benchmark.yml

name: Run Simple R Script on HPC via Slurm

on:
  push:
    branches:
      - feature/ci-cd-pipeline

jobs:
  test-hpc:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout Repository
      uses: actions/checkout@v3

    - name: Set Up SSH Access
      run: |
        mkdir -p ~/.ssh
        echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/id_rsa
        chmod 600 ~/.ssh/id_rsa
        ssh-keyscan -H login-00.discovery.neu.edu >> ~/.ssh/known_hosts

    - name: Transfer Files to HPC
      run: |
        scp benchmark/benchmark.R benchmark/config.slurm raina.ans@login-00.discovery.neu.edu:/home/raina.ans/R

    - name: Submit Slurm Job
      run: |
        ssh raina.ans@login-00.discovery.neu.edu "cd R && sbatch config.slurm"

    - name: Monitor Slurm Job
      run: |
        ssh raina.ans@login-00.discovery.neu.edu "
          while squeue -u raina.ans | grep -q 'R-test-job'; do
            echo 'Job is still running...'
            sleep 10
          done
        "

    - name: Fetch Output
      run: |
        scp raina.ans@login-00.discovery.neu.edu:/home/raina.ans/R/job_output.txt job_output.txt
        scp raina.ans@login-00.discovery.neu.edu:/home/raina.ans/R/job_error.txt job_error.txt

    - name: Upload Output as Artifact
      uses: actions/upload-artifact@v4
      with:
        name: benchmark-output
        path: |
          job_output.txt
          job_error.txt