Qmap Submit

Description

How to submit jobs to the Cluster using Qmap.

Qmap documentation: https://qmap.readthedocs.io

Howto

1. Prepare .qmap file (example)

[params]
memory=50G

[pre]
 . "/home/$USER/miniconda3/etc/profile.d/conda.sh"
conda activate sciclone-env

[jobs]
Rscript run.R ../data/vafs.dat bmm 3 ./results.beta.3
Rscript run.R ../data/vafs.dat gaussian.bmm 3 ./results.gaussian.3
Rscript run.R ../data/vafs.dat binomial.bmm 3 ./results.binomial.3

2. Run "qmap submit" from the login node

$ qmap submit filename.qmap

Aditional info

Extra parameters

If you need to provide any extra parameter directly to SLURM, you can do it defining a new profile.config file. E.g.

executor = slurm

[params]
extra = -p bigmem

By default, the queue used is bigrun.

Reference

• Federica Brando
• Miguel Grau