We are using PBS locally and had our cluster admin set this up, but I think the 
same principle applies across most job runners/mgrs.  As Peter mentioned, there 
should be a way for cluster admin to add your server as an allowed submitting 
host, the PBS variant is here:  

   
http://www.clusterresources.com/torquedocs/2.1jobsubmission.shtml#submitaccess

There also may be additional tweaking required due to firewalls, etc.

After that, run some simple job submission tests (we ran a simple 'sleep 60') 
from your server to check whether you can submit jobs, see submitted job 
status, etc.  

I found it helped when debugging to log in on both Galaxy server and cluster 
sides, and if the cluster admin allows it monitor the job manager logs on the 
cluster side if you run into problems (we found this very handy when debugging 
local LDAP issues).  

chris

On May 2, 2012, at 4:16 PM, Anne Pajon wrote:

> Yes we do have an LSF cluster. Thanks indeed for all the information, Peter. 
> I'll contact our cluster administrator tomorrow and keep you posted on my 
> progress. 
> 
> Kind regards,
> Anne.
> 
> On 2 May 2012, at 22:07, Peter Cock wrote:
> 
>> On Wed, May 2, 2012 at 9:58 PM, Anne Pajon <anne.pa...@cancer.org.uk> wrote:
>>> Hi Peter,
>>> 
>>> Thanks for the clarification, it is really helpful.
>>> 
>>> Would you mind sharing what needs to be done in
>>> term of configuration and instalation to transform
>>> the galaxy server into a submitting job to the cluster?
>>> Thanks.
>> 
>> You said you have an LSF cluster - so I have no idea,
>> sorry :(
>> 
>> We're using SGE here. I'm presuming similar concepts
>> apply - in our case a key step was getting qsub/qstat/qdel
>> to work from the Galaxy server as well as the cluster
>> head node - which required our cluster administrator to
>> setup our Galaxy server as an SGE submit node.
>> 
>> Regards,
>> 
>> Peter
> 
> --
> Anne Pajon, Ph.D.
> Cancer Research UK - Cambridge Research Institute
> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
> anne.pa...@cancer.org.uk | +44 (0)7958 511 353
> 
> 
> NOTICE AND DISCLAIMER
> This e-mail (including any attachments) is intended for the above-named 
> person(s). If you are not the intended recipient, notify the sender 
> immediately, delete this email from your system and do not disclose or use 
> for any purpose. 
> 
> We may monitor all incoming and outgoing emails in line with current 
> legislation. We have taken steps to ensure that this email and attachments 
> are free from any virus, but it remains your responsibility to ensure that 
> viruses do not adversely affect you. 
> Cancer Research UK
> Registered in England and Wales
> Company Registered Number: 4325234.
> Registered Charity Number: 1089464 and Scotland SC041666
> Registered Office Address: Angel Building, 407 St John Street, London EC1V 
> 4AD.
> 
> ___________________________________________________________
> 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:
> 
>  http://lists.bx.psu.edu/


___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to