FMA_UNITS_STANDALONE=1 \
    -DGMX_X86_GCC_INLINE_ASM=1 \
    -DSIMD_AVX_512_CXX_SUPPORTED=1 \
    -o /gromacs/bin.AVX_512/identifyavx512fmaunits \
    /gromacs-src/src/gromacs/hardware/identifyavx512fmaunits.cpp

# 
# Create the architecture-detection script
RUN mkdir -p /gromacs/bin && echo '#!/bin/sh\n\
FLAGS=`cat /proc/cpuinfo | grep ^flags | head -1`\n\
if echo $FLAGS | grep " avx512f " > /dev/null && test -d /gromacs/bin.AVX_512 && echo `/gromacs/bin.AVX_512/identifyavx512fmaunits` | grep "2" > /dev/null; then\n\
    ARCH="AVX_512"\n\
elif echo $FLAGS | grep " avx2 " > /dev/null && test -d /gromacs/bin.AVX2_256; then\n\
    ARCH="AVX2_256"\n\
elif echo $FLAGS | grep " avx " > /dev/null && test -d /gromacs/bin.AVX_256; then\n\
    ARCH="AVX_256"\n\
else\n\
    ARCH="SSE2"\n\
fi\n\
/gromacs/bin.${ARCH}/gmx $@\n' > /gromacs/bin/gmx && chmod +x /gromacs/bin/gmx

###############################################################################
# Final stage
###############################################################################
FROM nvidia/cuda:9.0-runtime-ubuntu16.04

# install required packages
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    libgomp1 \
    libopenmpi-dev \
    openmpi-bin \
    openmpi-common \
    python \
  && rm -rf /var/lib/apt/lists/*

# copy fftw libraries
COPY --from=builder /usr/local/lib /usr/local/lib

# copy gromacs install
COPY --from=builder /gromacs /gromacs
ENV PATH=$PATH:/gromacs/bin

# setup labels
LABEL com.nvidia.gromacs.version="${GROMACS_VERSION}"

# NVIDIA-specific stuff?
#WORKDIR /workspace
#COPY examples examples 

#
# Enable the entrypoint to use the dockerfile as a GROMACS binary
#ENTRYPOINT [ "/gromacs/bin/gmx" ]

Moved to https://github.com/bioexcel/gromacs-docker