[R-SIG-Mac] [R] How to interrupt an R process that hangs

(Ted Harding) Ted.Harding at manchester.ac.uk
Mon Mar 15 21:49:59 CET 2010 

[Though I'm not using a Mac, OS X is a Unix variant and should
have the commands used below installed]

Did you *literally* do
  kill -s INT <PID>
without substituting the R PID for "<PID"? If so, then here's a tip.
In Mac console, do

  ps aux | grep R

On my Linux machine this currently responds with (amongst some
irrelevant lines):

ted  8625  0.0  3.2  41568 34096 pts/6  S+ Mar13 0:07
  /usr/lib/R/bin/exec/R --no-save

showing that the PID of the R process is 8625. Then you can do
whatever corresponds to

  kill -s INT 8625

(replacing "8625" with what you get from ps). However, when I
just tried it, it didn't work for me either. So I changed the
Signal from "INT" to "HUP", and this time it did work. Maybe
try this instead?

Other ways of using 'kill' include
(a) Use the signal number (1 for HUP, 2 for INT) like

  kill -1 8625    or     kill -2 8625

(b) Don't search for the numeric Process ID (PID) but kill it
    by name ('killall' command):

  killall -1 R    or    killall -2 R

However, this will kill every running instance of R (if you
two or more running simultaneously), and you may not want that!

Hoping this helps,
Ted.



On 15-Mar-10 20:20:29, Matthew Keller wrote:
> Hi all,
> 
> Thanks Simon and Duncan for the help. Sorry to be dense, but I'm still
> unsure how to interrupt such processes. Here's an example:
> 
> for (i in 1:100000){
>       a <- matrix(rnorm(100000*100000),ncol=100000)
>       b <- svd(a)     }
> 
> If you run this, R will hang (i.e., it's a legitimate execution, it
> will just take a really long time to execute). The most obvious
> solution is to write code that doesn't do unintended things, but
> that's not always possible. Is there a way to interrupt it? I tried:
> 
> kill -s INT <PID>
> 
> and at least on Mac it had no effect. Thanks again,
> 
> Matt
> 
> 
> 
> On Mon, Mar 15, 2010 at 1:19 PM, Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>>
>> On Mar 15, 2010, at 14:42 , Adam D. I. Kramer wrote:
>>
>>> +1--this is the single most-annoying issue with R that I know of.
>>>
>>> My usual solution, after accomplishing nothing as R spins idly for a
>>> couple
>>> hours, is to kill the process and lose any un-saved work.
>>> Â_save.history()
>>> is
>>> my friend, but is a big delay when you work with big data sets as I
>>> do, so
>>> I
>>> don't run it after every command.
>>>
>>> I have cc'd r-help here, however, because I experience this problem
>>> with
>>> non-OSX R as well...when I run it in Linux or from the OSX
>>> command-line (I
>>> compile R for Darwin without aqua/R-framework), the same thing
>>> happens.
>>>
>>> Is there some way around this? Is this a known problem?
>>>
>>
>> "Hanging" for a long period of time is usually caused by poorly
>> written
>> C/Fortran code. You can always interrupt R as long as it is in the R
>> code.
>> Once you load a package that uses native code (C/Fortran/..) you have
>> to
>> rely on the sanity of the developer to call R_CheckUserInterrupt() or
>> rchkusr() often enough (see 6.12 in R-ext). If you have some
>> particular
>> package that does not do that, I would suggest alerting the author. By
>> definition this requires cooperation from authors, because
>> interrupting
>> random code forcefully (as it was possible many years ago) creates
>> leaks and
>> unstable states.
>>
>> Cheers,
>> Simon
>>
>>
>>
>>> Google searching suggests no solution, timeline, or anything, but the
>>> problem has been annoying users for at least twelve years:
>>> http://tolstoy.newcastle.edu.au/R/help/9704/0151.html
>>>
>>> Cordially,
>>> Adam
>>>
>>> On Mon, 15 Mar 2010, Matthew Keller wrote:
>>>
>>>> HI all,
>>>>
>>>> Apologies for this question. I'm sure it's been asked many times,
>>>> but
>>>> despite 20 minutes of looking, I can't find the answer. I never use
>>>> the GUI, I use emacs, but my postdoc does, so I don't know what to
>>>> tell her about the following:
>>>>
>>>> Occasionally she'll mess up in her code and cause R to hang
>>>> indefinitely (e.g., R is trying to do something that will take
>>>> days).
>>>> In these situations, is there an option other than killing R (and
>>>> the
>>>> work you've done on your script to that point)?
>>>>
>>>> Thank you,
>>>>
>>>> Matthew Keller
>>>>
>>>>
>>>> --
>>>> Matthew C Keller
>>>> Asst. Professor of Psychology
>>>> University of Colorado at Boulder
>>>> www.matthewckeller.com
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
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>>>
>>>
>>
>>
> 
> 
> 
> -- 
> Matthew C Keller
> Asst. Professor of Psychology
> University of Colorado at Boulder
> www.matthewckeller.com
> 
> ______________________________________________
> 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.

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E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 15-Mar-10                                       Time: 20:49:57
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