7:30 p.m.
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
5:06 p.m.
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.fernandez(a)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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6:09 p.m.
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:jmchilton@gmail.com]
Envoyé : November-25-14 12:07 PM
À : Fernandez Edgar
Cc : galaxy-dev(a)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.fernandez(a)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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this and other
Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
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John Chilton