I was doing some stress tests and came across a handful of issues. Version: R 2.0.1 downloaded from CRAN, standard install. Using 3 December 2004 version of R.app from ( http://www.rosuda.org/R/nightly/other/R-GUI.dmg ). All tests done on a 12" PowerBook G4 (original) with 640 MB of RAM. ------------------ Source code leading to crash: library(cluster) data(xclara) plot(hclust(dist(xclara))) This leads to a long wait where the application is frozen (spinning status bar going the entire time), a quartz window displays without any content, and then the following application crash occurs: Date/Time: 2004-12-04 20:15:00 -0600 OS Version: 10.3.6 (Build 7R28) Report Version: 2 Command: R Path: /Applications/R.app/Contents/MacOS/R Version: 1.02-pre build 795 (1.02-pre build 795) PID: 1654 Thread: 0 Exception: EXC_BAD_ACCESS (0x0001) Codes: KERN_INVALID_ADDRESS (0x0001) at 0x049b2940 Thread 0 Crashed: 0 libR.dylib 0x010bd2ec drawdend + 0x168 (plot.c:3358) 1 libR.dylib 0x010bd1e8 drawdend + 0x64 (plot.c:3346) 2 libR.dylib 0x010bd2bc drawdend + 0x138 (plot.c:3356) 3 libR.dylib 0x010bd2bc drawdend + 0x138 (plot.c:3356) 4 libR.dylib 0x010bd1e8 drawdend + 0x64 (plot.c:3346) 5 libR.dylib 0x010bd2bc drawdend + 0x138 (plot.c:3356) 6 libR.dylib 0x010bd2bc drawdend + 0x138 (plot.c:3356) 7 libR.dylib 0x010bd1e8 drawdend + 0x64 (plot.c:3346) 8 libR.dylib 0x010bd660 do_dend + 0x278 (plot.c:3438) 9 libR.dylib 0x0109f670 do_internal + 0x170 (names.c:1067) 10 libR.dylib 0x0106bf9c Rf_eval + 0x428 (eval.c:376) 11 libR.dylib 0x0106d894 do_begin + 0x88 (eval.c:1051) 12 libR.dylib 0x0106bf9c Rf_eval + 0x428 (eval.c:376) 13 libR.dylib 0x0106c5e0 Rf_applyClosure + 0x3b8 (eval.c:570) 14 libR.dylib 0x0109fb04 applyMethod + 0x1d8 (objects.c:119) 15 libR.dylib 0x010a020c Rf_usemethod + 0x420 (objects.c:300) 16 libR.dylib 0x010a05e0 do_usemethod + 0x1f4 (objects.c:389) 17 libR.dylib 0x0106bf9c Rf_eval + 0x428 (eval.c:376) 18 libR.dylib 0x0106bf9c Rf_eval + 0x428 (eval.c:376) 19 libR.dylib 0x0106d894 do_begin + 0x88 (eval.c:1051) 20 libR.dylib 0x0106bf9c Rf_eval + 0x428 (eval.c:376) 21 libR.dylib 0x0106c5e0 Rf_applyClosure + 0x3b8 (eval.c:570) 22 libR.dylib 0x0106c1c8 Rf_eval + 0x654 (eval.c:411) 23 libR.dylib 0x010918ec Rf_ReplIteration + 0x1d0 (main.c:253) 24 libR.dylib 0x01091a48 R_ReplConsole + 0x88 (main.c:302) 25 libR.dylib 0x010923bc run_Rmainloop + 0x6c (main.c:656) 26 com.apple.Foundation 0x909f30e4 __NSFireTimer + 0x68 27 com.apple.CoreFoundation 0x90194620 __CFRunLoopDoTimer + 0xf4 28 com.apple.CoreFoundation 0x90191980 __CFRunLoopRun + 0x5c8 29 com.apple.CoreFoundation 0x90195e94 CFRunLoopRunSpecific + 0x148 30 com.apple.HIToolbox 0x927d5f88 RunCurrentEventLoopInMode + 0xac 31 com.apple.HIToolbox 0x927dc6f0 ReceiveNextEventCommon + 0x17c 32 com.apple.HIToolbox 0x927fe6c8 BlockUntilNextEventMatchingListInMode + 0x60 33 com.apple.AppKit 0x92dd227c _DPSNextEvent + 0x180 34 com.apple.AppKit 0x92de8c24 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 0x74 35 com.apple.AppKit 0x92dfcf8c -[NSApplication run] + 0x21c 36 com.apple.AppKit 0x92eb948c NSApplicationMain + 0x1d0 37 org.R-project.R 0x000029c8 _start + 0x188 (crt.c:267) 38 dyld 0x8fe1a558 _dyld_start + 0x64 Thread 1: 0 libSystem.B.dylib 0x9000b20c select + 0xc 1 org.R-project.R 0x00003b30 -[RController readThread:] + 0x1b4 2 com.apple.Foundation 0x90a39b74 forkThreadForFunction + 0x6c 3 libSystem.B.dylib 0x900246e8 _pthread_body + 0x28 Thread 2: 0 libSystem.B.dylib 0x90012568 syscall_thread_switch + 0x8 1 com.apple.Foundation 0x90a029c8 +[NSThread sleepUntilDate:] + 0x98 2 com.apple.AppKit 0x92dca420 -[NSUIHeartBeat _heartBeatThread:] + 0x494 3 com.apple.Foundation 0x90a39b74 forkThreadForFunction + 0x6c 4 libSystem.B.dylib 0x900246e8 _pthread_body + 0x28 PPC Thread State: srr0: 0x010bd2ec srr1: 0x0200f030 vrsave: 0x00000000 cr: 0x24022286 xer: 0x20000004 lr: 0x010bd294 ctr: 0x900f5f70 r0: 0x010bd294 r1: 0xbfffb7c0 r2: 0x049b2948 r3: 0x00000b26 r4: 0x00000000 r5: 0xa09faf40 r6: 0xbfffb234 r7: 0x05175200 r8: 0x00000464 r9: 0x049ad018 r10: 0x00000118 r11: 0x24022282 r12: 0x900f5f70 r13: 0x011cc51c r14: 0x0118fdf4 r15: 0x05428acc r16: 0x01e09588 r17: 0x05188f10 r18: 0x0189a4e8 r19: 0x01e095f8 r20: 0x05428a94 r21: 0x00000017 r22: 0x00000bb8 r23: 0x011bcb38 r24: 0x00000bb7 r25: 0x0189761c r26: 0x05427748 r27: 0xbfffb940 r28: 0xbfffb948 r29: 0x0035d450 r30: 0x000023f8 r31: 0x010bd18c Binary Images Description: 0x1000 - 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0x97214fff com.apple.WebCore 125.8.10 /System/Library/Frameworks/WebKit.framework/Versions/A/ Frameworks/WebCore.framework/Versions/A/WebCore 0x97490000 - 0x97490fff com.apple.securitynssasn1 1.2 (12) /System/Library/PrivateFrameworks/SecurityNssAsn1.framework/ Versions/A/SecurityNssAsn1 0x97510000 - 0x97518fff libbsm.dylib /usr/lib/libbsm.dylib dist(xclara)->xclara.dist Works okay, though when attempting to display those results it freezes up the entire system, probably as the result of memory threshing/starvation if the top results are any indicator: 1661 R 8.5% 9:36.12 3 92 567 368M+ 3.88M 350M- 828M Sincerely, David
R.app crash report
3 messages · ap_llywelyn@mac.com, Simon Urbanek, Martin Maechler
On Dec 4, 2004, at 9:50 PM, ap_llywelyn@mac.com wrote:
Source code leading to crash: library(cluster) data(xclara) plot(hclust(dist(xclara))) This leads to a long wait where the application is frozen (spinning status bar going the entire time), a quartz window displays without any content, and then the following application crash occurs:
Please post this to the maintainers of the cluster library (if at all), since this has nothing to do with the GUI (behaves the same in X11). The above doesn't make much sense anyway - you definitely want to use cutree before you plot that dendogram ... Cheers, Simon
"Simon" == Simon Urbanek <simon.urbanek@math.uni-augsburg.de>
on Sun, 5 Dec 2004 19:39:07 -0500 writes:
Simon> On Dec 4, 2004, at 9:50 PM, ap_llywelyn@mac.com
Simon> wrote:
>> Source code leading to crash:
>>
>> library(cluster)
>> data(xclara)
>> plot(hclust(dist(xclara)))
>>
>> This leads to a long wait where the application is frozen
>> (spinning status bar going the entire time), a quartz
>> window displays without any content, and then the
>> following application crash occurs:
Simon> Please post this to the maintainers of the cluster
Simon> library (if at all),
Well, this is a *package*, not a library {please, please!}
And really, that has nothing to do with the 'cluster' package
(whose maintainer I am), as David only uses its data set.
hclust() and dist() are in the standard 'stats' package.
Btw, this can be accomplished more cleanly, i.e., without
attaching "cluster", by
data(xclara, package = "cluster")
Simon> this has nothing to do
Simon> with the GUI (behaves the same in X11). The above
Simon> doesn't make much sense anyway - you definitely want
Simon> to use cutree before you plot that dendogram ...
Indeed!
A bit more explicitly for David:
xclara has 3000 observations,
i.e. 3000*2999/2 ~= 4.5 Mio distances {i.e., a bit more than 36
MBytes to keep in memory and about 48 mio characters to display
when you use default options(digits=7)}.
I don't think you can really make much of printing these many
numbers onto your console as you try with
David> dist(xclara) -> xclara.dist
David> Works okay, though when attempting to display those results it freezes
David> up the entire system, probably as the result of memory
David> threshing/starvation if the top results are any indicator:
David> 1661 R 8.5% 9:36.12 3 92 567 368M+ 3.88M 350M- 828M
"freezes up the entire system" when trying to print something
too large actually has something to do with user interface.
AFAIK, it doesn't work 'nicely' on any R console,
but at least in ESS on Linux, it's just that one Emacs,
displaying the "wrist watch" (and I can easily tell emacs "not
to wait" by pressing Ctrl g"). Also, just trying it now {on a
machine with large amounts of RAM}: After pressing return, it at
least starts printing (displaying to the *R* buffer) after a bit
more than 1 minute.. and that does ``seem'' to never finish.
I can signal a break (via the [Signals] Menu or C-c C-c in
Emacs), and still have to wait about 2-3 minutes for the output
stops; but it does, and I can work on.. {well, in theory; my Emacs
seems to have become v..e..r..y s...l...o....w} We only
recently had a variation on this theme in the ESS-help mailing
list, and several people were reporting they couldn't really
stop R from printing and had to kill the R process...
So after all, there's not quite a trivial problem "hidden" in
David's report : What should happen if the user accidentally
wants to print a huge object to console... how to make sure R
can be told to stop.
And as I see it now, there's even something like an R "bug" (or
"design infelicity") here:
I've now done it again {on a compute server Dual-Opteron with 4
GB RAM}: After stopping, via the ESS [Signals] [Break (C-c C-c)] menu,
Emacs stops immediately, but R doesn't return quickly,
and rather, watching "top" {the good ol' unix process monitor} I
see R using 99.9% CPU and it's memory footage ("VIRT" and
"SHR") increasing and increasing..., upto '1081m', a bit more
than 1 GB, when R finally returns (displays the prompt) after
only a few minutes --- but then, as said, this is on a remote
64bit machine with 4000 MB RAM.
BTW, when I then remove the 'dist' (and hclust) objects in R,
and type gc(),
(or maybe do some other things in R; the R process has about
halfed its apparent memory usage to 500something MB.
more stats:
during printing: 798 m
after "break" : 798, for ~5 seconds, then starting to
grow; slowly (in my top, in steps of ~ 10m)
upto 1076m
then the R prompt is displayed and top shows "1081m".
It stays there , until I do
> gc()
where it goes down to VIRT 841m (RES 823m)
and after removing the large distance object, and gc() again,
it lowers to 820m (RES 790m) and stays there.
Probably this thread should be moved to R-devel -- and hence I
crosspost for once.
Martin