[BioC] Trying to create parallel cluster, but makePSOCKcluster() hangs

[Dan Tenenbaum]

On Sat, Dec 1, 2012 at 7:59 PM, Mortimer, Steven <MortimeS at advisory.com> wrote:
> 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)
>

Hi Steven,

Use this command instead:

cl <- makePSOCKcluster(hosts,
    master=system("hostname -i", intern=TRUE))

I've updated the AMI web page to reflect this change.
Thanks,
Dan


>
> Steven Mortimer
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