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Submitting jobs to Denovo


Submitting your job

If you are submitting your job on Denovo using SLURM you do NOT need to source any batch settings. If you are submitting your job on Denovo using UGE you do DO need to source UGE batch settings. The batch environment can be loaded into your path using modules.  If qsub is not working properly, check to make sure that the uge module is loaded:

module load uge

Alternatively, add it to your ~/.bashrc.ext

[ "$NERSC_HOST" == denovo ] && module load uge

If you are submitting a job from an external submit host you need to source the appropriate

source /opt/uge/denovo/uge/denovo/common/ 

UGE interactive jobs on Denovo

 CHOS is available, but not enabled by default on Denovo. To submit interactive jobs with the same environment as genepool, you can pass the appropriate chos environment with qrsh

$ qrsh -pty y -v CHOS=deb6gp /bin/chos /bin/bash -l

SLURM interactive jobs on Denovo

Slurm is available for testing on Denovo and the module is loaded for all users.

 $ srun --pty /bin/bash

Shifter jobs on Denovo

Shifter has been made available on Denovo as well. For testing shifter jobs, we recommend that you debug your code using an interactive session first via SLURM or UGE. It is only available on compute nodes.

$ srun --pty /bin/bash

$ shifterimg pull debian:latest

2017-01-15T15:40:56 Pulling Image: docker:debian:latest, status: READY

$ shifterimg images
mendel  docker   READY  1f025ed91d   2016-11-14T09:19:40 debian:latest

$ shifter —volume=`pwd`:/my_dir --image=docker:debian:latest /bin/bash