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
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