Command-Line Worldview - John Dennison

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Jan 4

Long running R commands: unix screen, nohup and R

I wanted to write a quick post about a useful linux tool for using R. I sometimes have long running R sessions for model training. One solution that I have alluded to is to call your script with Rscript.

The nohup command in linux with push this to the back ground. Even adding mutt(or other email program) to the bottom of your script is extremely useful.

You can save the details of the training into output.txt and then place this command in your R file

system(mutt -s “Master, this is an email from HAL 9000, your commands have been completed” john@foo.com < ~/R/output.txt)

Then you can call the script with nohup Rscript foo.R &

The nohup command runs a command in the background and the ampersand is unix for return the prompt. This will redirect all standard output to a file nohup.out file placed in the directory you called it. However, if you have multiple R file running and one breaks the error gets lost in the common log. Total mess, trust me. The solution is to redirect the output log to individual files with this little thing:

nohup Rscript foo.R > ~/R/logs/foo.out 2>&1 &

This redirects the standard out to a file ~/R/logs/foo.out as well as place all standard error there as well. that is what: 2>&1 is doing.

This is all well and good but we know that most R is written interactively not in nifty self contained scripts. To do this linux has a great program call screen. I and not going to get too fancy with screen but a it has been extremely useful to me. Again i am sshing to remote reserved servers or EC2 instances but this is also useful on a home machine for kicking of an R command and going back to what ever you do on you machine. (ANSII porn or http://xkcd.com/981/). The command is:

screen -S R

This will open a seemingly identical terminal prompt. From here use R(type R…) as you would. When you hit a long running process. Hit Ctrl-a d. This is the screen command to access all screen commands. Ctrl-a d will bring you back to your home prompt. Ctrl-a then typing :quit will exit the screen. When you want to get back, you can type:

screen

Now the -S R options you typed before are optional and if you only have one screen open. I have many screens running (mainly interactive sessions to my databases or ssh to EC2 machines) and getting back to them is a pain unless you name the screens the -S FOO will open a screen called FOO. To reopen type:

screen -Dr FOO

or in our case:

screen -Dr R

The D arg will detach the screen if you exited in a less then graceful manner.

One more trick: if you paste the R train command and the above system command email system() as one text block in the R screen session, then detach you will receive a lovely email when you are done.

Good Luck hacking this the New Year!!!

John