workflow.yaml

# yaml-language-server: $schema=https://activate.parallel.works/workflow.schema.json
---
# ==============================================================================
# Hello World Batch Submitter
# ==============================================================================
# A simple example workflow demonstrating how to submit batch jobs using the
# job_runner/v4.0 marketplace action. This workflow accepts a series of
# commands, packages them into a script, and submits via the reusable
# job_runner.
#
# This pattern leverages marketplace/job_runner/v4.0 for:
#   - Scheduler support (SLURM/PBS)
#   - Job monitoring and output streaming
#   - Automatic cancellation handling
#
# Usage:
#   1. Select a compute resource
#   2. Enter commands to execute (one per line)
#   3. Choose execution mode (SSH direct or scheduler)
#   4. Run the workflow
#
# For more information, see README.md
# ==============================================================================

jobs:
  # ============================================================================
  # PREPROCESSING - Create the command script on the remote system
  # ============================================================================
  preprocessing:
    working-directory: "${PW_PARENT_JOB_DIR}"
    ssh:
      remoteHost: ${{ inputs.resource.ip }}
    steps:
      - name: Create working directory
        run: |
          set -e
          mkdir -p "${PW_PARENT_JOB_DIR}"
          echo "$(date) Working directory: ${PW_PARENT_JOB_DIR}"

      - name: Create command script
        run: |
          set -e
          echo "$(date) Creating command script..."

          # Create the main execution script with header
          cat > commands.sh << 'HEADER_EOF'
          #!/bin/bash
          set -e

          echo "=============================================="
          echo "  Hello World from Parallel Works ACTIVATE"
          echo "=============================================="
          echo ""
          echo "System Information:"
          echo "  Hostname:    $(hostname)"
          echo "  Date:        $(date)"
          echo "  User:        $(whoami)"
          echo "  Directory:   $(pwd)"
          echo "  Job ID:      ${PW_JOB_ID:-N/A}"
          echo ""
          echo "----------------------------------------------"
          echo "  Executing Commands"
          echo "----------------------------------------------"
          echo ""
          HEADER_EOF

          # Append user commands to the script
          cat >> commands.sh << 'USER_COMMANDS_EOF'
          ${{ inputs.commands }}
          USER_COMMANDS_EOF

          # Add completion footer
          cat >> commands.sh << 'FOOTER_EOF'

          echo ""
          echo "----------------------------------------------"
          echo "  All commands completed"
          echo "----------------------------------------------"
          echo ""
          echo "Finished at: $(date)"
          echo "=============================================="
          FOOTER_EOF

          chmod +x commands.sh

          echo "$(date) Script created successfully:"
          echo "--- commands.sh ---"
          cat commands.sh
          echo "--- end of script ---"

  # ============================================================================
  # JOB RUNNER - Submit via v4.0 marketplace action
  # ============================================================================
  job_runner:
    needs: [preprocessing]
    working-directory: "${PW_PARENT_JOB_DIR}"
    ssh:
      remoteHost: ${{ inputs.resource.ip }}
    steps:
      - name: Submit batch job
        early-cancel: any-job-failed
        uses: marketplace/job_runner/v4.0
        with:
          resource: ${{ inputs.resource }}
          rundir: "${PW_PARENT_JOB_DIR}"
          poll_interval: 10
          use_existing_script: true
          script_path: "${PW_PARENT_JOB_DIR}/commands.sh"
          scheduler: ${{ inputs.scheduler }}
          slurm:
            is_disabled: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}
            account: ${{ inputs.slurm.account }}
            partition: ${{ inputs.slurm.partition }}
            qos: ${{ inputs.slurm.qos }}
            time: ${{ inputs.slurm.time }}
            nodes: ${{ inputs.slurm.nodes }}
          pbs:
            is_disabled: ${{ inputs.resource.schedulerType != 'pbs' || inputs.scheduler == false }}
            account: ${{ inputs.pbs.account }}
            queue: ${{ inputs.pbs.queue }}
            walltime: ${{ inputs.pbs.walltime }}

      - name: Show job output
        run: |
          echo "=============================================="
          echo "  Job Output"
          echo "=============================================="
          OUTPUT_FILE="run.${PW_JOB_ID}.out"
          if [ -f "${OUTPUT_FILE}" ]; then
            cat "${OUTPUT_FILE}"
          else
            echo "Output file not found: ${OUTPUT_FILE}"
            echo "Files in directory:"
            ls -la
          fi

      - name: Notify job ended
        early-cancel: any-job-failed
        run: touch job.ended

# ==============================================================================
# INPUT DEFINITIONS
# ==============================================================================
"on":
  execute:
    inputs:
      # ========================================================================
      # Core Settings
      # ========================================================================
      resource:
        label: Compute Resource
        type: compute-clusters
        autoselect: true
        optional: false
        tooltip: Select the compute resource where the job will run

      # ========================================================================
      # Commands Configuration
      # ========================================================================
      commands:
        label: Commands to Execute
        type: editor
        optional: false
        default: |
          # Enter your commands below (one per line)
          # These will be packaged into a script and executed on the remote system

          hostname
          date
          whoami
          pwd
          uname -a

          echo "Environment variables:"
          env | sort | head -20
        tooltip: |
          Enter the commands you want to execute on the remote system.
          Each line will be executed in sequence.

          Example commands:
            hostname          - Display the compute node name
            date              - Show current date/time
            module avail      - List available modules
            nvidia-smi        - Show GPU status (if available)

      # ========================================================================
      # Execution Mode
      # ========================================================================
      scheduler:
        type: boolean
        default: false
        label: Submit via Scheduler?
        hidden: ${{ inputs.resource.schedulerType == '' }}
        tooltip: |
          Enable to submit job through the cluster scheduler (SLURM/PBS).
          Disable for direct SSH execution.

      # ========================================================================
      # SLURM Configuration
      # ========================================================================
      slurm:
        type: group
        label: SLURM Settings
        hidden: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}
        items:
          account:
            label: Account
            type: slurm-accounts
            resource: ${{ inputs.resource }}
            optional: true
            tooltip: SLURM account for job submission (--account)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          partition:
            type: slurm-partitions
            label: Partition
            resource: ${{ inputs.resource }}
            optional: true
            tooltip: SLURM partition for job submission (--partition)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          qos:
            label: Quality of Service
            type: slurm-qos
            resource: ${{ inputs.resource }}
            optional: true
            tooltip: SLURM QoS setting (--qos)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          time:
            label: Walltime
            type: string
            default: "00:30:00"
            tooltip: Maximum job duration, e.g., 00:30:00 (--time)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          nodes:
            label: Nodes
            type: number
            default: 1
            min: 1
            optional: true
            tooltip: Number of nodes to request (--nodes)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          cpus_per_task:
            label: CPUs per Task
            type: number
            default: 1
            min: 1
            optional: true
            tooltip: Number of CPUs per task (--cpus-per-task)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          gres:
            label: Generic Resources (GPUs)
            type: string
            placeholder: "gpu:1"
            optional: true
            tooltip: Generic resource specification, e.g., gpu:1, gpu:a100:2 (--gres)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          mem:
            label: Memory
            type: string
            placeholder: "8G"
            optional: true
            tooltip: Memory per node, e.g., 8G, 32000M (--mem)
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

          scheduler_directives:
            type: editor
            label: Additional Directives
            optional: true
            tooltip: |
              Additional SLURM directives (one per line, include #SBATCH prefix)
              Example:
                #SBATCH --exclusive
                #SBATCH --mail-type=END
            ignore: ${{ inputs.resource.schedulerType != 'slurm' || inputs.scheduler == false }}

      # ========================================================================
      # PBS Configuration
      # ========================================================================
      pbs:
        type: group
        label: PBS Settings
        hidden: ${{ inputs.resource.schedulerType != 'pbs' || inputs.scheduler == false }}
        items:
          account:
            label: Account
            type: string
            optional: true
            tooltip: PBS account for job submission (-A)
            ignore: ${{ inputs.resource.schedulerType != 'pbs' || inputs.scheduler == false }}

          queue:
            label: Queue
            type: string
            optional: true
            tooltip: PBS queue name (-q)
            ignore: ${{ inputs.resource.schedulerType != 'pbs' || inputs.scheduler == false }}

          walltime:
            label: Walltime
            type: string
            default: "00:30:00"
            tooltip: Maximum job duration, e.g., 00:30:00 (-l walltime=)
            ignore: ${{ inputs.resource.schedulerType != 'pbs' || inputs.scheduler == false }}

          select:
            label: Resource Selection
            type: string
            placeholder: "1:ncpus=1"
            optional: true
            tooltip: PBS resource selection string (-l select=)
            ignore: ${{ inputs.resource.schedulerType != 'pbs' || inputs.scheduler == false }}

          scheduler_directives:
            label: Additional Directives
            type: editor
            optional: true
            tooltip: |
              Additional PBS directives (one per line, include #PBS prefix)
              Example:
                #PBS -V
                #PBS -m ae
            ignore: ${{ inputs.resource.schedulerType != 'pbs' || inputs.scheduler == false }}