[torqueusers] Success setting up a new Torque Environment in University

Ken Nielson knielson at adaptivecomputing.com
Fri Sep 2 06:45:02 MDT 2011


----- Original Message -----
> From: "Guilherme Rocha" <guilherme.consultor at gmail.com>
> To: torqueusers at supercluster.org
> Sent: Friday, September 2, 2011 3:17:45 AM
> Subject: [torqueusers] Success setting up a new Torque Environment in	University
> 
> 
> Hello folks,
> 
> 
> My name is Guilherme and this is my first post here.
> Thanks for this great project.
> 
> We're setting-up a Torque Cluster with 23 nodes and will be used to
> bioinformatics tasks.
> 
> I'm completely newbie to all of this, so after hard steps of
> troubleshooting, we finally
> received good news in logs. We did a small alginment using clustalw.
> 
> But we have some doubts about how to use a program in parallel, like:
> 
> 
> Question 1) I need to have clustalw (or the script programs installed
> in all nodes?)
> Clustalw is only installed in head node by now.
> 
> Question 2: Can we use/open GUI program's interfaces to work using
> torque?
> 
> Question 3: When I submit a job, even requesting 10 nodes, clustal
> are being runned
> only in one node. What can be wrong?
When TORQUE launches a mulit-node (parallel) job only one of the execution nodes receives the request from pbs_server. That node is called the mother superior. The mother superior then contacts the other sister nodes for the job and requests the sisters join the job. The script submitted on the qsub command line is then executed on the mother superior. In order to have the job also execute on the sister nodes you need something like MPI or you can write your own program to use the task management API in TORQUE. There is also a utility in TORQUE called pbsdsh that can be used in the job script to make the program requested run on all of the nodes requested in the job.

Regards

Ken Nielson
Adaptive Computing
> 
> 
> thanks in advance
> 
> thanks in advance,
> 
> --
> --
> Guilherme Rocha
> GF7 Doc & Systems - Soluções Tecnológicas
> Pesquisa e Desenvolvimento - World Wide
> R. João Goulart, 170 - Rio Pardo - RS - CEP 96640-000
> Mobile: +55 51 81400360 - Home Page: http://www.gf7.com.br
> 
> 
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