Running Nextflow on SLURM

Introduction

Nextflow is a powerful workflow management system that can be integrate with SLURM.

Configuring Nextflow for SLURM

To run Nextflow on SLURM, you need to create a configuration file (nextflow.config) in your project directory:


process {
    executor = 'slurm'
    queue = 'your_queue_name'
    clusterOptions = '--account=your_account'
}

This configuration tells Nextflow to use SLURM as the executor and specifies the queue to use. Adjust the 'queue' and 'clusterOptions' as needed for your specific SLURM setup.

Understanding Process Configuration and SLURM Integration

Process Configuration

The 'process' block in the configuration file defines settings that apply to all processes in your Nextflow script:

executor = 'slurm': This tells Nextflow to use SLURM for job submission and management.
queue = 'your_queue_name': Specifies the SLURM partition (queue) to which jobs will be submitted. Replace 'your_queue_name' with the appropriate partition name for your cluster.
clusterOptions = '--account=your_account': Allows you to specify additional SLURM options. In this example, it sets the account to be charged for the job. Modify this according to your cluster's requirements.

You can also define process-specific settings in your Nextflow script:


process example_task {
    cpus 4
    memory '8 GB'
    time '2h'

    script:
    """
    your_command_here
    """
}

These settings (cpus, memory, time) will be translated into appropriate SLURM resource requests when the job is submitted.

SLURM and Executor Management

It's important to understand that when using SLURM with Nextflow, SLURM itself handles most of the job execution and resource management tasks. The 'executor' settings in Nextflow are primarily used for local execution or when using other executors. When using SLURM:

SLURM manages job queuing, scheduling, and resource allocation.
SLURM's own configurations and limits (set by cluster administrators) control aspects like maximum concurrent jobs, job priorities, and resource limits.
Nextflow's role is to submit jobs to SLURM and monitor their progress, rather than directly managing execution details.

Therefore, many of the 'executor' settings in Nextflow (like queueSize or submitRateLimit) are not typically necessary or used when working with SLURM. Instead, you would rely on SLURM's own configurations and use SLURM-specific options in your Nextflow process definitions.

SLURM-Specific Options

When using Nextflow with SLURM, you can take advantage of SLURM-specific options in your process definitions:


process resource_intensive_task {
    cpus 16
    memory '64 GB'
    time '12h'
    clusterOptions '--qos=high --exclude=node01,node02'

    script:
    """
    your_command_here
    """
}

In this example:

cpus, memory, time: These are translated into SLURM resource requests.
clusterOptions: This allows you to pass SLURM-specific options directly to the sbatch command, such as quality of service (--qos) or node exclusions.

Running Your Pipeline

To run your Nextflow pipeline on SLURM, use the following command:

nextflow run your_script.nf

Nextflow will automatically submit jobs to SLURM based on your configuration and script directives.