Cluster Execution

Snakemake can make use of cluster engines that support shell scripts and have access to a common filesystem, (e.g. Slurm or PBS). There exists a generic cluster support which works with any such engine (see Generic cluster support), and a specific support for Slurm (see Executing on SLURM clusters). When executing on a cluster, Snakemake implicitly assumes some default resources for all rules (see Default Resources).

Executing on SLURM clusters

SLURM is a widely used batch system for performance compute clusters. In order to use Snakemake with slurm, simply append --slurm to your Snakemake invocation.

Specifying Account and Partition

Most SLURM clusters have two mandatory resource indicators for accounting and scheduling, Account and Partition, respectivily. These resources are usually omitted from Snakemake workflows in order to keep the workflow definition independent from the platform. However, it is also possible to specify them inside of the workflow as resources in the rule definition (see Resources).

To specify them at the command line, define them as default resources:

$ snakemake --slurm --default-resources slurm_account=<your SLURM account> slurm_partition=<your SLURM partition>

If individual rules require e.g. a different partition, you can override the default per rule:

$ snakemake --slurm --default-resources slurm_account=<your SLURM account> slurm_partition=<your SLURM partition> --set-resources <somerule>:slurm_partition=<some other partition>

Usually, it is advisable to persist such settings via a configuration profile, which can be provided system-wide or per user.

Ordinary SMP jobs

Most jobs will be carried out by programs which are either single core scripts or threaded programs, hence SMP (shared memory programs) in nature. Any given threads and mem_mb requirements will be passed to SLURM:

rule a:
    input: ...
    output: ...
    threads: 8

This will give jobs from this rule 14GB of memory and 8 CPU cores. It is advisable to use resonable default resources, such that you don’t need to specify them for every rule. Snakemake already has reasonable defaults built in, which are automatically activated when using the --default-resources flag (see above, and also snakemake --help).

MPI jobs

Snakemake’s Slurm backend also supports MPI jobs, see snakefiles-mpi for details. When using MPI with slurm, it is advisable to use srun as MPI starter.

rule calc_pi:
      "{resources.mpi} -n {resources.tasks} calc-pi-mpi > {output} 2> {log}"

Note that the -n {resources.tasks} is not necessary in case of SLURM, but it should be kept in order to allow execution of the workflow on other systems, e.g. by replacing srun with mpiexec:

$ snakemake --set-resources calc_pi:mpi="mpiexec" ...

Advanced Resource Specifications

A workflow rule may support a number of resource specification. For a SLURM cluster, a mapping between Snakemake and SLURM needs to be performed.

You can use the following specifications:

SLURM Resource

Snakemake resource

Background Information



the partition a rule/job is to use



the walltime per job in minutes



may hold features on some clusters



memory in MB a cluster node must provide



memory per reserved CPU



number of concurrent tasks / ranks



number of cpus per task (in case of SMP, rather use threads)



number of nodes

Each of these can be part of a rule, e.g.:

    input: ...
    output: ...
        partition: <partition name>
        runtime: <some number>

Please note: as --mem and --mem-per-cpu are mutually exclusive on SLURM clusters, there corresponding resource flags mem_mb and mem_mb_per_cpu are mutually exclusive, too. You can only reserve memory a compute node has to provide or the memory required per CPU (SLURM does not make any distintion between real CPU cores and those provided by hyperthreads). SLURM will try to sastify a combination of mem_mb_per_cpu and cpus_per_task and nodes, if nodes is not given.

Note that it is usually advisable to avoid specifying SLURM (and compute infrastructure) specific resources (like constraint) inside of your workflow because that can limit the reproducibility on other systems. Consider using the --default-resources and --set-resources flags to define such resources on the command line.

Additional custom job configuration

SLURM installations can support custom plugins, which may add support for additional flags to sbatch. In addition, there are various sbatch options not directly supported via the resource definitions shown above. You may use the slurm_extra resource to specify additional flags to sbatch:

    input: ...
    output: ...
        slurm_extra="--qos=long --mail-type=ALL --mail-user=<your email>"

Generic cluster support

To use the generic cluster support, Snakemake simply needs to be given a submit command that accepts a shell script as first positional argument:

$ snakemake --cluster qsub --jobs 32

Here, --jobs denotes the number of jobs submitted to the cluster at the same time (here 32). The cluster command can be decorated with job specific information, e.g.

$ snakemake --cluster "qsub {threads}"

Thereby, all keywords of a rule are allowed (e.g. rulename, params, input, output, threads, priority, resources, …). For example, you could encode the expected running time in minutes into a resource runtime_min:


and forward it to the cluster scheduler:

$ snakemake --cluster "qsub --runtime {resources.runtime}"

In order to avoid specifying runtime_min for each rule, you can make use of the --default-resources flag, see snakemake --help.

If your cluster system supports DRMAA, Snakemake can make use of that to control jobs. With DRMAA, no qsub command needs to be provided, but system specific arguments can still be given as a string, e.g.

$ snakemake --drmaa " -q username" -j 32

Note that the string has to contain a leading whitespace. Else, the arguments will be interpreted as part of the normal Snakemake arguments, and execution will fail.

Adapting to a specific cluster can involve quite a lot of options. It is therefore a good idea to setup a a profile.

Job Properties

When executing a workflow on a cluster using the --cluster parameter (see below), Snakemake creates a job script for each job to execute. This script is then invoked using the provided cluster submission command (e.g. qsub). Sometimes you want to provide a custom wrapper for the cluster submission command that decides about additional parameters. As this might be based on properties of the job, Snakemake stores the job properties (e.g. name, rulename, threads, input, output, params etc.) as JSON inside the job script (for group jobs, the rulename will be “GROUP”, otherwise it will be the same as the job name). For convenience, there exists a parser function snakemake.utils.read_job_properties that can be used to access the properties. The following shows an example job submission wrapper:


#!/usr/bin/env python3
import os
import sys

from snakemake.utils import read_job_properties

jobscript = sys.argv[1]
job_properties = read_job_properties(jobscript)

# do something useful with the threads
threads = job_properties[threads]

# access property defined in the cluster configuration file (Snakemake >=3.6.0)

os.system("qsub -t {threads} {script}".format(threads=threads, script=jobscript))