Dockerfile installs latest conda, texlive, cuda

Dockerfile

@@ -1,4 +1,162 @@
-FROM jchodera/omnia-linux-anvil:texlive18
+FROM centos:6
+
+MAINTAINER omnia <[email protected]>
+
+# Set locale and encoding to make things work smoothly
+# See http://jaredmarkell.com/docker-and-locales/
+#RUN locale-gen en_US.UTF-8 # not present in CentOS 6
+RUN localedef -c -i en_US -f UTF-8 en_US.UTF-8
+ENV LANG en_US.UTF-8  
+ENV LANGUAGE en_US:en  
+ENV LC_ALL en_US.UTF-8  
+
+# Add a file for users to source to activate the `conda`
+# environment `root` and the devtoolset compiler. Also
+# add a file that wraps that for use with the `ENTRYPOINT`.
+COPY entrypoint_source /opt/docker/bin/entrypoint_source
+COPY entrypoint /opt/docker/bin/entrypoint
+
+# Add a timestamp for the build. Also, bust the cache.
+#ADD https://now.httpbin.org/when/now /opt/docker/etc/timestamp
+
+# Resolves a nasty NOKEY warning that appears when using yum.
+RUN rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-6
+
+# Install basic requirements.
+RUN yum update -y && \
+    yum install -y \
+                   bzip2 \
+                   make \
+                   patch \
+                   sudo \
+                   tar \
+                   which \
+                   libXext-devel \
+                   libXrender-devel \
+                   libSM-devel \
+                   libX11-devel \
+                   mesa-libGL-devel && \
+    yum clean all
+
+# Install devtoolset 2.
+RUN yum update -y && \
+    yum install -y \
+                   centos-release-scl \
+                   yum-utils && \
+    yum-config-manager --add-repo http://people.centos.org/tru/devtools-2/devtools-2.repo && \
+    yum update -y && \
+    yum install -y \
+                   devtoolset-2-binutils \
+                   devtoolset-2-gcc \
+                   devtoolset-2-gcc-gfortran \
+                   devtoolset-2-gcc-c++ && \
+    yum clean -y --quiet expire-cache && \
+    yum clean -y --quiet all
+
+
+# Install conda
+
+# give sudo permission for conda user to run yum (user creation is postponed
+# to the entrypoint, so we can create a user with the same id as the host)
+RUN echo 'conda ALL=NOPASSWD: /usr/bin/yum' >> /etc/sudoers
+
+# Install Miniconda with Python 3 and update everything.
+# NOTE: This step differs from condaforge/linux-anvil
+RUN curl -s -L https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh && \
+    sha256sum miniconda.sh | grep bb2e3cedd2e78a8bb6872ab3ab5b1266a90f8c7004a22d8dc2ea5effeb6a439a && \
+    bash miniconda.sh -b -p /opt/conda && \
+    rm miniconda.sh && \
+    export PATH=/opt/conda/bin:$PATH && \
+    conda config --set show_channel_urls True && \
+    conda config --add channels conda-forge && \
+    touch /opt/conda/conda-meta/pinned && \
+    conda upgrade --yes conda && \
+    conda update --all --yes && \
+    conda install --yes --quiet conda-build anaconda-client jinja2 setuptools git && \
+    conda build purge-all && \
+    #export CONDA_CONDA_INFO=( `conda list conda | grep conda` ) && \
+    #echo "conda ${CONDA_CONDA_INFO[1]}" >> /opt/conda/conda-meta/pinned && \
+    rm -rf /opt/conda/pkgs/*
+
+# Install conda build and deployment tools
+# NOTE: This step differs from condaforge/linux-anvil
+RUN export PATH="/opt/conda/bin:${PATH}" && \
+    export CONDA_BUILD_INFO=( `conda list conda-build | grep conda-build` ) && \
+    echo "conda-build ${CONDA_BUILD_INFO[1]}" >> /opt/conda/conda-meta/pinned && \
+    conda build purge-all && \
+    rm -rf /opt/conda/pkgs/*
+
+# Install docker tools.
+RUN export PATH="/opt/conda/bin:${PATH}" && \
+    conda install --yes gosu && \
+    export CONDA_GOSU_INFO=( `conda list gosu | grep gosu` ) && \
+    echo "gosu ${CONDA_GOSU_INFO[1]}" >> /opt/conda/conda-meta/pinned && \
+    conda install --yes tini && \
+    export CONDA_TINI_INFO=( `conda list tini | grep tini` ) && \
+    echo "tini ${CONDA_TINI_INFO[1]}" >> /opt/conda/conda-meta/pinned && \
+    . /opt/conda/bin/activate root && \
+    conda build purge-all && \
+    rm -rf /opt/conda/pkgs/*
+
+#
+# Install TeXLive on top of conda-forge linux-anvil image
+#
+
+#
+# Install EPEL and extra packages
+#
+
+# CUDA requires dkms libvdpau
+# TeX installation requires wget and perl
+# The other TeX packages installed with `tlmgr install` are required for OpenMM's sphinx doc
+# libXext libSM libXrender are required for matplotlib to work
+
+# Download and install EPEL, install extra packages for TeX, AMD, and CUDA, cleanup yum
+RUN curl -L http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm --output epel-release-6-8.noarch.rpm && \
+    rpm -i --quiet epel-release-6-8.noarch.rpm && \
+    rm -rf epel-release-6-8.noarch.rpm && \
+    yum install -y --quiet perl dkms libvdpau git wget libXext libSM libXrender groff && \
+    yum clean -y --quiet expire-cache && \
+    yum clean -y --quiet all
+
+#
+# Install GLIBC 2.14 for TeXLive 2018 which needs full C++11 to run
+
+RUN curl -L https://ftp.gnu.org/gnu/libc/glibc-2.14.tar.gz --output glibc-2.14.tar.gz && \
+    tar -zxf glibc-2.14.tar.gz && \
+    cd glibc-2.14 && \
+    mkdir build && \
+    cd build && \
+    source /opt/docker/bin/entrypoint_source && \
+    ../configure --prefix=/opt/glibc-2.14 && \
+    make -s && make -s install && \
+    cd / && rm -rf glibc*
+
+#
+# Install TeXLive 2018
+#
+
+# Add config file from repo
+ADD texlive.profile .
+# Download, untar, install, remove install files, install additional packages, make symlinks for all users
+RUN export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/glibc-2.14/lib && \
+    curl -L http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz --output install-tl-unx.tar.gz && \
+    tar -xzf install-tl-unx.tar.gz && \
+    cd install-tl-* && ./install-tl -profile /texlive.profile && cd - && \
+    rm -rf install-tl-unx.tar.gz install-tl-* texlive.profile && \
+    /usr/local/texlive/2018/bin/x86_64-linux/tlmgr install \
+          cmap fancybox titlesec framed fancyvrb threeparttable \
+          mdwtools wrapfig parskip upquote float multirow hyphenat caption \
+          xstring fncychap tabulary capt-of eqparbox environ trimspaces \
+          varwidth latexmk etoolbox framed \
+          xcolor fancyvrb float wrapfig parskip upquote \
+          capt-of needspace && \          
+    ln -s /usr/local/texlive/2018/bin/x86_64-linux/* /usr/local/sbin/
+ENV PATH=/usr/local/texlive/2018/bin/x86_64-linux:$PATH
+
+# Show current packages.
+RUN export PATH="/opt/conda/bin:${PATH}" && \
+    conda list
 
 # Install NVIDIA driver
 RUN wget -q http://us.download.nvidia.com/XFree86/Linux-x86_64/390.67/NVIDIA-Linux-x86_64-390.67.run && \
@@ -22,6 +180,15 @@ RUN wget -q https://developer.nvidia.com/compute/cuda/9.2/Prod/patches/1/cuda_9.
     ./cuda_9.2.88.1_linux -s --accept-eula && \
     rm -f cuda_9.2.88.1_linux
 
+
+# Ensure that all containers start with tini and the user selected process.
+# Activate the `conda` environment `root` and the devtoolset compiler.
+# Provide a default command (`bash`), which will start if the user doesn't specify one.
+ENTRYPOINT [ "/opt/conda/bin/tini", "--", "/opt/docker/bin/entrypoint" ]
+CMD [ "/bin/bash" ]
+
 # Clean up
 RUN yum clean -y --quiet expire-cache && \
     yum clean -y --quiet all
+
+

entrypoint

@@ -0,0 +1,23 @@
+#!/bin/bash -il
+
+# Create conda user with the same uid as the host, so the container can write
+# to mounted volumes
+# Adapted from https://denibertovic.com/posts/handling-permissions-with-docker-volumes/
+USER_ID=${HOST_USER_ID:-9001}
+useradd --shell /bin/bash -u $USER_ID -o -c "" -m conda
+export HOME=/home/conda
+export USER=conda
+export LOGNAME=conda
+export MAIL=/var/spool/mail/conda
+export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/conda/bin
+chown conda:conda $HOME
+chown -R conda:conda /opt/conda
+cp -R /etc/skel $HOME && chown -R conda:conda $HOME/skel && (ls -A1 $HOME/skel | xargs -I {} mv -n $HOME/skel/{} $HOME) && rm -Rf $HOME/skel
+cp /root/.condarc $HOME/.condarc && chown conda:conda $HOME/.condarc
+cd $HOME
+
+# Source everything that needs to be.
+. /opt/docker/bin/entrypoint_source
+
+# Run whatever the user wants.
+exec /opt/conda/bin/gosu conda "$@"

entrypoint_source

@@ -0,0 +1,11 @@
+# Enable the compiler toolset.
+#
+# Must do this before activating conda or
+# the system Python interpreter is not used.
+# This is a problem for many reasons. One being
+# that the Python scripts used to activate the
+# toolset are not Python 3 compatible.
+. scl_source enable devtoolset-2
+
+# Activate the `root` conda environment.
+. /opt/conda/bin/activate root