slurm

This profile configures Snakemake to run on the SLURM Workload Manager

Setup

Deploy profile

To deploy this profile, run

mkdir -p ~/.config/snakemake
cd ~/.config/snakemake
cookiecutter https://github.com/Snakemake-Profiles/slurm.git

Then, you can run Snakemake with

snakemake --profile slurm ...

Submission scripts

There are two submission scripts that configure jobs for job submission. slurm-submit.py, the default, will use the supplied parameters untouched, making no attempt to modify the job submission to comply with the cluster partition configuration. On the other hand, slurm-submit-advanced.py will attempt to modify memory, time and number of tasks if these exceed the limits specified by the slurm configuration. If possible, the number of tasks will be increased if the requested memory is larger than the available memory, defined as the requested number of tasks times memory per cpu unit.

Resources

The following resources are supported by on a per-rule basis:

mem, mem_mb: set the memory resource request in mb.
walltime, runtime: set the time resource in min.

Cluster configuration file

As of 2018-10-08, the profile supports setting options in the cluster configuration file. The options must be named according to sbatch long option names. Note that setting memory or time will override resources specified by rules. Therefore, setting time or memory in the __default__ section will effectively override all resource specifications that set these parameters.

As an example, you can specify constraints in the cluster configuration file:

__default__:
  constraint: mem500MB
  
large_memory_requirement_job:
  constraint: mem2000MB

Tests

Test-driven development is enabled through the tests folder. Provided that the user has installed docker and enabled docker swarm, the SLURM tests will download two images:

In addition, testing of the cookiecutter template itself is enabled through the pytest plugin for Cookiecutters. You can run the tests by issuing

pytest -v -s

ChangeLog

2019-09-03

add qos option

2019-08-21

replace pytest_namespace with pytest_configure
make days optional (#18)

2018-10-18

add cookiecutter options to set sbatch output and error defaults

2018-10-09

add support for mem_mb in resources
add support for cluster configuration file
add advanced slurm-submit file
adjust resource requirements if they exceed partition configuration settings (#11)

hertzsprung/slurm