Stopping a nohup parallel simulation in R

Question

I need to cancel a parallel processing simulation that I started on a Linux server using R.

Last night I connected to the server using ssh and started the simulation from the shell with the nohup command: nohup R CMD BATCH mysimulation.R

The mysimulation.R file uses the mclapply command in the multicore package to spawn additional instances of R to run the simulation in parallel. For instance, when I run top in the shell I see ten different instances of R running, then finishing a run of the simulation, then starting again to continue with the additional simulation replications.

I have almost no experience working directly with a Linux server (the extent of my knowledge is cd, ls, and the nohup command mentioned above). I searched around a bit for a solution and thought killing the process might work. I tried:

kill -9 mypid (which said it killed the process).

However, the simulation continues to run. I can see the instances of R continuing to run, close, and respawn. Can anyone point me to resources or walk me through the specific steps I need to take to shut down this simulation? Thanks.

score 2 · Answer 1 · edited May 23 '17 at 12:18

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It seems you need to kill several processes at once. Maybe one of the answers to the post Best way to kill all child processes might help you.

edited May 23 '17 at 12:18

Community

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answered Oct 03 '12 at 20:52

Håvard

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I could not make the top answers work from the link, but manually went through and killed the individual child processes listed and that seemed to work. Thanks for the pointer. – user1715965 Oct 03 '12 at 22:25

score 0 · Answer 2 · answered Oct 04 '12 at 00:30

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You may see this page. I hope this would help

answered Oct 04 '12 at 00:30

Ali

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Stopping a nohup parallel simulation in R

2 Answers2