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

Bas van der Vlies basv at sara.nl
Fri Sep 16 07:34:09 MDT 2011


On 16 sep 2011, at 13:34, Guilherme Rocha wrote:

> 
> 
> 
> Hello folks,
> 
> 
> 
> thanks a lot for all answers, I'm doing a troubleshooting now, considering your answers, in order to get my target acquired.
> Thanks a lot once more.
> 
> I already start to research how to use MPI, in fact we have the clustalw-mpi installed on the head node,
> but no in the nodes (yet), I will try to do your recommendations now.
> 
> We alson have open-mpi installed.
> 
> 
> We are using Debian, all software installed via #aptitude. 
> 
> 
> I have this question from my teacher, the lab coordinator
> Is possible to run X programs (like clustalx)  interactivelly under Torque?
> 
qsub - I -X

-I: interactively 
-X: X11 forwarding

You get a shell prompt:
 * xcalc

PS) man qsub 

> 
> 
> 
> 
> 2011/9/2 Coyle, James J [ITACD] <jjc at iastate.edu>
>   You’ll need and MPI application to use multiple nodes.
> 
>  
> 
>   Perhaps this application would be  Clustalw-MPI .
> 
> It looks like this is available at:
> 
> http://www.bii.a-star.edu.sg/achievements/applications/clustalw/download.php
> 
> Information on this can be found at:
> 
> http://www.bii.a-star.edu.sg/docs/software/README.clustalw-mpi
> 
>  
> 
>  
> 
>   Torque just reserves node, you need something like MPi and program written in MPI to use
> 
> multiple nodes.
> 
>  
> 
>   If you need a suggestion on MPI,  I use OpenMPI because it installs easily and can use
> 
> multiple network interconnects, it also works well with Torque.
> 
>  
> 
> Ethernet works, but is slow, however, that is likely what you have.
> 
> We use Infiniband and Myrinet networks in addition to Ethernet. They give much better
> 
> performance for our workloads, but the cards and switches are very expensive.
> 
>  
> 
>  
> 
> From: torqueusers-bounces at supercluster.org [mailto:torqueusers-bounces at supercluster.org] On Behalf Of Guilherme Rocha
> Sent: Friday, September 02, 2011 4:18 AM
> To: torqueusers at supercluster.org
> 
> 
> 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?
> 
> 
> 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
> 
> 
> _______________________________________________
> torqueusers mailing list
> torqueusers at supercluster.org
> http://www.supercluster.org/mailman/listinfo/torqueusers
> 
> 
> 
> 
> -- 
> -- 
> 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 
> 
> <ATT00001..txt>

--
Bas van der Vlies
basv at sara.nl



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