Documentation changes #70
Workflow file for this run
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| name: Run Simple R Script on HPC via Slurm | |
| on: | |
| push: | |
| branches: | |
| - feature/multiple-scripts | |
| # - devel | |
| jobs: | |
| Benchmarking-pipeline: | |
| runs-on: ubuntu-latest | |
| env: | |
| FDR_THRESHOLD: 0.21 | |
| 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 "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/id_rsa | |
| ssh-keyscan -H login-00.discovery.neu.edu >> ~/.ssh/known_hosts || exit 1 | |
| - name: Transfer Files to HPC | |
| run: | | |
| scp -O benchmark/benchmark_Dowell2021-HEqe408_LFQ.R benchmark/benchmark_Puyvelde2022-HYE5600735_LFQ.R benchmark/scriptController.json benchmark/calculateMetrics.R benchmark/config.slurm raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking || exit 1 | |
| - name: Submit Slurm Job and Capture Job ID | |
| id: submit_job | |
| run: | | |
| ssh raina.ans@login-00.discovery.neu.edu "cd /work/VitekLab/Projects/Benchmarking && sbatch config.slurm" | tee slurm_job_id.txt | |
| slurm_job_id=$(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 -O raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/job_output.txt job_output.txt | |
| scp -O raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/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 |