[prev in list] [next in list] [prev in thread] [next in thread] 

List:       r-sig-mac
Subject:    Re: [R-SIG-Mac] Need help using Rmpi
From:       Prof Brian Ripley <ripley () stats ! ox ! ac ! uk>
Date:       2010-10-22 5:44:45
Message-ID: alpine.LFD.2.00.1010220637540.28385 () gannet ! stats ! ox ! ac ! uk
[Download RAW message or body]

Rmpi needs help (I'd say a bugfix) if your MPI is not lam (and you 
have not told us).  See the Rmpi/README file, but the effect is more 
serious in 2.12.0 (and the maintainer was informed weeks ago).

I don't understand your notation, but am assuming lines starting with 
# are both your comments *and* error messages from R.

On Thu, 21 Oct 2010, Cutler, Gene wrote:

> I've been trying to get some sort of parallel computing setup 
> running across my two Macs, one with 8 cores the other with 4.  So 
> far, I've mainly been trying to get MPI to work, but without a lot 
> of success.  For example:
> 
> Attempt 1:
> > /usr/local/openmpi/bin/mpirun --prefix /usr/local/openmpi -hostfile ~/hostfile \
> > /Library/Frameworks/R.framework/Versions/2.12/Resources/library/snow/RMPISNOW
> # this drops me into R and I can see messages from multiple R instances starting \
> up, so far so good... library('Rmpi')
> library('snow')
> cl <- getMPIcluster()
> cl
> # NULL
> cl <- makeMPIcluster()
> # cl <- makeMPIcluster()
> # Error in makeMPIcluster() : no nodes available.
> # Execution halted
> # --------------------------------------------------------------------------
> # mpirun noticed that the job aborted, but has no info as to the process
> # that caused that situation.
> # --------------------------------------------------------------------------
> 
> Note, that in fact any error such as just typing a stray character will cause R to \
> quite with that same 'aborted' notice. 
> Attempt 2:
> /usr/local/openmpi/bin/mpirun --prefix /usr/local/openmpi -hostfile ~/hostfile -n 1 \
> R --slave library(doMPI)
> cl <- startMPIcluster()
> # Error in system("lamnodes", TRUE, ignore.stderr = TRUE) :
> #   error in running command
> # Calls: startMPIcluster -> mpi.universe.size -> grep -> system
> # Execution halted
> # --------------------------------------------------------------------------
> # mpirun noticed that the job aborted, but has no info as to the process
> # that caused that situation.
> # --------------------------------------------------------------------------
> 
> 
> I've also looked into PVM, but that doesn't seem to support multiple cpus per \
> machine.  Using sockets with snow was also giving me problems, but I'll try that \
> again only after completely giving up on MPI. 
> Does anyone have some suggestions for getting this to work?
> 
> Thanks in advance,
> Gene
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


[prev in list] [next in list] [prev in thread] [next in thread]