[Bioclusters] interpro queuing system

[David Allouche]

hello concerning interpro scan parallelisation.
do you have the plane to use Jobarray (PBS et SGE) ?

( i.e ==> jobs identifier correspond on multiple sub job iteration )


example : qsub -J 1000  myjob.sh


 3440338[].host <==>  with 1000 iteration each one correspond

at  3440338[01].host  , 3440338[02].host  ..... 3440338[1000].host


regards dave


Bernard Li wrote:

>If we do not already have a SGE-Interpro HOWTO, perhaps it is time to
>start one :-)
>
>Thanks,
>
>Bernard 
>
>  
>
>>-----Original Message-----
>>From: bioclusters-bounces+bli=bcgsc.ca at bioinformatics.org 
>>[mailto:bioclusters-bounces+bli=bcgsc.ca at bioinformatics.org] 
>>On Behalf Of Chris Dagdigian
>>Sent: Monday, August 28, 2006 12:06
>>To: HPC in Bioinformatics
>>Subject: Re: [Bioclusters] interpro queuing system
>>
>>
>>In many cases LSF is actually simpler to set up and configure than  
>>any of the competing systems (from an administrators view).
>>
>> From the perspective of Interpro integration it may be a different  
>>story, of course! I believe that there are a few people on this list  
>>using the SGE (Grid Engine) queuing system with Interpro.  Perhaps  
>>they can lend a hand? You can find more information about 
>>grid engine  
>>online at http://gridengine.sunsource.net
>>
>>Also, a google search for "sge+interpro" yields some interesting hits.
>>
>>
>>
>>-Chris
>>
>>
>>
>>On Aug 28, 2006, at 10:49 AM, Michael Gang wrote:
>>
>>    
>>
>>>Dear all,
>>>I want to run interpro on an linux cluster.
>>>We are trying to setup interpro with the queuing system qsub.
>>>Is there another queuing system which is easier to setup (other  
>>>than LSF) ?
>>>
>>>Thanks in advance,
>>>Michael
>>>_______________________________________________
>>>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>>>https://bioinformatics.org/mailman/listinfo/bioclusters
>>>      
>>>
>>_______________________________________________
>>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>>    
>>
>_______________________________________________
>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bioclusters
>
>
>  
>


-- 
-----------
Dr David   Allouche  Tel:+33 (0)5 61 28 52 77 Fax:+33 (0)5 61 28 53 35
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