benchmark.yml

name: Run Simple R Script on HPC via Slurm

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

jobs:
  Benchmarking-pipeline:
    runs-on: ubuntu-latest

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

    - name: Set Up SSH Access
      run: |
        mkdir -p ~/.ssh
        touch ~/.ssh/id_rsa
        chmod 600 ~/.ssh/id_rsa
        echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/id_rsa
        ssh-keyscan -H login-00.discovery.neu.edu >> ~/.ssh/known_hosts || exit 1

    - name: Transfer Files to HPC
      run: |
        scp benchmark/benchmark.R benchmark/config.slurm raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking || exit 1

    - name: Submit Slurm Job and Capture Job ID
      id: submit_job
      run: |
        ssh raina.ans@login-00.discovery.neu.edu "cd R && sbatch config.slurm" | tee slurm_job_id.txt 
        slurm_job_id=$(grep -oP '\d+' slurm_job_id.txt) 
        echo "Slurm Job ID is $slurm_job_id"
        echo "slurm_job_id=$slurm_job_id" >> $GITHUB_ENV  

    - name: Monitor Slurm Job
      run: |
        ssh raina.ans@login-00.discovery.neu.edu "
          while squeue -j ${{ env.slurm_job_id }} | grep -q ${{ env.slurm_job_id }}; do
            echo 'Job Id : ${{ env.slurm_job_id }} is still running...'
            sleep 10
          done
          echo 'Job has completed.'
        "

    - name: Fetch Output
      run: |
        # scp raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/job_output.txt job_output.txt
        # scp raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/job_error.txt job_error.txt
        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: Check Metrics in Output
      run: |
        THRESHOLD_FPR=0.2

        METRICS=$(tail -n 20 job_output.txt | grep -E 'FPR|Accuracy|Recall|FDR' | tail -n 3)
		echo METRICS
        
        FPR=$(echo "$METRICS" | grep -oP 'FPR\s+\K[0-9.]+')
        ACCURACY=$(echo "$METRICS" | grep -oP 'Accuracy\s+\K[0-9.]+')
        RECALL=$(echo "$METRICS" | grep -oP 'Recall\s+\K[0-9.]+')

        echo "Extracted Metrics - FPR: $FPR, Accuracy: $ACCURACY, Recall: $RECALL"

        if (( $(echo "$FPR > $THRESHOLD_FPR" | bc -l) )) || 
           (( $(echo "$ACCURACY < $THRESHOLD_ACCURACY" | bc -l) )) || 
           (( $(echo "$RECALL < $THRESHOLD_RECALL" | bc -l) )); then
            echo "Metrics did not meet the thresholds."
            exit 1
        else
            echo "Metrics are within acceptable range."
        fi


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