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how to set param to run cellranger on cluster

Posted By: katherinehuang, on Jul 6, 2018 at 1:26 PM

I am running cellranger on the large cluster with the SLURM scheduler and would like to know how to set the Martian Runtime parameters properly, i.e. --jobmode, --mempercore, --maxjobs and --jobinterval. Or just use the default "local" mode? Thanks.

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Re: how to set param to run cellranger on cluster

Posted By: Leah, on Jul 9, 2018 at 8:02 AM

Hello Katherine,

 

Cell Ranger can be run in either --jobmode=local or --jobmode=[cluster type] on a cluster:

1. --jobmode=local (default) on a cluster:

Submitting an instance of a Cell Ranger pipeline analysis to run locally.

2. --jobmode=[sge/lsf/slurm] on cluster:

Configuring the Cell Ranger pipeline to submit different stages and job chunks for a given pipeline run as separate jobs to be scheduled by the cluster:
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/clust...

 

The --mempercore is described in the section "Requesting Memory via Cores."

The --maxjobs  --jobinterval are described in "Rate Limiting Job Submissions."

 

As noted in the cluster mode page, there is more limited documentation and support for clusters other than SGE and LSF. There are unsupported starter templates for other clusters such as slurm.

 

Best,