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

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

In general, I prefer the forum as more people read it.

I didn't get Thomas' email for some reason.

There is a Queue parameter -maxConcurrentRun N that limits the number of 
concurrent jobs from Queue's point of view.  In a cluster environment, 
this is the maximum number submitted to the cluster at once.  In a 
parallel shell environment, it's the number of concurrent shell jobs.

I don't now how the slurm drmaa api would interact with .sbatch (i.e. 
whether it reads it, which takes precedence). The -jobNative parameters 
are passed through the drmaa api.

-Bob

On 6/28/18 11:41 AM, Wusheng Zhang wrote:
> Hi Thoma,
>
> Thank you very much for sharing your experience. I am working on a 
> cluster with slurm 17.11.7 but without Drma, and I am trying to 
> persuade the administrator to install it. If is it possible, could you 
> share how you setup the corresponding flag? For example, is the 
> following correct?
>
>
> …
>
> -jobRunner Drmaa
>
> -gatkJobRunner 
> <http://software.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_QCommandLine.html#--gatkJobRunner>Drmaa
>
> …
>
>
> And do I need to setup -jobNative? Because based on my understanding, 
> this flag is used to passing the parameters such as the 
> nodes_per_tasks, memory, walltime, and so on to the system — is this 
> correct? But since in the slurm, we will use the .sbatch script to 
> submit the job and setup the parameters above, I am not sure how to 
> make -jobNative consistent with the sbatch script. May I have your 
> suggestion?
>
>
> Thank you very much.
>
>
> Best regards,
>
> Wusheng
>
>
>
> Thomas Faraut <Tho...@in... <mailto:Tho...@in...>> 
> 于2018年5月22日周二 上午4:29写道：
>
>     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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>
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