Hello,
This might belong in the R-devel category, but I am not a C / C++
programmer, so I thought I'd start here. I have just written my first R
extension using Rcpp, and it is SO much faster than my best R efforts,
thank you for such a wonderful package! Instead of writing a separate text
file, I used the following:
### begin R ###
require(Rcpp)
cppFunction('
double s2nICm(NumericVector ICvec, int m, double In, double sampleSize) {
int n = ICvec.size();
double covSum = 0.0;
double s2n = 0.0;
double ss = sampleSize*sampleSize;
for(int i=0; i<=m-1; i++){
for(int k=0; k<=i+m; k++){
covSum += ICvec[i]*ICvec[k];
}
}
for(int i=m; i<=n-m-1; i++){
for(int k=i-m; k<=i+m; k++){
covSum += ICvec[i]*ICvec[k];
}
}
for(int i=n-m; i<=n; i++){
for(int k=i-m; k<=n; k++){
covSum += ICvec[i]*ICvec[k];
}
}
s2n = (In/ss) * covSum;
return s2n;
}
')
### end R ###
This works perfectly on my laptop (Macbook air). Now I need to use this
function as a part of a large simulation on my school's cluster (running
Sun Grid Engine) using Rmpi. I included the above function in a text file,
sourced that file in the master and sent the function above to my slaves
using
mpi.bcast.Robj2slave(s2nICm)
I've been trying to get this to work for about a week now, but no luck.
(The original Rmpi simulation code that included the old, slow R version of
the function above worked without error). Until recently, I've been getting
a steady stream of informative error messages that I've forwarded to our
sys admin - problems with g++, etc. Now I'm not getting any error messages,
I'm just not getting any results. There may still be a problem with our
cluster, but I'm wondering if perhaps I'm doing something wrong, too. I'd
really like to understand how Rcpp and Rmpi interact. Is it OK to call
cppFunction('...') in the master and then send the resulting R function to
slaves using mpi.bcast.Robj2slave()? Or do I need to send a text version of
the cppFunction('...') to each slave and evaluate the text within each
slave? What's the proper way to use Rcpp within the context of Rmpi? Does
anyone know of any good resources out there that can help me understand
what's going on under the hood?
Thanks very much for your time,
Molly Davies
Biostatistics Graduate Student
UC Berkeley
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