micromamba container has too many missing OS components to work correctly, switch to ubuntu setup

Author: jimboid

gromacs/.condarc

@@ -0,0 +1,6 @@
+# Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
+
+auto_update_conda: false
+show_channel_urls: true
+channels:
+  - conda-forge

gromacs/Dockerfile

@@ -1,37 +1,157 @@
-FROM ghcr.io/mamba-org/micromamba:2.4.0-ubuntu24.04
+ARG BASE_IMAGE=ubuntu:24.04
+FROM $BASE_IMAGE
 
 LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"
 
-ARG AIIDAVERSION=2.6.1
+# Define customisable args
+ARG AIIDAVERSION=2.6.3
 ARG GMXVERSION=2025.4
 ARG PLUMEDVERSION=2.9.2
 ARG PYTHONVERSION=3.11
-ARG NEW_MAMBA_USER=aiida
-ARG NEW_MAMBA_USER_ID=1001
-ARG NEW_MAMBA_USER_GID=121
+ARG SYSTEM_USER=aiida
+ARG SYSTEM_UID=1001
+ARG SYSTEM_GID=121
+
+# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
+# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
 USER root
 
-RUN if grep -q '^ID=alpine$' /etc/os-release; then \
-      # alpine does not have usermod/groupmod
-      apk add --no-cache --virtual temp-packages shadow; \
-    fi && \
-    usermod "--login=${NEW_MAMBA_USER}" "--home=/home/${NEW_MAMBA_USER}" \
-        --move-home "-u ${NEW_MAMBA_USER_ID}" "${MAMBA_USER}" && \
-    groupmod "--new-name=${NEW_MAMBA_USER}" \
-        "-g ${NEW_MAMBA_USER_GID}" "${MAMBA_USER}" && \
-    if grep -q '^ID=alpine$' /etc/os-release; then \
-      # remove the packages that were only needed for usermod/groupmod
-      apk del temp-packages; \
+# Set OS level deps
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update --yes && \
+    apt-get upgrade --yes && \
+    apt-get install --yes --no-install-recommends \
+    bison \
+    build-essential \
+    bzip2 \
+    ca-certificates \
+    cmake \
+    curl \
+    flex \
+    erlang \
+    gfortran \
+    git \
+    libbz2-dev \
+    locales \
+    openssh-client \
+    sudo \
+    vim \
+    wget \
+    xz-utils \
+    zlib1g-dev && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* && \
+    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+# Configure env vars
+ENV CONDA_DIR=/opt/conda \
+    SHELL=/bin/bash \
+    SYSTEM_USER="${SYSTEM_USER}" \
+    SYSTEM_UID=${SYSTEM_UID} \
+    SYSTEM_GID=${SYSTEM_GID} \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    LANGUAGE=en_US.UTF-8
+ENV PATH="${CONDA_DIR}/bin:${PATH}" \
+    HOME="/home/${SYSTEM_USER}"
+
+# Create SYSTEM_USER with name aiida  with UID=1001 and in the 'users' group
+# and make sure these dirs are writable by the `users` group.
+RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
+    sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
+    sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
+    addgroup --gid "${SYSTEM_GID}" "${SYSTEM_USER}" && \
+    useradd -l -m -s /bin/bash -N --uid "${SYSTEM_UID}" --gid "${SYSTEM_GID}" "${SYSTEM_USER}" && \
+    mkdir -p "${CONDA_DIR}" && \
+    chown "${SYSTEM_USER}:${SYSTEM_GID}" "${CONDA_DIR}" "${HOME}" && \
+    chmod g+w /etc/passwd
+
+# make a github actions mount point.
+RUN mkdir /github && \
+    chown "${SYSTEM_USER}:${SYSTEM_GID}" /github
+
+USER ${SYSTEM_UID}
+
+# Download and install Micromamba, and initialize Conda prefix.
+COPY --chown="${SYSTEM_UID}:${SYSTEM_GID}" .condarc "${CONDA_DIR}/.condarc"
+WORKDIR /tmp
+RUN set -x && \
+    arch=$(uname -m) && \
+    if [ "${arch}" = "x86_64" ]; then \
+        # Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
+        arch="64"; \
     fi && \
-    # Update the expected value of MAMBA_USER for the
-    # _entrypoint.sh consistency check.
-    echo "${NEW_MAMBA_USER}" > "/etc/arg_mamba_user" && \
-    :
-ENV MAMBA_USER=$NEW_MAMBA_USER
-USER $MAMBA_USER
+    wget --progress=dot:giga -O /tmp/micromamba.tar.bz2 \
+        "https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && \
+    tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && \
+    rm /tmp/micromamba.tar.bz2 && \
+    ./micromamba install \
+        --root-prefix="${CONDA_DIR}" \
+        --prefix="${CONDA_DIR}" \
+        --yes \
+        'mamba' && \
+    rm micromamba
+
+# Add ~/.local/bin to PATH where the dependencies get installed via pip
+# This require the package installed with `--user` flag in pip
+ENV PATH=${PATH}:/home/${SYSTEM_USER}/.local/bin
 
 # Install dependencies
-RUN micromamba install -c conda-forge python=$PYTHONVERSION aiida-core=$AIIDAVERSION aiida-core.services=$AIIDAVERSION && \
-    micromamba install -c conda-forge gromacs=$GMXVERSION plumed=$PLUMEDVERSION && \
-    micromamba clean --all --yes
+RUN mamba install -c conda-forge mamba python=$PYTHONVERSION aiida-core=$AIIDAVERSION aiida-core.services=$AIIDAVERSION && \
+    mamba clean --all --yes
+
+# Change to root and build in /tmp.
+USER root
+WORKDIR /tmp
+
+# Grab the specified version of plumed and untar the source.
+RUN wget https://github.com/plumed/plumed2/archive/refs/tags/v${PLUMEDVERSION}.tar.gz && \
+    tar xvf v${PLUMEDVERSION}.tar.gz && \
+    rm v${PLUMEDVERSION}.tar.gz
+
+# Configure, compile and install plumed.
+WORKDIR /tmp/plumed2-${PLUMEDVERSION}
+RUN ./configure --prefix=/opt/plumed2-${PLUMEDVERSION}
+RUN make -j8
+RUN make install
+
+# Add plumed to the various paths.
+ENV PATH=/opt/plumed2-${PLUMEDVERSION}/bin:$PATH
+ENV LIBRARY_PATH=/opt/plumed2-${PLUMEDVERSION}/lib:$LIBRARY_PATH
+ENV LD_LIBRARY_PATH=/opt/plumed2-${PLUMEDVERSION}/lib:$LD_LIBRARY_PATH
+ENV PLUMED_KERNEL=/opt/plumed2-${PLUMEDVERSION}/lib/libplumedKernel.so
+ENV PLUMED_VIMPATH=/opt/plumed2-${PLUMEDVERSION}/vim
+ENV PYTHONPATH=/opt/plumed2-${PLUMEDVERSION}/python:$PYTHONPATH
+
+# Back to tmp
+WORKDIR /tmp
+
+# Grab the specified version of gromacs and untar the source.
+RUN wget ftp://ftp.gromacs.org/gromacs/gromacs-${GMXVERSION}.tar.gz && \
+    tar xvf gromacs-${GMXVERSION}.tar.gz && \
+    rm gromacs-${GMXVERSION}.tar.gz
+
+# Patch gmx with plumed and make build dir
+WORKDIR /tmp/gromacs-${GMXVERSION}
+#RUN plumed patch -p -e gromacs-2025.4
+RUN mkdir build
+
+# Build gromacs without mpi and without cuda.
+WORKDIR /tmp/gromacs-${GMXVERSION}/build
+RUN cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs-${GMXVERSION} -DGMX_BUILD_OWN_FFTW=ON -DGMX_OPENMP=ON -DGMXAPI=OFF -DCMAKE_BUILD_TYPE=Release
+
+RUN make -j8
+RUN make install
+
+# Cleanup and fix permissions.
+RUN rm -r /tmp/gromacs-${GMXVERSION}
+RUN chown ${SYSTEM_UID}:${SYSTEM_GID} -R /opt/gromacs-${GMXVERSION}
+
+# Add the exec to the path.
+ENV PATH=/opt/gromacs-${GMXVERSION}/bin:$PATH
 
+# Switch back to USER aiida to avoid accidental container runs as root
+USER ${SYSTEM_UID}
+WORKDIR "${HOME}"