[R] Mpirun with R CMD scripts

Srividya Valivarthi srividya.v at gmail.com
Tue Apr 4 20:48:09 CEST 2006


   I am working on a 64-bit rocks cluster and am relatively new to the
R package. I am trying to get Snow working with R and Rmpi and have
run into the following issue. R is able to load the Rmpi and snow
libraries and is able to run simple commands both interactively and
batch as follows:

[srividya at cheaha ~]$ R
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0  (2005-10-06 r35749)
ISBN 3-900051-07-0
> library(snow)
> c1<-makeCluster(3, type="MPI")
Loading required package: Rmpi
        3 slaves are spawned successfully. 0 failed.
> clusterCall(c1,function() Sys.info()[c("nodename","machine")])
           nodename             machine
"cheaha.ac.uab.edu"            "x86_64"

            nodename              machine
"compute-0-12.local"             "x86_64"

            nodename              machine
"compute-0-13.local"             "x86_64"

> stopCluster(c1)
[1] 1
> q()

But on running the same script with mpirun i get the following error.
[srividya at cheaha ~]$ mpirun -np 3 R -slave R CMD BATCH TestSnow.R
/home/srividya/R/library/snow/RMPInode.sh: line 9: 19431 Segmentation
fault      ${RPROG:-R} --vanilla  >${OUT:-/dev/null} 2>&1 <<EOF



I am not sure about what the error could be and any help is greatly


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