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

Coyle, James J [ITACD] jjc at iastate.edu
Fri Sep 2 13:49:29 MDT 2011


  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
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