Re: [R] Unix batch to different nodes

From: stephen sefick <ssefick_at_gmail.com>
Date: Thu, 30 Sep 2010 06:48:20 -0500

This, I think, all depends on how the server is set up.

On Thu, Sep 30, 2010 at 1:21 AM, Daisy Englert Duursma <daisy.duursma_at_gmail.com> wrote:
> Hello,
>
> I am struggling with computing nodes in Unix.
>
> I have the use of a Unix server that has 30 nodes and I would like to
> batch scripts.
>
> Here is an R example that results in 72 repeated tasks based on the 2
> loops. If I wanted to send these out to the different nodes, each node
> has 1 task and the remaining 42 tasks are put in a queue, what would I
> do?
>
> #Example:
>
> proj.dir<-"C:/test/"
> setwd(proj.dir)
>
>
> group.vars <- c("biol1","biol4","biol5","biol6","biol12","biol15","biol16","biol17")
> species <- c("aa", "bb", "cc", "dd", "ee", "ff", "gg", "hh", "ii")
>
> for (gv in 1:length(group.vars)){
> for (sp in 1:length(species)){
>
> zzz <- file(paste(group.vars[gv],species[sp],".TXT",sep=""),"w")
>        cat(paste(group.vars[gv]),file=zzz)
>        cat(paste(species[sp]),file=zzz)
> close(zzz)
> }
> }
>
> I know it is a silly script test but the division is similar to my
> real task which is repeated 459 times and each run takes 18 hours
>
> At this point I am confused what should be written in Unix and then at
> what point should I call R. I have read an abundance of things but I
> feel like I am missing something essential. Or perhaps I have read all
> the wrong things.
>
>
> Thanks,
> Daisy
>
>
> --
> Daisy Englert Duursma
>
> Room E8C156
> Dept. Biological Sciences
> Macquarie University  NSW  2109
> Australia
>
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>

-- 
Stephen Sefick
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annoying little problems of being mammals.

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Received on Thu 30 Sep 2010 - 11:51:41 GMT

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