have R halt the EC2 machine it's running on

Question

I have a few work flows where I would like R to halt the Linux machine it's running on after completion of a script. I can think of two similar ways to do this:

1. run R as root and then call system("halt")
2. run R from a root shell script (could run the R script as any user) then have the shell script run halt after the R bit completes.

Are there other easy ways of doing this?

The use case here is for scripts running on AWS where I would like the instance to stop after script completion so that I don't get charged for machine time post job run. My instance I use for data analysis is an EBS backed instance so I don't want to terminate it, simply suspend. Issuing a halt command from inside the instance is the same effect as a stop/suspend from AWS console.

Answer 1

I'm impressed that works. (For anyone else surprised that an instance can stop itself, see notes 1 & 2.)

You can also try "sudo halt", as you wouldn't need to run as a root user, as long as the user account running R is capable of running sudo. This is pretty common on a lot of AMIs on EC2.

Be careful about what constitutes an assumption of R quitting - believe it or not, one can crash R. It may be better to have a separate script that watches the R pid and, once that PID is no longer active, terminates the instance. Doing this command inside of R means that if R crashes, it never reaches the call to halt. If you call it from within another script, that can be dangerous, too. If you know Linux well, what you're looking for is the PID from starting R, which you can pass to another script that checks ps, say every 1 second, and then terminates the instance once the PID is no longer running.

I think a better solution is to use the EC2 API tools (see: http://docs.amazonwebservices.com/AWSEC2/latest/APIReference/ for documentation) to terminate OR stop instances. There's a difference between the two of these, and it matters if your instance is EBS backed or S3 backed. You needn't run as root in order to terminate the instance - the fact that you have the private key and certificate shows Amazon that you're the BOSS, way above the hoi polloi who merely have root access on your instance.

Because these credentials can be used for mischief, be careful about running API tools from a given server, you'll need your certificate and private key on the server. That's a bad idea in the event that you have a security problem. It would be better to message to a master server and have it shut down the instance. If you have messaging set up in any way between instances, this can do all the work for you.

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Note 1: Eric Hammond reports that the halt will only suspend an EBS instance, so you still have storage fees. If you happen to start a lot of such instances, this can clutter things up. Your original question seems unclear about whether you mean to terminate or stop an instance. He has other good advice on this page

Note 2: A short thread on the EC2 developers forum gives advice for Linux & Windows users.

Note 3: EBS instances are billed for partial hours, even when restarted. (See this thread from the developer forum.) Having an auto-suspend close to the hour mark can be useful, assuming the R process isn't working, in case one might re-task that instance (i.e. to save on not restarting). Other useful tools to consider: setTimeLimit and setSessionTimeLimit, and various checkpointing tools (I have a Q that mentions a couple). Using an auto-kill is useful if one has potentially badly behaved code.

Note 4: I recently learned of the shutdown command in package fun. This is multi-platform. See this blog post for commentary, and code is here. Dangerous stuff, but it could be useful if you want to adapt to Windows. I haven't tried it, though.

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Update 1. Three more ideas:

• You could use .Last() and runLast = TRUE for q() and quit(), which could shut down the instance.
• If using littler or a script that invokes the script via Rscript, the same command line functions could be used.
• My favorite package of today, tcltk2 has a neat timer mechanism, called tclTaskSchedule() that can be used to schedule the execution of an expression. You could then go crazy with the execution of stuff just before a hourly interval has elapsed.

Answer 2

system("echo 'rootpassword' | sudo halt")

However, the downside is having your root password in plain text in the script.