Re: [svtoolkit-help] Is it possible to install Genome STRiP on an HPC cluster with SLURM as the man
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Re: [svtoolkit-help] Is it possible to install Genome STRiP on an HPC cluster with SLURM as the management software?
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From: Thomas F. <Tho...@in...> - 2018-06-29 15:30:45
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Hi Wusheng,
The options I use for running SVDiscovery (and CNVDiscoveryPipeline) on
our cluster with slurm and Drmaa are :
-jobRunner Drmaa
-gatkJobRunner Drmaa
-jobNative "--mem-per-cpu={cluster.mem}000 --time={cluster.time}"
-jobQueue workq
where indeed -jobNative specifies the options to be passed to slurm.
This is how genomeSTRIP with interact with the cluster.
Putting the genomeSTRIP command in a batch script is a different
issue, it will simply delegate the genomeSTRIP master process
to a job send on the cluster (so both things are independent)
A simple reminder, SVDiscovery can work as a single process, while
the CNVDiscoveryPipeline will send jobs to the cluster without
asking for permission. So the latter will not work with a slurm
cluster without Drmaa.
Best regards,
Thomas
Le 28/06/2018 à 17:41, Wusheng Zhang a écrit :
> 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
>
> New email add...@in... <mailto:Tho...@in...>
>
> UMR 1388 INRA-INPT GenPhySE
> Tel: +33 (0)5 61 28 54 57
> http://genphyse.toulouse.inra.fr
>
> ------------------------------------------------------------------------------
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--
Thomas Faraut
New email address Tho...@in...
UMR 1388 INRA-INPT GenPhySE
Tel: +33 (0)5 61 28 54 57
http://genphyse.toulouse.inra.fr
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