submit a job to PBS cluster

Submitted by Jianhao on Fri, 2015-12-25 09:19

Forums

Frealign

Dear all,

I am trying to submit a job to PBS cluster in working directory, but I don't know how to write a right script.
I tried the following script and with a output file with message "No PBS system available. Submit jobs to local machine (y/N)?"
What should I do to chang my job script?

Best regards!
Jianhao

Job Script:
#!/bin/bash
#PBS -q QUEUE
#PBS -l nodes=3:ppn=12
#PBS -j oe
#PBS -N frealign
#PBS -V
cd $PBS_O_WORKDIR
mpiexec -np 120 --bynode frealign_run_refine

Output File:
21:54:19 up 17 days, 10:31, 0 users, load average: 0.21, 0.20, 0.13
USER TTY FROM LOGIN@ IDLE JCPU PCPU WHAT

No PBS system available. Submit jobs to local machine (y/N)?
No PBS system available. Submit jobs to local machine (y/N)?
...

niko Sun, 2015-12-27 20:37

This error message means that the command

qstat

produces an error on the machine you are trying to launch Frealign on. This command should be available on a PBS cluster head node.

Jianhao Tue, 2015-12-29 07:49

Thank Alexis and Niko!
Does head node means that the node for logining?
For our cluster, all jobs only are submitted on the logining node.
If I want to use serval nodes to run, what parameter should I change?

Alexis Wed, 2015-12-30 14:34

Yes, usually, the login node is also the head node, from which jobs are submitted.

Please see this page for instructions:
http://grigoriefflab.janelia.org/frealign_getting_started

Make sure you use frealign_template to generate your initial mparameters file. Then, read the comments in the mparameters file to understand what the parameters mean. For example, to set the number of processors to use on the cluster, amend nprocessor_ref and nprocessor_rec

Alexis Sun, 2015-12-27 20:39

Dear Jianhao,

The script frelign_run_refine will do the job submission itself. So it needs to be run on a node which is permitted to submit jobs to the cluster - typically the head node.

So all you should need to do is:

  1. Edit mparameters to indicate "pbs" for the cluster type
  2. Log in to the head node for the cluster
  3. Run "frealign_run_refine"

There should be no need to write a scripts or to specify pbs options. If you find you do need to pass options to qsub, you can edit the "qsub_string_ref" and "qsub_string_rec" parameters in mparameters. For example, in your case you could set these parameters to "-q QUEUE".

Hope this helps
Alexis