How to interrupt an R process that hangs
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: "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
?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. ?_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