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

Mon Mar 15 22:38:37 CET 2010

On 15-Mar-10 21:10:03, 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
> ;)

Well, it was a "just in case" assumption, not based on a prior!

> Anyway, all your kill statements merely kill R, script included,
> which doesn't really do what I'd like.

On the matter of killing an R script, I have tested kill -s INT
with a script "test.R":

  while(TRUE){ x <- 1} ## trivially light-weight, but ...

And then, in R,

  source("test.R")

It duly puts the command prompt to sleep. WHen I type ^C at the
keyboard, it stops and the command prompt returns.

So I start it again, and this time from another console enter

   kill -s INT  13863

(the PID for that instance of R) and again the script is interuppted
and the command prompt returns. So this adds weight to the theory
that your script (for some reason) is not interruptible, i.e. R
is not able to apply the INT to the script.

Ted.

> Thus, summary of responses:
> 
> Question:
> "How do I interrupt an R process that's taking too long?"
> 
> Answer:
> "You don't. Kill R. And don't make mistakes."
> 
> Matthew
> 
> 
> 
> 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
>> Â_kill -s INT <PID>
>> without substituting the R PID for "<PID"? If so, then here's a tip.
>> In Mac console, do
>>
>> Â_ps aux | grep R
>>
>> On my Linux machine this currently responds with (amongst some
>> irrelevant lines):
>>
>> ted Â_8625 Â_0.0 Â_3.2 Â_41568 34096 pts/6 Â_S+ Mar13 0:07
>> Â_/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
>>
>> Â_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
>>
>> Â_kill -1 8625 Â_ Â_or Â_ Â_ kill -2 8625
>>
>> (b) Don't search for the numeric Process ID (PID) but kill it
>> Â_ Â_by name ('killall' command):
>>
>> Â_killall -1 R Â_ Â_or Â_ Â_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){
>>> Â_ Â_ Â_ a <- matrix(rnorm(100000*100000),ncol=100000)
>>> Â_ Â_ Â_ b <- svd(a) Â_ Â_ }
>>>
>>> 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.
>>>>> Ã‚_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 Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_ Â_
>> Â_ 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
> 
> ______________________________________________
> 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: 21:38:33
------------------------------ XFMail ------------------------------