running Rmpi with SGE on a cluster

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running Rmpi with SGE on a cluster

Jérémie Juste

Hello,

I would like to know how to use Rmpi on a cluster but usually the
workflow of the cluster uses sun grid engine to launch jobs.

I found this reference on the web
http://borisv.lk.net/howtos/grid-mpi-r-howto.html.

But I could not even reproduce that example some errors with
> n.cores <- mpi.universe.size()

But regardless of this error do you have any resources on running R on a
cluster?


Best regards,

Jeremie

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Re: running Rmpi with SGE on a cluster

David Winsemius

> On Jul 1, 2018, at 6:32 AM, Jeremie Juste <[hidden email]> wrote:
>
>
> Hello,
>
> I would like to know how to use Rmpi on a cluster but usually the
> workflow of the cluster uses sun grid engine to launch jobs.
>
> I found this reference on the web
> http://borisv.lk.net/howtos/grid-mpi-r-howto.html.
>
> But I could not even reproduce that example some errors with
>> n.cores <- mpi.universe.size()
>

"Some errors"? I'm not sure how you could be any more vague.


> But regardless of this error do you have any resources on running R on a
> cluster?
>
>
> Best regards,
>
> Jeremie
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   -Gehm's Corollary to Clarke's Third Law

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Re: running Rmpi with SGE on a cluster

Loris Bennett-2
David Winsemius <[hidden email]> writes:

>> On Jul 1, 2018, at 6:32 AM, Jeremie Juste <[hidden email]> wrote:
>>
>>
>> Hello,
>>
>> I would like to know how to use Rmpi on a cluster but usually the
>> workflow of the cluster uses sun grid engine to launch jobs.
>>
>> I found this reference on the web
>> http://borisv.lk.net/howtos/grid-mpi-r-howto.html.
>>
>> But I could not even reproduce that example some errors with
>>> n.cores <- mpi.universe.size()
>>
>
> "Some errors"? I'm not sure how you could be any more vague.
>
>
>> But regardless of this error do you have any resources on running R on a
>> cluster?

In keeping with the vagueness of the posting, I can contribute my
experience that installing Rmpi on a cluster is in general not trivial.
You potentially have to ensure that your are using the correct
combination of compiler and MPI implementation to build the packages and
then ensure that the environment is correspondingly set up for the jobs
you submit to the cluster.

I would maintain that installing Rmpi should normally be done by the
cluster administrator and the he/she should then be able to provide the
users with the information about how to use it.

Cheers,

Loris

--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin         Email [hidden email]

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Re: running Rmpi with SGE on a cluster

Jérémie Juste
Hello,

Many thanks to you.

Best regards,

Jeremie



On Mon, Jul 2, 2018 at 7:54 AM, Loris Bennett <[hidden email]>
wrote:

> David Winsemius <[hidden email]> writes:
>
> >> On Jul 1, 2018, at 6:32 AM, Jeremie Juste <[hidden email]>
> wrote:
> >>
> >>
> >> Hello,
> >>
> >> I would like to know how to use Rmpi on a cluster but usually the
> >> workflow of the cluster uses sun grid engine to launch jobs.
> >>
> >> I found this reference on the web
> >> http://borisv.lk.net/howtos/grid-mpi-r-howto.html.
> >>
> >> But I could not even reproduce that example some errors with
> >>> n.cores <- mpi.universe.size()
> >>
> >
> > "Some errors"? I'm not sure how you could be any more vague.
> >
> >
> >> But regardless of this error do you have any resources on running R on a
> >> cluster?
>
> In keeping with the vagueness of the posting, I can contribute my
> experience that installing Rmpi on a cluster is in general not trivial.
> You potentially have to ensure that your are using the correct
> combination of compiler and MPI implementation to build the packages and
> then ensure that the environment is correspondingly set up for the jobs
> you submit to the cluster.
>
> I would maintain that installing Rmpi should normally be done by the
> cluster administrator and the he/she should then be able to provide the
> users with the information about how to use it.
>
> Cheers,
>
> Loris
>
> --
> Dr. Loris Bennett (Mr.)
> ZEDAT, Freie Universität Berlin         Email [hidden email]
>



--
Jérémie Juste

        [[alternative HTML version deleted]]

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