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.hard...@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.urba...@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
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--
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com
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--------------------------------------------------------------------
E-Mail: (Ted Harding) <ted.hard...@manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 15-Mar-10 Time: 20:49:57
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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@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.
