Mortimer, Steven | 2 Dec 04:59 2012

Trying to create parallel cluster, but makePSOCKcluster() hangs

I have been using my Amazon Web Servies account and the directions on
http://www.bioconductor.org/help/bioconductor-cloud-ami/#parallel to bootstrap a cluster of
Bioconductor AMIs.  After running the lines of code below, it hangs on the makePSOCKcluster call.  This
error happens quite frequently to me, but not always.  Any ideas for how to get reliable results or is there
workaround?  Thanks for your time and consideration.

library(parallel)
lines <- readLines("/usr/local/Rmpi/hostfile.plain")
hosts <- character()
for (line in lines)
{
    x <- (strsplit(line[[1]], " "))
    hosts <-
        c(hosts, rep.int(x[[1]][1], as.integer(x[[1]][2])))
}
#THIS LINE HANGS
#HOSTS IS A CHARACTER VECTORS OF IP ADDRESSES FOR BIOCONDUCTOR AMIs CREATED FROM STACK TEMPLATE
cl <- makePSOCKcluster(hosts)

Steven Mortimer
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