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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]
ml load anaconda3  #OR . "/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

[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

The only difference is how you load conda. On the IRB cluster, you can use either of the following options:

1) Use the pre-installed conda module (ml load anaconda3)

2) If you use mamba or prefer to use your own conda installation, load it the same way you do on the BBG cluster:

. "/home/$USER/miniforge3/etc/profile.d/conda.sh"

For micromamba:

eval "$(micromamba shell hook --shell=bash)"

2. Run "qmap submit" from the login node

interactive
spack load py-qmap
qmap submit filename.qmap

qmap submit filename.qmap

Additional 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 = -G 1

executor = slurm

[params]
extra = -p bigmem

By default, the queue used in the BBG cluster is bigrun.

For Qmap runs using GPUs, use -G 1.

Reference

  • Federica Brando
  • Miguel Grau