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basnijholtbasnijholt
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Add .devcontainer (#243)
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‎.devcontainer/Dockerfile

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ARG BASE_IMAGE=git-515d637-jammy
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FROM ghcr.io/mamba-org/micromamba-devcontainer:$BASE_IMAGE
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# Ensure that all users have read-write access to all files created in the subsequent commands.
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ARG DOCKERFILE_UMASK=0000
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# Install the fix-permissions script
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ADD --chmod=755 https://raw.githubusercontent.com/jupyter/docker-stacks/d8c60bc42cad227c5a35214a43a29c157c0a345e/images/docker-stacks-foundation/fix-permissions /usr/local/bin/fix-permissions
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# Create a fixed group for /opt/conda in case the user GID changes
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RUN sudo groupadd --gid 46328 mamba-admin && sudo usermod -aG mamba-admin "${MAMBA_USER}"
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# Install the Conda packages.
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ARG ENVIRONMENT_YAML=environment.yml
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COPY --chown=$MAMBA_USER:$MAMBA_USER ${ENVIRONMENT_YAML} /tmp/environment.yml
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RUN echo "use_lockfiles: false" >> ~/.mambarc && \
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micromamba config append channels conda-forge && \
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micromamba install --yes --name base --file /tmp/environment.yml && \
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micromamba clean --all --force-pkgs-dirs --yes && \
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sudo -E "NB_GID=mamba-admin" fix-permissions "${MAMBA_ROOT_PREFIX}"
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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# Create and set the workspace folder
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ARG CONTAINER_WORKSPACE_FOLDER=/workspaces/default-workspace-folder
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RUN mkdir -p "${CONTAINER_WORKSPACE_FOLDER}"
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WORKDIR "${CONTAINER_WORKSPACE_FOLDER}"
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# On WSL the repo is mounted with permissions 1000:1000, but the mambauser inside the container has a different UID.
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# So we change the UID of the mambauser inside the container to match the UID of the user on the host.
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USER root
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ARG USER_UID=1000
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ARG USER_GID=$USER_UID
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RUN groupmod --gid $USER_GID $MAMBA_USER \
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&& usermod --uid $USER_UID --gid $USER_GID $MAMBA_USER \
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&& chown -R $USER_UID:$USER_GID /home/$MAMBA_USER
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# Install SLURM and Munge
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RUN apt-get update && apt-get install -y \
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slurm-wlm \
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munge \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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# Set up SLURM configuration
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COPY .devcontainer/slurm.conf /etc/slurm/slurm.conf
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RUN chmod 644 /etc/slurm/slurm.conf && \
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mkdir -p /var/spool/slurmd && \
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mkdir -p /var/run/slurm && \
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mkdir -p /var/log/slurm && \
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mkdir -p /var/lock/slurm && \
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mkdir -p /var/spool/slurm && \
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chown -R slurm:slurm /var/spool/slurmd /var/run/slurm /var/log/slurm /var/lock/slurm /var/spool/slurm
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# Create a startup script to ensure SLURM services are running
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RUN echo '#!/bin/bash' > /usr/local/bin/startup.sh && \
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echo 'service munge start' >> /usr/local/bin/startup.sh && \
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echo 'service slurmd start' >> /usr/local/bin/startup.sh && \
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echo 'service slurmctld start' >> /usr/local/bin/startup.sh && \
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echo 'exec "$@"' >> /usr/local/bin/startup.sh && \
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chmod +x /usr/local/bin/startup.sh
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USER root
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CMD ["/bin/bash"]

‎.devcontainer/devcontainer.json

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{
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"name": "micromamba",
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"runArgs": [
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"--hostname",
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"devcontainer",
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"--name",
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"${localEnv:USER}_devcontainer_micromamba",
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"--privileged" // Add this to allow SLURM to manage processes
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],
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"containerEnv": {
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}",
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"CONTAINER_WORKSPACE_FOLDER": "${containerWorkspaceFolder}"
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},
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"build": {
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"dockerfile": "Dockerfile",
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"context": "..",
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"args": {
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"CONTAINER_WORKSPACE_FOLDER": "${containerWorkspaceFolder}",
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"BASE_IMAGE": "git-515d637-jammy",
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"ENVIRONMENT_YAML": "environment.yml"
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}
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},
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"overrideCommand": true, // allow the entrypoint to run
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"mounts": [
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"source=pre-commit-cache-${localEnv:USER},target=/home/mambauser/.cache/pre-commit,type=volume",
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"source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind,consistency=cached",
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"source=${localWorkspaceFolder}/.devcontainer/slurm.conf,target=/etc/slurm-llnl/slurm.conf,type=bind"
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],
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"remoteUser": "mambauser",
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"customizations": {
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"vscode": {
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"extensions": [
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"ms-python.python",
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"ms-python.mypy-type-checker",
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"charliermarsh.ruff",
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"ms-toolsai.jupyter",
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"ms-azuretools.vscode-docker",
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"donjayamanne.githistory",
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"eamodio.gitlens",
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"mutantdino.resourcemonitor",
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"github.copilot",
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"davidanson.vscode-markdownlint"
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],
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"settings": {
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// Files to completely exclude from view
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// (see also search.exclude and files.watcherExclude)
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"files.exclude": {
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// Ignore cached files
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"**/__pycache__": true,
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// Ignore files created for development installs
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"**/*.egg-info": true,
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// Ignore Jupyter checkpoint files
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"**/.ipynb_checkpoints": true,
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// Ignore cache directory, except for files which start with . (e.g. .gitignore)
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".devcontainer/cache/*/[!\\.]*": true
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},
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"[python]": {
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"editor.defaultFormatter": "charliermarsh.ruff"
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},
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"ruff.path": [
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"/opt/conda/bin/ruff"
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],
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"ruff.interpreter": [
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"/opt/conda/bin/python"
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],
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// Ruler for "black"-formatted line widths
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"editor.rulers": [
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88
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],
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// Disable barely usable scrollbar
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"workbench.editor.wrapTabs": true,
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// Turn on autosave
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"files.autoSave": "afterDelay",
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// Show whitespace as tiny grey dots
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"editor.renderWhitespace": "boundary",
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// Use Pylance
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"python.languageServer": "Pylance",
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"python.analysis.typeCheckingMode": "basic",
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// Interpret lines beginning with "# !%" as ipython magic commands
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"jupyter.interactiveWindow.textEditor.magicCommandsAsComments": true,
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// Path of the default Python environment
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"python.defaultInterpreterPath": "/opt/conda/bin/python",
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// Disable the "conda activate base" command when opening a new terminal
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"python.terminal.activateEnvironment": false,
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// Automatically keep Git up-to-date with remotes
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"git.autofetch": "all",
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// Make sure that key combos like Ctrl+K are not intercepted by VS Code
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// when using the terminal
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"terminal.integrated.allowChords": false,
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"extensions.verifySignature": false
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}
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}
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},
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"postCreateCommand": "sudo /usr/local/bin/startup.sh && sudo scontrol show config && sudo scontrol show nodes && sudo scontrol show partitions",
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"postStartCommand": "pip install -e ."
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}

‎.devcontainer/slurm.conf

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ClusterName=devcluster
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SlurmctldHost=localhost
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MpiDefault=none
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ProctrackType=proctrack/linuxproc
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ReturnToService=1
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SlurmctldPidFile=/var/run/slurmctld.pid
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SlurmdPidFile=/var/run/slurmd.pid
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SlurmdSpoolDir=/var/spool/slurmd
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SlurmUser=slurm
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StateSaveLocation=/var/spool/slurm
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SwitchType=switch/none
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TaskPlugin=task/affinity
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InactiveLimit=0
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KillWait=30
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MinJobAge=300
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SlurmctldTimeout=120
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SlurmdTimeout=300
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Waittime=0
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SchedulerType=sched/backfill
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SelectType=select/cons_res
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SelectTypeParameters=CR_Core
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# COMPUTE NODES
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NodeName=localhost NodeAddr=127.0.0.1 CPUs=1 State=UNKNOWN
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PartitionName=debug Nodes=localhost Default=YES MaxTime=INFINITE State=UP

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