[R] Running R on a grid engine
ramasamy at cancer.org.uk
Thu Oct 28 20:41:18 CEST 2004
See comments below.
On Thu, 2004-10-28 at 18:49, S Peri wrote:
> Dear Group,
> I am using DEAL package for modeling signal
> transduction nets. This process is deal slow on a
> SunFire server with 8 gigs ram.
> we have a grid that can process much faster that one
> individual server.
> However, to start the process in Grid, I have to give
> a command or submit a batch process.
> Is there any way, I can run R in bach process.
> I tried the following:
> R CMD | library(deal) | data <-
Something like this works in *NIX
echo " print(mean(rnorm(10))) " | R --no-save
HOWEVER you will run into nightmares soon trying to backslash all the
quotes and other special characters. And try to recall a long sequence
of commands you typed in a few days ago ...
Better to put all your codes into a file, say script.R and do
R --no-save < script.R > log_script.R &
> Here I do not know know :
> 1. How can I point my data files to a function.
Two ways :
1) Hard code the path inside the script.R
2) Take advantage of commandArgs().
Example. If your script.R contains
data.path <- as.character( commandArgs() )
load (data.path) # or read.delim or whatever
Then you can pass the path to test.rda via command line
R --no-save < script.R /home/speri/data/test.rda > log_script.R &
One thing to keep in mind is to pass the absolute paths and not relative
paths (e.g. ../../data/test.rda). Using relative path may not always
> 2. creating a function (other than in R environment)
Huh ? You can put all your functions into a file, say functions.R, and
you can source("/path/to/functions.R") in your script.R/
> Could any one help me.
> Thank you in advance.
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