job-deploy.yml

name: job-deploy

on:
  workflow_dispatch:
    inputs:
      target:
        description: 'Deploy to (workstation or cluster)'
        type: choice
        required: true
        default: 'workstation'
        options:
          - workstation
          - cluster
      command:
        description: 'Command passed to docker compose'
        required: true
        default: 'scripts/sampler.py'
      args:
        description: 'Arguments passed to job script'
        required: false
        default: '-U http://mlflow:5000 --num_cpus 34 --memory 4'

jobs:
  deploy2workstation:
    name: Deploy to workstation
    if: github.event.inputs.target == 'workstation'
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Echo target
        run: echo "Deploying to targeted machine - ${{ github.event.inputs.target }}"

      - name: Rsync repo to workstation
        uses: burnett01/rsync-deployments@5.2
        with:
          switches: -avzr --delete
          remote_path: '~/projects/mbl'
          remote_host: ${{ secrets.WORKSTATION_HOST }}
          remote_user: ${{ secrets.USERNAME }}
          remote_key: ${{ secrets.KEY }}

      - name: Deploy built docker image to workstation
        uses: appleboy/ssh-action@master
        with:
          host: ${{ secrets.WORKSTATION_HOST }}
          username: ${{ secrets.USERNAME }}
          key: ${{ secrets.KEY }}
          script: |
            cd projects/mbl &&
            docker compose run --service-ports -d mbl \
            ${{ github.event.inputs.command }} \
            ${{ github.event.inputs.args }}

      - name: Prune dangling images
        uses: appleboy/ssh-action@master
        with:
          host: ${{ secrets.WORKSTATION_HOST }}
          username: ${{ secrets.USERNAME }}
          key: ${{ secrets.KEY }}
          script: |
            yes | docker system prune

  #######################################################

  deploy2cluster:
    name: Deploy to cluster
    if: github.event.inputs.target == 'cluster'
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Echo target
        run: echo "Deploying to targeted machine - ${{ github.event.inputs.target }}"

      - name: Rsync repo to cluster
        uses: burnett01/rsync-deployments@5.2
        with:
          switches: -avzr --delete
          remote_path: '~/projects/mbl'
          remote_host: ${{ secrets.CLUSTER_HOST }}
          remote_user: ${{ secrets.USERNAME }}
          remote_key: ${{ secrets.KEY }}

      - name: Build singularity and run sampler
        uses: appleboy/ssh-action@master
        with:
          host: ${{ secrets.CLUSTER_HOST }}
          username: ${{ secrets.USERNAME }}
          key: ${{ secrets.KEY }}
          script: |
            cd projects/mbl &&
            singularity build --fakeroot mbl.sif singularity.def &&
            conda activate &&
            nohup python scripts/sampler.py > foo.out 2> foo.err < /dev/null &
#            singularity exec -B /etc/slurm,/etc/passwd,/run/munge,/usr/lib64,/usr/bin/squeue,/usr/bin/sbatch,/usr/bin/scancel --bind ~/data:/data mbl.sif python scripts/sampler.py