Generated Dockerfiles

The generated Dockerfiles for all images are shown below. See also the image specification YAML.

base Dockerfile

Dockerfile.base

#syntax=docker/dockerfile:1

ARG BASE_NAME=archlinux
ARG BASE_TAG=latest

FROM ${BASE_NAME}:${BASE_TAG}

ARG IMAGE_NAME=base
ARG NTHREADS=4
ARG USER_NAME=clas12user
ARG GROUP_NAME=clas12user
ARG USER_ID=10001
ARG GROUP_ID=10001

LABEL name=$IMAGE_NAME
LABEL maintainer="Christopher Dilks"
LABEL architecture="amd64"

USER root

# CA certificates
ADD https://pki.jlab.org/JLabCA.crt /tmp/JLabCA.crt
RUN trust anchor --store /tmp/JLabCA.crt && rm /tmp/JLabCA.crt

# define user
RUN groupadd \
  --gid ${GROUP_ID}\
  ${GROUP_NAME} && \
useradd \
  --no-log-init \
  --create-home \
  --shell /usr/sbin/bash \
  --uid ${USER_ID} \
  --gid ${GROUP_ID} \
  ${USER_NAME}

# context
RUN mkdir -p /opt
COPY bashrc /home/${USER_NAME}/.bashrc
COPY memmon /usr/local/bin/
COPY container_info /usr/local/bin/

# include info about this image
COPY images.yaml /usr/local/etc/
COPY info.yaml /usr/local/etc/

# dump runner specs
RUN spec() { echo "::::: $@ :::::" && $@ ; } && \
echo '======= RUNNER SPECS ========' && \
spec nproc && \
spec lscpu && \
spec free -m && \
echo '===== CONSTRAINED SPECS =====' && \
spec cat /sys/fs/cgroup/cpu.max && \
echo "  (ncpu: divide the first number by the second)" && \
spec cat /sys/fs/cgroup/memory.max && \
echo "  (units: bytes)" && \
echo '============================='

# pacman configuration
# Try each mirror until we find one that works; sometimes slow mirrors cause
# problems, and `pacman` doesn't seem to fallback to the next mirror. We could
# use one of the official mirror ranking scripts, but to install those, we
# first need a working mirror; instead, here is our own mirror selector:
RUN for mirror in \
  'https://america.mirror.pkgbuild.com/$repo/os/$arch' \
  'https://us.arch.niranjan.co/$repo/os/$arch' \
  'https://arlm.tyzoid.com/$repo/os/$arch' \
  'https://arch.mirror.constant.com/$repo/os/$arch' \
  'https://mirrors.lug.mtu.edu/archlinux/$repo/os/$arch' ; do \
    echo "Server = $mirror" | tee /etc/pacman.d/mirrorlist && \
    pacman -Syu --noconfirm && \
    exit 0 ; \
  done ; \
  echo "ERROR: all pacman mirrors failed" >&2 && \
  exit 1

# system configuration
# NOTE: using `w /dev/stdout` in `sed -i` calls to print what gets replaced to `stdout`
RUN echo '=============== system configuration ===============' && \
echo '>>> set locale, by uncommenting the relevant locale line' && \
sed -i -e '/en_US\.UTF-8/ s;^#;;g w /dev/stdout' /etc/locale.gen && \
echo '>>> regenerate locales' && \
locale-gen && \
echo '>>> allow man pages to be installed, by commenting out the relevant `NoExtract` line' && \
sed -i -e '/^\<NoExtract\>.*\<man\>/ s;^;#; w /dev/stdout' /etc/pacman.conf && \
echo '>>> install manpage for pacman' && \
pacman -S --noconfirm pacman && \
echo '=============== done system configuration ==============='

# `/usr/local` is not in all default search paths
# - already included by default in `$PATH`
# - everything else uses the following env vars:
ENV CMAKE_PREFIX_PATH=/usr/local
ENV LD_LIBRARY_PATH=/usr/local/lib
ENV PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
ENV PYTHONPATH=/usr/local/python
ENV ROOT_INCLUDE_PATH=/usr/local/include

# install upstream packages with pacman
# NOTE: the pacman cache is cleared afterward to minimize image size
RUN pacman -Syu --noconfirm && \
pacman -S --noconfirm \
  bash \
  bc \
  clang \
  cmake \
  curl \
  diffutils \
  emacs \
  fish \
  gcc-fortran \
  gcc \
  git \
  groovy \
  jdk21-openjdk \
  jq \
  julia \
  llvm \
  make \
  man-db \
  man-pages \
  mariadb \
  maven \
  meson \
  nano \
  ninja \
  patch \
  pkgconf \
  plocate \
  python \
  rsync \
  ruby \
  scons \
  sqlite \
  tcsh \
  tree \
  vim \
  wget \
  which \
  xrootd \
  yq \
  zsh && \
yes | pacman -Scc

# make a temporary build directory; all build instructions below should
# assume /build is the current working directory
WORKDIR /build

# install rcdb, version v1.99.6
ENV RCDB_HOME=/opt/rcdb
ENV RCDB_CONNECTION=mysql://rcdb@clasdb.jlab.org/rcdb
ENV PATH=$RCDB_HOME/bin:$PATH
ENV PYTHONPATH=$RCDB_HOME/python:$PYTHONPATH
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch v1.99.6 \
  https://github.com/baltzell/rcdb.git \
  $RCDB_HOME

# install ccdb, version v1.99.6
ENV CCDB_HOME=/usr/local
ENV CCDB_USER=clas12user
ENV CCDB_CONNECTION=mysql://clas12reader@clasdb-farm.jlab.org/clas12
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch v1.99.6 \
  https://github.com/baltzell/ccdb.git && \
cmake -S ccdb -B ccdb_build --install-prefix $CCDB_HOME && \
cmake --build ccdb_build -j $NTHREADS && \
cmake --install ccdb_build

# install qadb, version v3.1.0
# NOTE: this is the only repo that uses JYPATH (for coatjava's `run-groovy`)
ENV QADB=/opt/clas12-qadb
ENV JYPATH=$QADB/src
ENV PATH=$QADB/bin:$PATH
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch v3.1.0 \
  https://github.com/JeffersonLab/clas12-qadb.git \
  --recurse-submodules \
  --shallow-submodules \
  $QADB

# install hipo, version 4.2.0
ENV HIPO=/usr/local
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch 4.2.0 \
  https://github.com/gavalian/hipo.git && \
meson setup hipo/build hipo \
  --prefix=$HIPO \
  -D buildtype=release \
  && \
meson compile -C hipo/build -j $NTHREADS && \
meson install -C hipo/build

# cleanup
WORKDIR /home/${USER_NAME}
RUN rm -rf /build

# remove .git directories, leftover from `git clone` to `/opt/`
RUN find /opt -type d -name .git | xargs -I{} sh -c 'echo "REMOVING {}" && rm -rf {}'

# update plocate DB
RUN updatedb

# set entrypoint
CMD ["/usr/sbin/bash", "--rcfile", "/home/clas12user/.bashrc"]

# switch back to non-root user
USER ${USER_NAME}

base_root Dockerfile

Dockerfile.base_root

#syntax=docker/dockerfile:1

ARG BASE_NAME=base
ARG BASE_TAG=latest

FROM ${BASE_NAME}:${BASE_TAG}

ARG IMAGE_NAME=base_root
ARG NTHREADS=4
ARG NTHREADS_ROOT=3

LABEL name=$IMAGE_NAME
LABEL maintainer="Christopher Dilks"
LABEL architecture="amd64"

# switch from non-root user to root
RUN user_name=$(whoami)
USER root

# include info about this image
COPY info.yaml /usr/local/etc/

# dump runner specs
RUN spec() { echo "::::: $@ :::::" && $@ ; } && \
echo '======= RUNNER SPECS ========' && \
spec nproc && \
spec lscpu && \
spec free -m && \
echo '===== CONSTRAINED SPECS =====' && \
spec cat /sys/fs/cgroup/cpu.max && \
echo "  (ncpu: divide the first number by the second)" && \
spec cat /sys/fs/cgroup/memory.max && \
echo "  (units: bytes)" && \
echo '============================='

# install upstream packages with pacman
# NOTE: the pacman cache is cleared afterward to minimize image size
RUN pacman -Syu --noconfirm && \
pacman -S --noconfirm \
  binutils \
  davix \
  glu \
  gsl \
  libx11 \
  libxext \
  libxft \
  libxpm \
  openssl && \
yes | pacman -Scc

# make a temporary build directory; all build instructions below should
# assume /build is the current working directory
WORKDIR /build

# install root, version v6-34-04
# prefer to isolate its installation, so we can more clearly see CLAS12-software in /usr/local
ENV ROOTSYS=/opt/root
ENV PATH=$ROOTSYS/bin:$PATH
ENV LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
ENV PYTHONPATH=$ROOTSYS/lib:$PYTHONPATH
ENV CMAKE_PREFIX_PATH=$ROOTSYS:$CMAKE_PREFIX_PATH
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch v6-34-04 \
  https://github.com/root-project/root.git \
  root && \
cmake -S root -B root_build \
  --install-prefix $ROOTSYS \
  -D builtin_glew=ON \
  -D fftw3=ON \
  -D mathmore=ON \
  -D proof=ON \
  && \
memmon 1 cmake --build root_build -j $NTHREADS_ROOT && \
cmake --install root_build

# install hipo, version 4.2.0
ENV HIPO=/usr/local
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch 4.2.0 \
  https://github.com/gavalian/hipo.git && \
meson setup hipo/build hipo \
  --prefix=$HIPO \
  -D buildtype=release \
  && \
meson compile -C hipo/build -j $NTHREADS && \
meson install -C hipo/build

# cleanup
WORKDIR /home/$user_name
RUN rm -rf /build

# remove .git directories, leftover from `git clone` to `/opt/`
RUN find /opt -type d -name .git | xargs -I{} sh -c 'echo "REMOVING {}" && rm -rf {}'

# update plocate DB
RUN updatedb

# switch back to non-root user
USER $user_name

recon Dockerfile

Dockerfile.recon

#syntax=docker/dockerfile:1

ARG BASE_NAME=base
ARG BASE_TAG=latest

FROM ${BASE_NAME}:${BASE_TAG}

ARG IMAGE_NAME=recon
ARG NTHREADS=4
ARG NTHREADS_ROOT=3

LABEL name=$IMAGE_NAME
LABEL maintainer="Christopher Dilks"
LABEL architecture="amd64"

# switch from non-root user to root
RUN user_name=$(whoami)
USER root

# include info about this image
COPY info.yaml /usr/local/etc/

# dump runner specs
RUN spec() { echo "::::: $@ :::::" && $@ ; } && \
echo '======= RUNNER SPECS ========' && \
spec nproc && \
spec lscpu && \
spec free -m && \
echo '===== CONSTRAINED SPECS =====' && \
spec cat /sys/fs/cgroup/cpu.max && \
echo "  (ncpu: divide the first number by the second)" && \
spec cat /sys/fs/cgroup/memory.max && \
echo "  (units: bytes)" && \
echo '============================='


# make a temporary build directory; all build instructions below should
# assume /build is the current working directory
WORKDIR /build

# install clas12-config, version main
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch main \
  https://github.com/JeffersonLab/clas12-config.git \
  /opt/clas12-config

# install clara, version main
ENV CLARA_HOME=/opt/clara-home
ENV PATH=$CLARA_HOME/bin:$PATH
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch main \
  https://code.jlab.org/hallb/clas12/clara-java.git && \
cd clara-java && \
./gradlew deploy

# install coatjava, version 11.1.1
ENV COATJAVA=/opt/coatjava
ENV CLAS12DIR=/opt/coatjava
ENV PATH=$COATJAVA/bin:$PATH
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch 11.1.1 \
  https://github.com/JeffersonLab/coatjava.git && \
cd coatjava && \
./build-coatjava.sh -T $NTHREADS && \
cd validation/advanced-tests && \
./run-eb-tests.sh electronproton && \
./run-eb-tests.sh electrongamma && \
./run-eb-tests.sh electronprotonC && \
./run-eb-tests.sh electronneutronC && \
./run-eb-tests.sh electronFTpion && \
cd - && \
mv coatjava /opt/ && \
mv validation/advanced-tests/out_*.hipo /opt/coatjava/etc/data/test

# install denoise, version 4.2.0
# NOTE: the Makefile is not thread safe
ENV DENOISING_NETWORKS=/usr/local/share/denoising
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch 4.2.0 \
  https://github.com/gavalian/driftchambers.git && \
make -C driftchambers && \
cp -v -R driftchambers/install/* /usr/local/

# install asprof, version master
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch master \
  https://github.com/async-profiler/async-profiler.git && \
cd async-profiler && \
make -j $NTHREADS && \
install -t /usr/local/lib ./build/lib/* && \
install -t /usr/local/bin ./build/bin/*

# cleanup
WORKDIR /home/$user_name
RUN rm -rf /build

# remove .git directories, leftover from `git clone` to `/opt/`
RUN find /opt -type d -name .git | xargs -I{} sh -c 'echo "REMOVING {}" && rm -rf {}'

# update plocate DB
RUN updatedb

# switch back to non-root user
USER $user_name

analysis Dockerfile

Dockerfile.analysis

#syntax=docker/dockerfile:1

ARG BASE_NAME=base_root
ARG BASE_TAG=latest

FROM ${BASE_NAME}:${BASE_TAG}

ARG IMAGE_NAME=analysis
ARG NTHREADS=4
ARG NTHREADS_ROOT=3

LABEL name=$IMAGE_NAME
LABEL maintainer="Christopher Dilks"
LABEL architecture="amd64"

# switch from non-root user to root
RUN user_name=$(whoami)
USER root

# include info about this image
COPY info.yaml /usr/local/etc/

# dump runner specs
RUN spec() { echo "::::: $@ :::::" && $@ ; } && \
echo '======= RUNNER SPECS ========' && \
spec nproc && \
spec lscpu && \
spec free -m && \
echo '===== CONSTRAINED SPECS =====' && \
spec cat /sys/fs/cgroup/cpu.max && \
echo "  (ncpu: divide the first number by the second)" && \
spec cat /sys/fs/cgroup/memory.max && \
echo "  (units: bytes)" && \
echo '============================='

# install upstream packages with pacman
# NOTE: the pacman cache is cleared afterward to minimize image size
RUN pacman -Syu --noconfirm && \
pacman -S --noconfirm \
  fmt \
  yaml-cpp && \
yes | pacman -Scc

# make a temporary build directory; all build instructions below should
# assume /build is the current working directory
WORKDIR /build

# install iguana, version v0.8.0
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch v0.8.0 \
  https://github.com/JeffersonLab/iguana.git && \
meson setup iguana/build iguana \
  --prefix=/usr/local \
  -D buildtype=release \
  -D bind_fortran=true \
  -D bind_python=true \
  -D install_examples=true \
  -D z_install_envfile=false \
  -D z_require_root=true \
  -D rcdb:home=$RCDB_HOME \
  && \
meson compile -C iguana/build -j $NTHREADS && \
meson install -C iguana/build

# install clas12root, version 1.8.5
ENV CLAS12ROOT=/opt/clas12root
ENV PATH=$CLAS12ROOT/bin:$PATH
ENV LD_LIBRARY_PATH=$CLAS12ROOT/lib:$LD_LIBRARY_PATH
ENV ROOT_INCLUDE_PATH=$CLAS12ROOT/Clas12Root:$CLAS12ROOT/Clas12Banks:$ROOT_INCLUDE_PATH
RUN git clone \
  --depth 1 \
  --single-branch \
  --branch 1.8.5 \
  https://github.com/JeffersonLab/clas12root.git \
  $CLAS12ROOT && \
cd $CLAS12ROOT && \
./installC12Root

# install clas12-mcgen, version v3.15
RUN cd /build && \
git clone \
  --depth 1 \
  --single-branch \
  --branch v3.15 \
  --recurse-submodules https://github.com/jeffersonlab/clas12-mcgen.git && \
cd clas12-mcgen && \
make -j $NTHREADS && \
make install && \
make prune


# cleanup
WORKDIR /home/$user_name
RUN rm -rf /build

# remove .git directories, leftover from `git clone` to `/opt/`
RUN find /opt -type d -name .git | xargs -I{} sh -c 'echo "REMOVING {}" && rm -rf {}'

# update plocate DB
RUN updatedb

# switch back to non-root user
USER $user_name