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

Simon Urbanek simon.urbanek at r-project.org
Mon Mar 15 22:28:50 CET 2010 

On Mar 15, 2010, at 17:10 , Matthew Keller wrote:

> Hi all,
>
> Thanks for the responses. Ted - thank you for your help. I had to
> laugh. I'm no computer guru, but I do know unix well enough to know
> not to type "<PID>". But then again, my original code did contain a
> matrix with >>2^31-1 elements, so maybe your assumption was reasonable
> ;)
>
> Anyway, all your kill statements merely kill R, script included, which
> doesn't really do what I'd like.
>
> Thus, summary of responses:
>
> Question:
> "How do I interrupt an R process that's taking too long?"
>

Answer 1: Press Stop or <Ctrl><C>
if that doesn't produce the desired effect in reasonable time, proceed  
to next answer


> Answer:
> "You don't. Kill R. And don't make mistakes."
>


Cheers,
Simon


>
> On Mon, Mar 15, 2010 at 2:49 PM, Ted Harding
> <Ted.Harding at manchester.ac.uk> wrote:
>> [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
>>>>> R-SIG-Mac at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> 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.
>>
>> --------------------------------------------------------------------
>> 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
>> ------------------------------ XFMail ------------------------------
>>
>> ______________________________________________
>> 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.
>>
>
>
>
> -- 
> Matthew C Keller
> Asst. Professor of Psychology
> University of Colorado at Boulder
> www.matthewckeller.com
>
>

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