[GE users] question concerning R on HPC

Rainer M. Krug r.m.krug at gmail.com
Tue Nov 25 17:32:27 GMT 2008


On 25 Nov 2008, at 19:12, andreas <andreas.haas at sun.com> wrote:

> On Tue, 25 Nov 2008, Rainer M Krug wrote:
>
>> 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.
>
> "No such file or directory" stands for the ENOENT as errno upon
> open()/fopen() failures. So you must look in the strace(1) output
> for a open()/fopen() that returns -1/NULL as error indication.
> Once you have the open()/fopen() you know also which file Rmpi
> tried to access.
>
Thanks - I'll do that and let you know.

Rainer

> Regards,
> Andreas
>
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