[R-sig-hpc] Easiest Road to Parallel R?

Thomas Hampton Thomas.H.Hampton at dartmouth.edu
Tue Jul 21 15:22:26 CEST 2009

Hi Brian,

As I understand it (I will check) MPI is the basis of everything they  
do in this computer in
terms of parallel computing, so we know that it works.

The Rmpi library loads fine, though that took a bit of doing.

papply() creates an error-free status message when it runs a trivial  
example, but it reports
that is is running in serial mode.

I can get on this machine easily and answer any specific questions you  
can come up with

Thanks very much for your assistance. I feel that the cavalry has  



On Jul 21, 2009, at 8:39 AM, Brian G. Peterson wrote:

> Thomas Hampton wrote:
>> We have a substantial beowulf cluster and would like to
>> get parallel R going. Our systems administrators attempted
>> without success to get the R function papply to run
>> properly without success. I passed their comments/questions on to  
>> this
>> list in a previous message. The way I understand it, the various  
>> pieces are
>> there and report no errors, but the final result is that no  
>> parallelism is achieved.
>> Is there some more bullet-proof route to parallel R than mpich2,  
>> Rmpi and papply?
>> We are on a beowulf cluster, red hat linux.
> In the future, it would be best if you simply "Reply All" to your  
> previous message to keep the thread intact.  It makes it easier to  
> find the thread.
> Have you verified that MPI is running correctly and can pass  
> messages between machines?  In any parallel system made up of many  
> parts, you need to verify each component independently.  Your prior  
> message was extremely short on details of what had been tried to  
> establish communications.
> Regards,
> - Brian
> -- 
> Brian G. Peterson
> http://braverock.com/brian/
> Ph: 773-459-4973
> IM: bgpbraverock

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