R help - Oct 2010 - running a long R process on Linux using putty - best practice to disconnect

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

----------------------------------------
> Date: Thu, 14 Oct 2010 18:07:02 +0200
> From: martin.tomko at geo.uzh.ch
> To: r-help at r-project.org
> Subject: [R] running a long R process on Linux using putty - best practice
to disconnect
>
> 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?
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

>
> Another option was using screen, btu that is not available on the server.
> Any help is welcome.
>
> Thanks
> Martin
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

On 14.10.2010 18:07, Martin Tomko wrote:
> 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?
Right, just do

nohup R CMD BATCH myscript.R &

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

Uwe Ligges

> Another option was using screen, btu that is not available on the server.
> Any help is welcome.
 >
> Thanks
> Martin
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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:
>
>
> On 14.10.2010 18:07, Martin Tomko wrote:
>> 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?
>
> Right, just do
>
> nohup R CMD BATCH myscript.R &
>
> and make sure you save all relevant results into files within myscript.R
>
> Uwe Ligges
>
>
>> Another option was using screen, btu that is not available on the 
>> server.
>> Any help is welcome.
> >
>> Thanks
>> Martin
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Martin Tomko
Postdoctoral Research Assistant

Geographic Information Systems Division
Department of Geography
University of Zurich - Irchel
Winterthurerstr. 190
CH-8057 Zurich, Switzerland

email: 	martin.tomko at geo.uzh.ch
site:	http://www.geo.uzh.ch/~mtomko
mob: 	+41-788 629 558
tel: 	+41-44-6355256
fax: 	+41-44-6356848