Singularity 5

apptainer.Dockerfile

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+FROM dsarchive/dsa_common:latest
+LABEL maintainer="Kitware, Inc. <kitware@kitware.com>"
+
+RUN add-apt-repository -y ppa:apptainer/ppa \
+    && apt update \
+    && apt install -y apptainer-suid

devops/singularity-5/.gitignore

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+assetstore
+db
+# opt
+# logs
+# fuse
+
+girder
+mongodb
+etc.hosts
+resolv.conf

devops/singularity-5/README.md

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+# Apptainer DSA (Girder 5)
+
+Launches DSA containers using `apptainer`.
+
+## Getting Started
+
+```bash
+# Build dsa_common with apptainer
+./build.sh
+
+# Pull DSA service images
+./pull_images.sh
+
+# Start DSA services
+./dsa_compose.sh
+```

devops/singularity-5/SIF/.gitignore

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+*
+!.gitignore

devops/singularity-5/build.sh

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+#!/usr/bin/env bash
+
+sudo apptainer build SIF/dsa_common.sif dsa_common.def

devops/singularity-5/dsa_common.def

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+Bootstrap: docker
+From: dsarchive/dsa_common_5
+
+%environment
+    export NVM_DIR=/root_opt/nvm
+    [ -s "$NVM_DIR/nvm.sh" ] && . "$NVM_DIR/nvm.sh"
+    [ -s /root_opt/venv/bin/activate ] && . /root_opt/venv/bin/activate
+
+%post -c /bin/bash
+    set -euxo pipefail
+
+    # install nvm / node properly
+    export NVM_DIR=/opt/nvm
+
+    git clone https://github.com/nvm-sh/nvm.git "$NVM_DIR"
+    . "$NVM_DIR/nvm.sh"
+
+    nvm install 24
+    nvm alias default 24
+    nvm use default
+
+    # install pyaml in virtual environment
+    . /opt/venv/bin/activate
+    /opt/venv/bin/pip install pyaml setuptools
+
+    # install apptainer
+    apt-get update
+    apt-get install -y --no-install-recommends \
+        ca-certificates \
+        fuse3 \
+        software-properties-common \
+        squashfs-tools \
+        uidmap \
+        wget
+
+    # Prefer distro package if available; otherwise install a pinned .deb from
+    # GitHub releases (works in environments where Launchpad PPAs are blocked).
+    if ! apt-get install -y --no-install-recommends apptainer; then
+        APPTAINER_VERSION="${APPTAINER_VERSION:-1.4.3}"
+        wget -O /tmp/apptainer.deb \
+            "https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb"
+        apt-get install -y /tmp/apptainer.deb
+        rm -f /tmp/apptainer.deb
+    fi
+    apptainer --version
+
+    # preserve image /opt so it can be copied into bind-mounted /opt at startup
+    mv /opt /root_opt
+
+    apt-get clean
+    rm -rf /var/lib/apt/lists/*
+
+%runscript
+    set -x
+
+    if [ -d /opt/nvm ]; then
+        export NVM_DIR=/opt/nvm
+        . "$NVM_DIR/nvm.sh"
+    else
+        export NVM_DIR=/root_opt/nvm
+        . "$NVM_DIR/nvm.sh"
+    fi
+
+    if [ -f /opt/venv/bin/activate ]; then
+        . /opt/venv/bin/activate
+    else
+        . /root_opt/venv/bin/activate
+    fi
+
+    exec bash -c "$@"
+
+%startscript
+    set -x
+
+    # assuming that the user mounts a local directory to /opt/
+    # this is necessary for getting the correct singularity permissions
+    echo " - Copying docker image's opt (/root_opt) to user mounted /opt"
+    echo " - Make sure you're mounting a local directory to /opt"
+    cp -r /root_opt/* /opt/
+    /opt/venv/bin/pip install pyaml setuptools

devops/singularity-5/dsa_compose.sh

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+#!/usr/bin/env bash
+set -euxo pipefail
+
+cd "$(dirname "$0")"
+GIRDER_SRC="${GIRDER_SRC:-$(realpath ../../../girder)}"
+if [ ! -d "$GIRDER_SRC" ]; then
+    echo "Missing GIRDER_SRC directory: $GIRDER_SRC"
+    exit 1
+fi
+
+apptainer instance stop -a || echo "No instances stopped"
+
+# Load Modules
+# module load slurm-drmaa
+
+# Start instances
+# MongoDB, RabbitMQ, Redis
+apptainer instance start \
+    --bind ./db:/data/db \
+    SIF/mongodb.sif dsa-mongodb-1
+
+apptainer instance start \
+    --env RABBITMQ_DEFAULT_USER=guest \
+    --env RABBITMQ_DEFAULT_PASS=guest \
+    --bind ./rabbitmqdata:/var/lib/rabbitmq/ \
+    SIF/rabbitMQ.sif dsa-rabbitMQ-1
+
+apptainer instance start SIF/redis.sif dsa-redis-1
+
+# # clean girder opt
+# find ./opt/* -not -path "*opt/local_*" -not -path "*opt/.gitignore" -delete
+
+# # set up worker opt
+# # rm -rf ./worker_opt/*
+# # cp -r ./opt/* ./worker_opt/
+rm -rf ./tmp/*
+mkdir -p ./tmp/sifs
+TMP_OPT_GIRDER=$(mktemp -d --tmpdir=./tmp)
+TMP_OPT_WORKER=$(mktemp -d --tmpdir=./tmp)
+
+## Start Girder and Worker
+apptainer instance start \
+    --bind ./assetstore:/assetstore \
+    --bind ./logs:/logs \
+    --bind ./tmp:/tmp \
+    --bind ./fuse:/fuse \
+    --bind ./girder.cfg:/etc/girder.cfg \
+    --bind ./start_girder.sh:/opt/start_girder.sh \
+    --bind ./provision.yaml:/opt/provision.yaml \
+    --bind ../ver5/provision.py:/opt/provision.py \
+    --bind "$GIRDER_SRC":/src/girder \
+    --bind $TMP_OPT_GIRDER:/opt \
+    SIF/dsa_common.sif test-dsarchive
+
+apptainer instance start \
+    --bind ./logs:/logs \
+    --bind ./start_worker.sh:/opt/start_worker.sh \
+    --bind ./provision.yaml:/opt/provision.yaml \
+    --bind ../ver5/provision.py:/opt/provision.py \
+    --bind "$GIRDER_SRC":/src/girder \
+    --bind $TMP_OPT_WORKER:/opt \
+    SIF/dsa_common.sif dsa-worker-1
+    # --bind ./worker_opt:/opt \
+
+    # --bind ./blue:/blue/pinaki.sarder/rc-svc-pinaki.sarder-web \
+    # --no-mount /cmsuf \
+    # --bind /blue/pinaki.sarder/rc-svc-pinaki.sarder-web/logs:/logs \
+    # --bind /apps \
+    # --bind /var/run/munge:/run/munge \
+    # --bind /opt/slurm \
+
+## Execute shells
+apptainer exec instance://dsa-mongodb-1 mongod > /dev/null &
+
+sleep 5 # TODO: WHY THE HELL IS THERE A RACE CONDITIONNNNNN
+        # the files seem to be not mounted properly before this stuff runs
+
+apptainer run \
+    --env SIF_IMAGE_PATH="$(pwd)/tmp/sifs/" \
+    --env TMPDIR="$(pwd)/tmp" \
+    --env LOGS="$(pwd)/logs" \
+    --env DSA_PROVISION_YAML=/opt/provision.yaml \
+    --env GIRDER_WORKER_BROKER=amqp://guest:guest@localhost:5672/ \
+    --env GIRDER_WORKER_BACKEND=rpc://guest:guest@localhost:5672/  \
+    --env CELERY_BROKER_URL=amqp://guest:guest@localhost:5672/ \
+    --env CELERY_RESULT_BACKEND=rpc://guest:guest@localhost:5672/ \
+    instance://dsa-worker-1 /opt/start_worker.sh &
+
+    # --env PATH=/opt/slurm/bin:$PATH \
+    # --env SLURM_QOS=pinaki.sarder-dsa \
+    # --env SLURM_ACCOUNT=pinaki.sarder-dsa \
+
+
+sleep 30
+
+apptainer run \
+    --env SIF_IMAGE_PATH="$(pwd)/tmp/sifs/" \
+    --env TMPDIR="$(pwd)/tmp" \
+    --env LOGS="$(pwd)/logs" \
+    --env DSA_PROVISION_YAML=/opt/provision.yaml \
+    --env CELERY_BROKER_URL=amqp://guest:guest@localhost:5672/ \
+    --env CELERY_RESULT_BACKEND=rpc://guest:guest@localhost:5672/ \
+    --env GIRDER_NOTIFICATION_REDIS_URL=redis://localhost:6379 \
+    --env LARGE_IMAGE_CACHE_BACKEND=redis \
+    --env LARGE_IMAGE_CACHE_REDIS_URL=localhost:6379 \
+    --env DSA_WORKER_API_URL=http://localhost:8080/api/v1 \
+    instance://test-dsarchive /opt/start_girder.sh
+
+    # --env PATH=/opt/slurm/bin:$PATH \
+    # --env SLURM_QOS=pinaki.sarder-dsa \
+    # --env SLURM_ACCOUNT=pinaki.sarder-dsa \

devops/singularity-5/fuse/.gitignore

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+*
+!.gitignore

devops/singularity-5/girder.cfg

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+[global]
+server.socket_host = "0.0.0.0"
+server.max_request_body_size = 1073741824
+
+[database]
+uri = "mongodb://localhost:27017/girder?socketTimeoutMS=3600000"

devops/singularity-5/logs/.gitignore

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+*
+!.gitignore

devops/singularity-5/provision.yaml

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+---
+# The provision script can take a yaml file with provision options
+# This is a dictionary of command-line arguments for the provisioning script
+force: False
+samples: False
+clean-delete-locks: True
+sample-collection: Samples
+sample-folder: Images
+# Set use-defaults to False to skip default settings
+use-defaults: True
+# Set mongo_compat to False to not automatically set the mongo feature
+# compatibility version to the current server version.
+mongo-compat: True
+# A list of additional pip modules to install; if any are girder plugins with
+# client-side code, that code must be built in the shell step.
+# pip:
+#   - girder-oauth
+#   - girder-ldap
+# Run additional shell commands before start
+# shell:
+#   - ls
+# Default admin user if there are no admin users
+admin:
+  login: admin
+  password: password
+  firstName: Admin
+  lastName: Admin
+  email: admin@nowhere.nil
+  public: True
+# Default assetstore if there are no assetstores
+assetstore:
+  method: createFilesystemAssetstore
+  name: Assetstore
+  root: /assetstore
+# Any resources to ensure exist.  A model must be specified.  This creates the
+# resource if there is no match for all specified values.  A value of
+# "resource:<path>" is converted to the resource document with that resource
+# path.  "resource:admin" uses the default admin, "resourceid:<path>" is the
+# string id for the resource path, and "resourceid:admin" is the string if for
+# default admin.
+#   You can add metadata to a resource.  The default key is meta.  If
+# metadata_update is False, metadata will not be set if any metadata
+# already exists.
+resources:
+  - model: collection
+    name: Tasks
+    creator: resource:admin
+    public: True
+  - model: folder
+    parent: resource:collection/Tasks
+    parentType: collection
+    name: "Slicer CLI Web Tasks"
+    creator: resource:admin
+    public: True
+    # metadata:
+    #   sample_key: sample_value
+    # metadata_key: meta
+    # metadata_update: True
+settings:
+  worker.api_url: "http://localhost:8080/api/v1"
+  worker.direct_path: True
+
+  core.brand_name: "Digital Slide Archive"
+  # core.http_only_cookies: True
+  histomicsui.webroot_path: "histomics"
+  histomicsui.alternate_webroot_path: "histomicstk"
+  histomicsui.delete_annotations_after_ingest: True
+  homepage.markdown: |-
+    # Digital Slide Archive
+    ---
+    ## Bioinformatics Platform
+
+    Welcome to the **Digital Slide Archive**.
+
+    Developers who want to use the Girder REST API should check out the
+    [interactive web API docs](api/v1).
+
+    The [HistomicsUI](histomics) application is enabled.
+  slicer_cli_web.task_folder: "resourceid:collection/Tasks/Slicer CLI Web Tasks"
+# List slicer-cli-images to pull, if not present, and load
+# slicer-cli-image:
+#   - dsarchive/histomicstk:latest
+# List slicer-cli-images to always pull, and load
+slicer-cli-image-pull:
+  # - dsarchive/histomicstk:latest
+# The worker can specify parameters for provisioning
+# worker-rabbitmq-host: localhost:5672
+worker-rabbitmq-user: guest
+worker-rabbitmq-pass: guest
+worker-rabbitmq-host: localhost
+worker-config: /src/girder/worker/girder_worker/worker.local.cfg
+# These have precedence over the top level values
+worker:
+  # rabbitmq-host: girder:8080
+  # rabbitmq-user: guest
+  # rabbitmq-pass: guest
+  # config: /opt/girder_worker/girder_worker/worker.local.cfg
+  # Install additional pip packages in the worker
+  # shell:
+  #   - pip -V
+  #   - python -V
+  # pip:
+  #   - -e /opt/local_girder_worker
+  #   - --force-reinstall -e /opt/local_girder_worker
+  #   - -e /opt/local_girder_worker/girder_worker/singularity
+  #   - -e /opt/local_girder_worker/girder_worker/slurm
+  #   - -e /opt/local_slicer_cli_web
+  #   - -e /opt/local_slicer_cli_web/slicer_cli_web/singularity
+  shell:
+    - pip install --force-reinstall -e /src/girder
+    - pip install --force-reinstall -e /src/girder/worker
+    - pip install --force-reinstall -e /src/girder/plugins/slicer_cli_web
+    - pip install --force-reinstall --no-deps -e /src/girder/worker/girder_worker/singularity
+    # - pip install --force-reinstall --no-deps -e /src/girder/worker/girder_worker/slurm
+    - pip install --force-reinstall --no-deps -e /src/girder/plugins/slicer_cli_web/slicer_cli_web/singularity
+    - pip install --upgrade "girder-client>=5.0.0a5"
+
+  # Run additional shell commands in the worker before start
+  # shell:
+  #   - pip -V
+  #   - pip freeze | grep worker
+  #   - pip install -e /opt/local_girder_worker
+  #   - pip freeze | grep worker
+  #   - ls
+pip:
+#  - -e /opt/local_girder_worker
+#  - -e /opt/local_girder_worker/girder_worker/singularity
+#  - -e /opt/local_girder_worker/girder_worker/slurm
+#  - -e /opt/local_slicer_cli_web
+#  - -e /opt/local_slicer_cli_web/slicer_cli_web/singularity
+shell:
+ - /bin/bash -lc 'cd /src/girder/plugins/slicer_cli_web/slicer_cli_web/web_client && if [ ! -f dist/style.css ]; then npm ci && npm run build; fi'
+ - pip install --force-reinstall -e /src/girder
+ - pip install --force-reinstall -e /src/girder/worker
+ - pip install --force-reinstall -e /src/girder/plugins/slicer_cli_web
+ - pip install --force-reinstall --no-deps -e /src/girder/worker/girder_worker/singularity
+#  - pip install --force-reinstall --no-deps -e /src/girder/worker/girder_worker/slurm
+ - pip install --force-reinstall --no-deps -e /src/girder/plugins/slicer_cli_web/slicer_cli_web/singularity
+ - pip install --upgrade "girder-client>=5.0.0a5"

devops/singularity-5/pull_images.sh

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+#!/usr/bin/env bash
+
+apptainer pull SIF/rabbitMQ.sif library://sylabs/examples/rabbitmq
+apptainer pull SIF/mongodb.sif docker://mongo:latest
+apptainer pull SIF/redis.sif docker://redis:latest

devops/singularity-5/rabbitmqdata/.gitignore

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+*
+!.gitignore