[GE users] question concerning R on HPC

Rainer M Krug r.m.krug at gmail.com
Tue Nov 25 16:53:18 GMT 2008


On Tue, Nov 25, 2008 at 5:15 PM, andreas <andreas.haas at sun.com> wrote:
> Hi Rainer,
>
> On Tue, 25 Nov 2008, Dr. Rainer M Krug wrote:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Hi
>>
>> I want to use R on an HPC via MPI.
>>
>> I managed to install Rmpi and to load it ionto R, but I get the
>> following errormessage when I try to create an MPI cluster and R hangs
>> (no response):
>>
>> library(Rmpi)
>> [head001:15781] mca: base: component_find: unable to open osc pt2pt:
>> file not found (ignored)
>>> library(snow)
>>> cl <- makeCluster(2, type = "MPI")
>> Rscript execution error: No such file or directory
>> Rscript execution error: No such file or directory
>
> try to run this under Linux strace(1) as to trace the system calls.
> This will show you what file/directory your application tries to access.

I tried this, but the output is HUGE and I don't know what I should be
looking for.

I used

strace -o trace.R R

and then executed the commands.

Rainer

>
> Regards,
> Andreas
>
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-- 
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

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