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

[Markus Schmidberger]

Thats a internal wiki from Revolution. I only got the pdf. But this 
should be the latest version.

Best
Markus

Rainer M Krug schrieb:
> 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
>>
>>
>>     
>
>
>
>   


-- 
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