1 a drmaa d
Envoyé depuis mon HTC
----- Reply message -----
De : "Fernandez Edgar" <edgar.fernan...@umontreal.ca>
Pour : "John Chilton" <jmchil...@gmail.com>
Cc : "galaxy-...@bx.psu.edu" <galaxy-...@bx.psu.edu>
Objet : [galaxy-dev] galaxy with torque
Date : mer., nov. 26, 2014 19:09
Hi John,
First, thank you very much for your prompt answer.
It's extremely appreciated.
Secondly, I have some other questions: whatever answers you can provide me
with, will be greatly helpful.
Please, forgive my beginner level understanding of an DRM system.
1. Once I compile, make and install the Torque Submit Node code against the
server running Galaxy, what exactly is the purpose for an DRMAA ?
2. What is exactly the PBS step describe here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
galaxy_user@galaxy_server% LIBTORQUE_DIR=/path/to/libtorque python
scripts/scramble.py -e pbs_python
What does it do exactly ?
3. All servers which includes my torque server, torque compute nodes and torque
submit node (a.k.a galaxy server) have the galaxy user defines and its home
shared on all of them. This means all of them have access (via NFS) of the
installation directory of galaxy. But what about the MySQL server access. Does
the torque server or the compute nodes need access to that service?
I hope I'm not sending too many emails/questions...
Thank you very much!
Cordialement / Regards,
Edgar Fernandez
-----Message d'origine-----
De : John Chilton [mailto:jmchil...@gmail.com]
Envoyé : November-25-14 12:07 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] galaxy with torque
I am not sure we have a walkthrough for Torque specifically - but if you have
Galaxy up and running and you can qsub commands to torque - hopefully you have
done all of the hard parts.
You will need a DRMAA library for your torque setup -
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
suggests compiling pbs_drmaa and outlines how to set it up. After that you just
need to add a plugin and default destination to your job_conf.xml file - also
outlined on that wiki page.
Other good resources to consult if you are scaling up your Galaxy this way are:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough
Good luck and let us know if you encounter any problems.
-John
On Fri, Nov 21, 2014 at 2:30 PM, Fernandez Edgar <edgar.fernan...@umontreal.ca>
wrote:
> Hello all,
>
>
>
> My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal.
>
> I’ve contacted you a while back about installing galaxy and I’ve
> successfully done it on a redhat 6 server.
>
>
>
> I see myself in a situation where I need to utilise all my redhat
> servers (who are identical to the server running the galaxy website).
>
>
>
> I’ve also successfully installed a server torque with compute notes
> and clients nodes.
>
>
>
> What are the last step to make the link between galaxy and torque?
>
> Also, once that connection is made, how will galaxy keep track of the
> jobs sent?
>
> I mean who will it know this job that just finished is for this user
> and not another ?
>
>
>
> Also, my torque installation is so that my server running galaxy is a
> submit node and a client node.
>
> I hope this is not a problem.
>
>
>
> Please help!
>
>
>
> Cordialement / Regards,
>
>
>
> Edgar Fernandez
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la
> Communication
>
> ( Bur. : 1-514-343-6111 poste 16568
>
>
>
> Université de Montréal
>
> PAVILLON ROGER-GAUDRY, bureau X-218
>
>
>
>
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___________________________________________________________
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___________________________________________________________
Please keep all replies on the list by using "reply all"
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To search Galaxy mailing lists use the unified search at:
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