Dask container recipe (#545)

dask/2023.10.1-py11-ol9/Dockerfile

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+ARG DASK_VERSION=2023.10.1
+
+FROM oraclelinux:9
+
+MAINTAINER biocontainers <[email protected]>
+
+LABEL base_image="oraclelinux:9"
+LABEL version="1"
+LABEL software="Dask"
+LABEL software.version="2023.10.1-py11-ol9"
+LABEL about.summary="Dask is a flexible library for parallel computing in Python."
+LABEL about.home="https://www.dask.org"
+LABEL about.license="BSD-3-Clause"
+LABEL about.license_file="https://github.com/dask/dask/blob/main/LICENSE.txt"
+LABEL about.documentation="https://docs.dask.org/en/stable/"
+LABEL extra.binaries="/opt/mambaforge/bin"
+LABEL extra.scripts="/opt/scripts/daskscripts"
+LABEL about.tags="implemented-in::python, interface::daemon, role::devel-lib"
+LABEL conda_forge.minforge.version="23.3.1-1"
+LABEL python.version="3.11"
+
+ARG TARGETPLATFORM
+
+ENV NVIDIA_VISIBLE_DEVICES=all
+ENV NVIDIA_DRIVER_CAPABILITIES=all
+
+RUN dnf update -y && \
+    dnf install -y \
+        tar wget \
+        hostname \
+        procps-ng \
+        net-tools \
+        which
+
+# Install miniconda
+RUN wget https://github.com/conda-forge/miniforge/releases/download/23.3.1-1/Mambaforge-23.3.1-1-Linux-$(uname -m).sh \
+    -O mamba-install.sh && \
+    bash mamba-install.sh -b -p /opt/mambaforge
+
+ENV PATH=/opt/mambaforge/bin:${PATH}
+
+COPY conda-env.yml /tmp/
+
+RUN mamba env update -n base -f /tmp/conda-env.yml
+
+RUN rm -rf /opt/mambaforge/pkgs
+
+WORKDIR /opt/scripts/daskscripts
+
+ENV DASK_CONFIG=/opt/scripts/daskscripts/config/dask-config.yml
+
+# Add scripts
+COPY scripts/* /opt/scripts/daskscripts/
+COPY config /opt/scripts/daskscripts/config
+
+RUN chmod 755 /opt/scripts/daskscripts/*.sh

dask/2023.10.1-py11-ol9/conda-env.yml

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+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - pip
+  - bokeh>=2.4.2,<3
+  - cachey=0.2.1
+  - cytoolz>=0.12
+  - dask=2023.10.1
+  - distributed=2023.10.1
+  - h5py
+  - jq=1.6
+  - jupyter-server-proxy
+  - lz4>=4.3.2
+  - msgpack-python
+  - nomkl=3.0
+  - numpy>=1.26.0
+  - pandas=1.5.1
+  - psutil>=5.7.2
+  - python-blosc=1.10.6
+  - s3fs>=2021.9.0
+  - scipy>=1.9.1
+  - streamz=0.6.3
+  - tblib>=1.6.0
+  - zarr=2.16.1
+  - pip:
+    - cloudpickle==3.0.0

dask/2023.10.1-py11-ol9/config/dask-config.yml

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+distributed:
+    admin:
+        tick:
+            interval: 500ms # time between event loop health checks
+            limit: 2h # time allowed between triggering a warning
+
+    comm:
+        retry:
+            count: 10
+
+        timeouts:
+            connect: 600s
+
+    distributed:
+        nanny:
+            pre-spawn-environ:
+                MALLOC_TRIM_THRESHOLD_: 0
+
+    scheduler:
+        allowed-failures: 5 # default 3
+        worker-ttl: 120s # default 5min
+        unknown-task-duration: 120s
+
+        locks:
+            lease-timeout: 900s
+            lease-validation-interval: 300s
+
+    worker:
+        use-file-locking: False
+
+        lifetime:
+            stagger: '5 minutes'
+
+        memory:
+            transfer: 0.5 # default 0.1
+            target: 0.9 # default 0.6
+            spill: 0.9 # default 0.7
+            pause: false # default 0.8
+            terminate: false # default 0.95
+            recent-to-old-time: 300s
+            monitor-interval: 500ms # default 100ms
+
+            rebalance:
+                sender-min: 0.5
+                recipient-max: 0.5
+
+        profile:
+            interval: 50ms # default 10ms

dask/2023.10.1-py11-ol9/scripts/determine_ip.sh

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+#!/bin/bash
+# Determine the IP address of the current host
+
+container_engine=$1
+
+local_ip=
+if [ "$container_engine" = "docker" ]; then
+    for interface in /sys/class/net/{eth*,en*,em*}; do
+        [ -e $interface ] && \
+        [ `cat $interface/operstate` == "up" ] && \
+        local_ip=$(ifconfig `basename $interface` | grep "inet " | awk '$1=="inet" {print $2; exit}' | sed s/addr://g)
+        if [[ "$local_ip" != "" ]]; then
+            echo "Use IP: $local_ip"
+            break
+        fi
+    done
+    if [[ -z "${local_ip}" ]] ; then
+        echo "Could not determine local IP: local_ip is empty"
+        exit 1
+    fi
+else
+    # Take the last IP that's listed by hostname -i.
+    # This hack works on Janelia Cluster and AWS EC2.
+    local_ip=`hostname -i | rev | cut -d' ' -f1 | rev`
+    echo "Use Spark IP: $local_ip"
+    if [[ -z "${local_ip}" ]] ; then
+        echo "Could not determine local IP: local_ip is empty"
+        exit 1
+    fi
+fi

dask/2023.10.1-py11-ol9/scripts/prepare.sh

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+#!/bin/bash -ue
+# Prepare the given dir by creating it, or cleaning it 
+# of Dask content if it already exists.
+work_dir=$1
+
+if [[ ! -d "${work_dir}" ]] ; then
+    echo "Creating work directory: ${work_dir}"
+    mkdir -p "${work_dir}"
+else
+    echo "Cleaning existing work directory: ${work_dir}"
+    rm -rf ${work_dir}/* || true
+fi

dask/2023.10.1-py11-ol9/scripts/startmanager.sh

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+#!/bin/bash -ue
+# Start the Dask scheduler process and wait for terminate signal
+DIR=$(cd "$(dirname "$0")"; pwd)
+
+container_engine=
+scheduler_pid_file=
+terminate_file=
+scheduler_start_timeout=
+scheduler_poll_interval=
+scheduler_work_dir=.
+args=()
+
+while [[ $# > 0 ]]; do
+    key="$1"
+    shift # past the key
+    case $key in
+        --container-engine)
+            container_engine="$1"
+            shift
+            ;;
+        --pid-file)
+            scheduler_pid_file=$1
+            args=("${args[@]}" "--pid-file" "${scheduler_pid_file}")
+            shift
+            ;;
+        --scheduler-start-timeout)
+            scheduler_start_timeout=$1
+            shift
+            ;;
+        --scheduler-poll-interval)
+            scheduler_poll_interval=$1
+            shift
+            ;;
+        --scheduler-work-dir)
+            scheduler_work_dir=$1
+            shift
+            ;;
+        --terminate-file)
+            terminate_file=$1
+            shift
+            ;;
+        *)
+            args=("${args[@]}" "${key}")
+            ;;
+    esac
+done
+
+function cleanup() {
+    echo "Killing scheduler background processes"
+    if [[ -f "${scheduler_pid_file}" ]]; then
+        local dpid=$(cat "${scheduler_pid_file}")
+        kill "$dpid"
+    fi
+    exit 0
+}
+trap cleanup INT TERM EXIT
+
+echo "Determining scheduler IP address..."
+. $DIR/determine_ip.sh $container_engine
+
+# start scheduler in background
+echo "Run: dask scheduler --host ${local_ip} ${args[@]}"
+dask scheduler --host ${local_ip} ${args[@]} \
+    2> >(tee ${scheduler_work_dir}/dask-scheduler.log >&2) \
+    &
+
+# wait for PID file
+# make sure there is a timeout param since the default wait does not timeout
+${DIR}/waitforanyfile.sh 0 "${terminate_file},${scheduler_pid_file}" ${scheduler_start_timeout}
+
+if [[ -e "${scheduler_pid_file}" ]] ; then
+    scheduler_pid=$(cat "${scheduler_pid_file}")
+    echo "Scheduler started: pid=$scheduler_pid"
+
+    # scheduler was started - wait until terminate
+    echo "Wait for termination event: ${terminate_file}"
+    ${DIR}/waitforanyfile.sh ${scheduler_pid} "${terminate_file}"
+else
+    echo "Scheduler pid file not found"
+    scheduler_pid=0
+fi

dask/2023.10.1-py11-ol9/scripts/startworker.sh

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+#!/bin/bash -ue
+# Start the Dask worker process and wait for terminate signal
+DIR=$(cd "$(dirname "$0")"; pwd)
+
+container_engine=
+worker_name=
+worker_dir=
+worker_pid_file=
+terminate_file=
+worker_start_timeout=
+worker_poll_interval=
+scheduler_address=
+args=()
+
+while [[ $# > 0 ]]; do
+    key="$1"
+    shift # past the key
+    case $key in
+        --container-engine)
+            container_engine="$1"
+            shift
+            ;;
+        --pid-file)
+            worker_pid_file=$1
+            args=("${args[@]}" "--pid-file" "${worker_pid_file}")
+            shift
+            ;;
+        --name)
+            worker_name=$1
+            args=("${args[@]}" "--name" "${worker_name}")
+            shift
+            ;;
+        --worker-dir)
+            worker_dir=$1
+            shift
+            ;;
+        --scheduler-address)
+            scheduler_address=$1
+            shift
+            ;;
+        --worker-start-timeout)
+            worker_start_timeout=$1
+            shift
+            ;;
+        --worker-poll-interval)
+            worker_poll_interval=$1
+            shift
+            ;;
+        --terminate-file)
+            terminate_file=$1
+            shift
+            ;;
+        *)
+            args=("${args[@]}" "${key}")
+            ;;
+    esac
+done
+
+function cleanup() {
+    echo "Killing background processes for ${worker_name}"
+    if [[ -f "${worker_pid_file}" ]]; then
+        local wpid=$(cat "${worker_pid_file}")
+        kill "$wpid"
+    fi
+    exit 0
+}
+trap cleanup INT TERM EXIT
+
+echo "Determining worker ${worker_name} IP address..."
+. $DIR/determine_ip.sh $container_engine
+
+if [[ -n ${worker_dir} ]] ; then
+    mkdir -p ${worker_dir}
+fi
+
+# start worker in background
+echo "Run: dask worker \
+    --host ${local_ip} \
+    --local-directory ${worker_dir} \
+    ${args[@]} \
+    ${scheduler_address}"
+dask worker \
+    --host ${local_ip} \
+    --local-directory ${worker_dir} \
+    ${args[@]} \
+    ${scheduler_address} \
+    2> >(tee ${worker_dir}/${worker_name}.log >&2) \
+    &
+
+# wait for PID file
+# make sure there is a timeout param since the default wait does not timeout
+${DIR}/waitforanyfile.sh 0 "${terminate_file},${worker_pid_file}" ${worker_start_timeout}
+
+if [[ -e "${worker_pid_file}" ]] ; then
+    worker_pid=$(cat "${worker_pid_file}")
+    echo "Worker ${worker_name} started: pid=$worker_pid"
+
+    # worker was started - wait until terminate
+    echo "Worker ${worker_name} - wait for termination event: ${terminate_file}"
+    ${DIR}/waitforanyfile.sh ${worker_pid} "${terminate_file}"
+else
+    echo "Worker ${worker_name} pid file not found"
+    worker_pid=0
+fi