[R] Fwd: Re: [R-sig-hpc] Working doSNOW foreach openMPI example

[Mario Valle]

Whas missing the R in the command line:

"mpirun -n --hostfile /home/hostfile R --no-save -f rtest.R"

Hope this helps
                                  mario

On 13-Jan-11 22:08, Justin Moriarty wrote:
>  Hi,
>  Just wanted to share a working example of doSNOW and foreach for an openMPI cluster.  The function eddcmp() is just an example and returns some inocuous warnings.  The example first has each node return its nodename, then runs an example comparing dopar, do and a for loop.  In the directory containing rtest.R it is run from the command line with:
>  "mpirun -n --hostfile /home/hostfile --no-save -f rtest.R"
>
>  Here is the code for rtest.R:
>
>  #################
>  library(doSNOW)
>  library(panel)
>
>  cl<-makeMPIcluster(3)
>  registerDoSNOW(cl)
>
>  clusterEvalQ(cl,library(panel))
>
>  res<-clusterCall(cl, function(){Sys.info()["nodename"]})
>  print(do.call(rbind,res))
>
>  sme<- matrix(rnorm(100),10,10)
>  clusterExport(cl,"sme")
>
>  myfun<-function()
>  {
>  for(i in 1:1000)
>  {
>  x<-eddcmp(sme)
>  }
>  }
>
>  ged<-0
>
>  system.time({
>  ged<-foreach(i=1:10) %dopar%
>  {
>  myfun()
>  }
>  })
>
>  system.time({
>  ged<-foreach(i=1:10) %do%
>  {
>  myfun()
>  }
>  })
>
>  system.time({
>  for(i in 1:10)
>  {
>  ged<-myfun()
>  }
>  })
>
>  stopCluster(cl)
>  mpi.quit()
>
>  #################
>  Cheers,
>  Justin
>
>
>
>
>
>
>
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-- 
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82