Slim image based on mambaorg/micromamba

docker-compose.slim.yml

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+---
+version: '3.4'
+
+services:
+
+    database:
+        image: postgres:12.3
+        environment:
+            POSTGRES_USER: postgres
+            POSTGRES_PASSWORD: password
+        volumes:
+            - aiida-postgres-db:/var/lib/postgresql/data
+        healthcheck:
+            interval: 5s
+            timeout: 5s
+            retries: 10
+
+    messaging:
+        image: rabbitmq:3.8.3-management
+        environment:
+            RABBITMQ_DEFAULT_USER: guest
+            RABBITMQ_DEFAULT_PASS: guest
+        volumes:
+            - aiida-rmq-data:/var/lib/rabbitmq/
+
+    aiida:
+        image: 88ed76fefd33
+        environment:
+            RMQHOST: messaging
+            TZ: Europe/Zurich
+            SETUP_DEFAULT_AIIDA_PROFILE: 'true'
+        volumes:
+            - aiida-home-folder:/home/aiida
+        depends_on:
+            database:
+                condition: service_started
+            messaging:
+                condition: service_started
+        command: tail -f /dev/null
+
+volumes:
+    aiida-postgres-db:
+    aiida-rmq-data:
+    aiida-home-folder:

stack/slim/Dockerfile

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+FROM mambaorg/micromamba:0.27-jammy
+ARG NEW_MAMBA_USER=aiida
+ARG NEW_MAMBA_USER_ID=1000
+ARG NEW_MAMBA_USER_GID=1000
+
+USER root
+RUN 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}" && \
+    # 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
+
+COPY _init.sh /usr/local/bin/_init.sh
+RUN chmod +x /usr/local/bin/_init.sh
+
+COPY prepare-aiida.sh /usr/local/bin/prepare-aiida.sh
+RUN chmod +x /usr/local/bin/prepare-aiida.sh
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
+RUN micromamba install -y -n base -f /tmp/env.yaml && \
+    micromamba clean --all --yes
+
+USER $MAMBA_USER
+
+# Configure AiiDA profile.
+COPY config-quick-setup.yaml /opt/config-quick-setup.yaml
+
+# Configure AiiDA.
+ENV SETUP_DEFAULT_AIIDA_PROFILE true
+ENV AIIDA_PROFILE_NAME default
+ENV AIIDA_USER_EMAIL aiida@localhost
+ENV AIIDA_USER_FIRST_NAME Giuseppe
+ENV AIIDA_USER_LAST_NAME Verdi
+ENV AIIDA_USER_INSTITUTION Khedivial
+
+# Make sure that the known_hosts file is present inside the .ssh folder.
+RUN mkdir -p --mode=0700 /home/${MAMBA_USER}/.ssh && \
+        touch /home/${MAMBA_USER}/.ssh/known_hosts
+
+RUN /usr/local/bin/_entrypoint.sh ssh-keygen -f /home/${MAMBA_USER}/.ssh/id_rsa -t rsa -b 4096 -m PEM -N ''
+
+WORKDIR /home/${MAMBA_USER}
+
+ENTRYPOINT [ "/usr/local/bin/_init.sh" ]

stack/slim/_init.sh

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+#!/bin/bash
+
+# Start the ssh-agent
+/usr/local/bin/_entrypoint.sh ssh-agent
+
+# setup aiida
+/usr/local/bin/_entrypoint.sh /usr/local/bin/prepare-aiida.sh
+
+exec "$@"

stack/slim/config-quick-setup.yaml

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+---
+db_engine: postgresql_psycopg2
+db_backend: psql_dos
+db_host: database
+db_port: 5432
+su_db_username: postgres
+su_db_password: password
+su_db_name: template1
+db_name: aiida_db
+db_username: aiida
+db_password: password
+broker_host: messaging
+broker_port: 5672
+broker_username: guest
+broker_password: guest

stack/slim/env.yaml

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+---
+# Using an environment name other than "base" is not recommended!
+# Read https://github.com/mamba-org/micromamba-docker#multiple-environments
+# if you must use a different environment name.
+name: base
+channels:
+    - conda-forge
+dependencies:
+    - python=3.9.13
+    - aiida-core=2.0.4
+    - openssh=9.1p1

stack/slim/prepare-aiida.sh

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+#!/bin/bash
+
+# This script is executed whenever the docker container is (re)started.
+
+# Debugging.
+set -x
+
+# Environment.
+export SHELL=/bin/bash
+
+# Check if user requested to set up AiiDA profile (and if it exists already)
+if [[ ${SETUP_DEFAULT_AIIDA_PROFILE} == true ]] && ! verdi profile show ${AIIDA_PROFILE_NAME} &> /dev/null; then
+    NEED_SETUP_PROFILE=true;
+else
+    NEED_SETUP_PROFILE=false;
+fi
+
+# Setup AiiDA profile if needed.
+if [[ ${NEED_SETUP_PROFILE} == true ]]; then
+
+    # Create AiiDA profile.
+    verdi quicksetup              \
+        --non-interactive                            \
+        --profile "${AIIDA_PROFILE_NAME}"            \
+        --email "${AIIDA_USER_EMAIL}"                \
+        --first-name "${AIIDA_USER_FIRST_NAME}"      \
+        --last-name "${AIIDA_USER_LAST_NAME}"        \
+        --institution "${AIIDA_USER_INSTITUTION}"    \
+        --config /opt/config-quick-setup.yaml
+
+    # Setup and configure local computer.
+    computer_name=localhost
+
+    # Determine the number of physical cores as a default for the number of
+    # available MPI ranks on the localhost. We do not count "logical" cores,
+    # since MPI parallelization over hyper-threaded cores is typically
+    # associated with a significant performance penalty. We use the
+    # `psutil.cpu_count(logical=False)` function as opposed to simply
+    # `os.cpu_count()` since the latter would include hyperthreaded (logical
+    # cores).
+    NUM_PHYSICAL_CORES=$(python -c 'import psutil; print(int(psutil.cpu_count(logical=False)))' 2>/dev/null)
+    LOCALHOST_MPI_PROCS_PER_MACHINE=${LOCALHOST_MPI_PROCS_PER_MACHINE:-${NUM_PHYSICAL_CORES}}
+
+    if [ -z $LOCALHOST_MPI_PROCS_PER_MACHINE ]; then
+      echo "Unable to automatically determine the number of logical CPUs on this "
+      echo "machine. Please set the LOCALHOST_MPI_PROCS_PER_MACHINE variable to "
+      echo "explicitly set the number of available MPI ranks."
+      exit 1
+    fi
+
+    verdi computer show ${computer_name} || verdi computer setup \
+        --non-interactive                                               \
+        --label "${computer_name}"                                      \
+        --description "this computer"                                   \
+        --hostname "${computer_name}"                                   \
+        --transport core.local                                          \
+        --scheduler core.direct                                         \
+        --work-dir /home/${MAMBA_USER}/aiida_run/                          \
+        --mpirun-command "mpirun -np {tot_num_mpiprocs}"                \
+        --mpiprocs-per-machine ${LOCALHOST_MPI_PROCS_PER_MACHINE} &&    \
+    verdi computer configure core.local "${computer_name}" \
+        --non-interactive                                               \
+        --safe-interval 0.0
+fi
+
+
+# Show the default profile
+verdi profile show || echo "The default profile is not set."
+
+# Make sure that the daemon is not running, otherwise the migration will abort.
+verdi daemon stop
+
+# Migration will run for the default profile.
+verdi storage migrate --force
+
+# Daemon will start only if the database exists and is migrated to the latest version.
+verdi daemon start || echo "AiiDA daemon is not running."