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running a long R process on Linux using putty - best practice to disconnect

4 messages · Mike Marchywka, Uwe Ligges, Martin Tomko

Original
Martin Tomko
# 
Dear all,
I am sure this has been solved before, googling did not help much,. 
Warning, I am not great with putty/linux servers

Situation: I have been given access to an R installation on a Linux 
server to do some larger number crunching that was killing my machine. I 
use putty to connect, and then go R, source("myscript") and all is fine
But this will take potentially days, and I would like to disconnect

What is the best practice? Someone mentionne nohup, but this would 
require starting the R script with an argument to R, I think. Is this 
doable?

Another option was using screen, btu that is not available on the server.
Any help is welcome.

Thanks
Martin
Mike Marchywka
# 
----------------------------------------
In short, I think "R CMD BATCH script " does what you want.
I routinely run R from scripts and use nohup, the two should work well
together AFAIK. I have encapsulated R stuff into a script ( "myR") 
and have something like this ,

if [ "$1" == "-run" ]
then
echo running $2
$R CMD BATCH $2
shift ; shift
fi


if [ "$1" == "-go" ]
then
echo starting R with no params
$R
shift
Uwe Ligges
#
On 14.10.2010 18:07, Martin Tomko wrote:
Right, just do

nohup R CMD BATCH myscript.R &

and make sure you save all relevant results into files within myscript.R

Uwe Ligges
>
Martin Tomko
# 
thank you guys, R CMD BATCH seems the way to go, and I will nudge my 
admin to install screen /byobu

Thanks heaps,
Martin
On 10/14/2010 7:21 PM, Uwe Ligges wrote: