Re: [svtoolkit-help] Is it possible to install Genome STRiP on an HPC cluster with SLURM as the management software?

[Bob H. <han...@br...>]

Thanks so much for sharing your experience. If you want to post this on 
the forum, that would be great.

It is great to know that Queue runs OK on a slurm system with drmaa 
support. My only experience with slurm was with a rather old version and 
we had to make modifications to the slurm code to fix problems in the 
drmaa API in order to get Genome STRiP to run.

There is a flag to Queue to do what I think you want: -maxConcurrentRun N

Limits the number of jobs that will be sent to the job scheduler 
simultaneously.

-Bob

On 5/22/18 4:28 AM, Thomas Faraut wrote:
> Dear Wusheng,
>
> I have been using genome STRIP on two clusters with SLURM.
>
> On the first one the Drmaa interface was available and
> very easy to use. You simply have to make sure that the
> Drmaa library file (libdrmaa.so) is in your LD_LIBRARY_PATH.
>
> On the second cluster there is no Drmaa interface (not
> implemented in part because of the scheduling policy).
> On this cluster I found no solution except to run Genome
> STRP as a single process which is clearly not convenient.
> If you find a solution for this I would be very much interested.
>
> By the way, it would be nice, when using the Queue workflow
> engine to control the maximum number of (simultaneous) submissions
> to reduce our footprint on the cluster Queue.
> I don't know if it is currently possible.
>
> Best regards,
> Thomas
>
>
> Le 18/05/2018 à 18:38, Wusheng Zhang a écrit :
>> Dear Genome STRiP users,
>>
>> I am new to this software and intend to install this software on my 
>> university HPC cluster. But the cluster management software the 
>> university is using is the SLURM rather than LSF or SGE. In this 
>> sense, is it still possible to install Genome STRiP on my university 
>> cluster and is there anything I need to change based on the original 
>> installation steps? Thank you very much.
>>
>> Best regards,
>> Wusheng
>>
>>
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> -- 
> Thomas Faraut
>
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