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

Guilherme Rocha guilherme.consultor at gmail.com
Fri Sep 16 05:34:52 MDT 2011


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?


I'm familiar to terminal, but biologists are not.



thanks once more dudes.



Guilherme





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
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