Qsub
From BIOcrunch
The cluster uses the qsub system. The Job scheduler is responsible to make all the houskeeping within the cluster.
- Start your job
- $ qsub 8 example.sh
- qsub is the command
- 8 is the numer of CPU you want to use this will be inserted in your jobfile in variable: $NSLOTS
- example.sh is the jobfile you transmitted to cluster.
system will give you an output like this:
Your job 403 ("example.sh.job") has been submitted
- Monitoring your job
You can monitor the status of your job with qstat:
- $ qstat
job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 403 0.00000 example mustermann qw 07/18/2014 13:51:09 8
The letters of 'state' are:
- r – running
- w – waiting
- t – transfering to the cluster nodes
- E – Error
- h – hold
- s/S – suspended
- q – in queue (qw is waiting in queue until enough resources are available)
- Deleting a Job
If you want to cancel a already started with qsub or delete a job witch had an error use qdel with the id shown in qstat:
- $ qdel <job_id>
- If an error occurs
You can get more information about a job including the error message by
- $ qstat -j <job_id>