[R-sig-hpc] [R] Running R under Sun Grid Engine with OpenMPI tight integration

[Rainer M Krug]

On Wed, Jan 28, 2009 at 10:54 AM, Markus Schmidberger
<schmidb at ibe.med.uni-muenchen.de> wrote:
> Hi,
>
> in Munich we use SGE with Lam/MPI and Rmpi (latest version). It is working
> very well now. There were only some small changes to the SGE configuration
> required.
>
> Attached a document form REvolution Computing for using SGE with OpenMPI. It
> is a nice installation guide. Thanks to REvolution for providing this
> document to the R community.

Thanks a lot for the document and the info - that sounds fantastic,
and I will try it out very soon.

Could you provide the link to the original document from Revolution,
so that I can check for updates on the document?

Cheers

Rainer

>
> Best
> Markus
>
>
> Rainer M Krug schrieb:
>>
>> On Tue, Jan 27, 2009 at 11:04 AM, Marce <marcemb at gmail.com> wrote:
>>
>>>
>>> 2009/1/27 Rainer M Krug <r.m.krug at gmail.com>:
>>>
>>>>
>>>> On Tue, Jan 27, 2009 at 2:30 AM, Peter Waltman <peter.waltman at gmail.com>
>>>> wrote:
>>>>
>>>>>
>>>>> Hi -
>>>>>
>>>>> I saw your posting on the R-help mailing list.  Were you ever able to
>>>>> get
>>>>> this working?  did you end up switching to use the rsge library?
>>>>>
>>>>
>>>> Yes - that is exactly what I did - I am using rsge or, which is in
>>>> most cases sufficient for me, starting several instances of R and run
>>>> the whole simulation (array processing).
>>>>
>>>> But I would still like to know how I can use the Rmpi and snow on the
>>>> Sun Grid Engine.
>>>>
>>>> Please keep me posted,
>>>>
>>>> Rainer
>>>>
>>>>>
>>>>> I'm trying to do the same, and not having very much luck getting it
>>>>> going.
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Peter Waltman
>>>>>
>>>>>
>>>>
>>>> --
>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
>>>> Biology, UCT), Dipl. Phys. (Germany)
>>>>
>>>> Centre of Excellence for Invasion Biology
>>>> Faculty of Science
>>>> Natural Sciences Building
>>>> Private Bag X1
>>>> University of Stellenbosch
>>>> Matieland 7602
>>>> South Africa
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> 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.
>>>>
>>>>
>>>
>>> Hi all,
>>> I have been installed R in SGE but with LAM tight integration, I don't
>>> k now if this help you :s . The problem I had with OpenMPI was that
>>> the load in all nodes waiting for a job and with an instance of R.
>>> Their load up to 100 %, and there isn't a job running on them.
>>> Even so, I will try to configure it with OpenMPI..when I have results
>>> I will post them ok?
>>>
>>
>> Yes please - could you please provide some info (and a small example)
>> on how you managed this with LAM?
>>
>> I think we should move this thread to r-sig-hpc, as it is more
>> appropriate there. I CC'd it to there - please respond there and not
>> on r-help.
>>
>> Thanks
>>
>> Rainer
>>
>>
>>>
>>> Saludos
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> 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.
>>>
>>>
>>
>>
>>
>>
>
>
> --
> Dipl.-Tech. Math. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at]
> ibe.med.uni-muenchen.de
> Tel: +49 (089) 7095 - 4497
>
>



-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Faculty of Science
Natural Sciences Building
Private Bag X1
University of Stellenbosch
Matieland 7602
South Africa