SGE Cluster Guide

Job Submition Host:

  • igm-atav-qsub01, IP: 10.73.52.20 (internal users)
  • igm-atav-qsub02, IP: 10.73.50.99 (external users)

Submitting Jobs:

Submitting jobs is done using the qsub command.

[zr2180@igm-atav-qsub01 ~]$ qsub -V ...
Your job 8186300 ("atav") has been submitted
  • The -V option to qsub states that the job should have the same environment variables as the shell executing qsub (recommended)

Example Command:

qsub -V /nfs/goldstein/software/sh/atav.sh \
--list-var-geno \
--sample /nfs/goldstein/software/atav_home/data/sample/ALS_1424_DukeGr_ctrl.txt \
--function /nfs/goldstein/software/atav_home/data/function/functional.txt \
--gene TBK1 \
--ctrl-maf 0.01 \
--min-coverage 10 \
--out ~/hello_atav

Monitoring Jobs in the Queue:

Now that ATAV job has been submitted, we can take a look at the job’s status in the queue using the command qstat:

[zr2180@igm-atav-qsub01]$ qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
-----------------------------------------------------------------------------------------------------------------
8186313 0.00000 atav       zr2180       qw    08/30/2017 11:57:42                                    5 

From this output, we can see that the job is in the qw state which stands for queued and waiting. After a few seconds, the job will transition into a r, or running, state at which point the job will begin executing.

[zr2180@igm-atav-qsub01 ~]$ qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
-----------------------------------------------------------------------------------------------------------------
8186315 0.56214 atav       zr2180       r     08/30/2017 11:59:03 all.q@igm-cluster067.igm.cumc.     5  

Once the job has finished, the job will be removed from the queue and will no longer appear in the output of qstat:

[zr2180@igm-atav-qsub01 ~]$ qstat
[zr2180@igm-atav-qsub01 ~]$

If you need to check details of one specific job, you can run -j with job number:

[zr2180@igm-atav-qsub01 ~]$ qstat -j 8186313

Deleting a Job from the Queue:

You can delete a job from the queue using the qdel command with job number:

[zr2180@igm-atav-qsub01 ~]$ qdel 8186525
zr2180 has deleted job 8186525