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

[Wusheng Z. <min...@gm...>]

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...> 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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