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lme4a crash

4 messages · Ben Bolker, Christopher Philipson

Ben Bolker
# 
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On 11-06-27 11:57 AM, Christopher Philipson wrote:
More details (especially including a reproducible example) would be
very helpful ... see e.g. https://gist.github.com/270442

  ... Ben Bolker
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1 day later
Christopher Philipson
# 
Hi Ben and mixed modellers,

My apologies.  The link you provided is useful, I am working on a simpler example that produces the problem.

The nlmer() model is:

power.law_light2 <- deriv(expression((( ( M0 )^(1-beta)) + (exp(Amax_Int + Amax_Slope * x2))*(1-beta)*x1)^(1/(1-beta))),
							c("M0", "Amax_Int","Amax_Slope", "beta"), function(x1, x2, M0, Amax_Int, Amax_Slope, beta) {})

nlmer1<-  nlmer(total.mass ~ power.law_light2(day, Treatment, M0, Amax_Int, Amax_Slope, beta) ~ 
					   0 + M0 + Amax_Int + Amax_Slope + beta
					 + (0 + M0 |Seedling_no2)
					 + (0 + Amax_Int|Seedling_no2)
	                                + (0 + beta |Seedling_no2), 
					 datNEW,			 
					 start=mystart,
					 verbose=TRUE);	


In the mean time I have established that R64, does not crash but produces the following error message:

Error in bobyqa(ans at re@theta, obj, ans at re@lower, control = control) : 
 non-finite objective values not allowed
In addition: Warning message:
In log(.expr8) : NaNs produced

I will try to produce an example that does repeats this

The sessionInfo() is: [note I have the same situation with r2.13]
R version 2.14.0 Under development (unstable) (2011-06-26 r56223)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lme4a_0.999375-67  MatrixModels_0.2-1 minqa_1.1.15       Rcpp_0.9.4         Matrix_0.999375-50 lattice_0.19-26   

loaded via a namespace (and not attached):
[1] codetools_0.2-8 grid_2.14.0     nlme_3.1-101    splines_2.14.0  tools_2.14.0 

Many thanks and apologies for lack of previous details.


Cheers
Chris

R 32-bit message when nlmer() crashes r.
Process:         R [3850]
Path:            /Applications/R.app/Contents/MacOS/R
Identifier:      org.R-project.R
Version:         R for Mac OS X GUI 1.40-devel Leopard build 32-bit (5862)
Code Type:       X86 (Native)
Parent Process:  launchd [112]

Date/Time:       2011-06-29 09:13:06.737 +0200
OS Version:      Mac OS X 10.6.8 (10K540)
Report Version:  6

Interval Since Last Report:          78981 sec
Crashes Since Last Report:           84
Per-App Interval Since Last Report:  1581 sec
Per-App Crashes Since Last Report:   1
Anonymous UUID:                      F882E507-864C-4DA4-BDFF-C104FBB881C2

Exception Type:  EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Application Specific Information:
abort() called

Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   libSystem.B.dylib             	0x923b4c5a __kill + 10
1   libSystem.B.dylib             	0x923b4c4c kill$UNIX2003 + 32
2   libSystem.B.dylib             	0x924475a5 raise + 26
3   libSystem.B.dylib             	0x9245d6e4 abort + 93
4   libstdc++.6.dylib             	0x99ba4fda __gnu_cxx::__verbose_terminate_handler() + 433
5   libstdc++.6.dylib             	0x99ba317a __cxxabiv1::__terminate(void (*)()) + 10
6   libstdc++.6.dylib             	0x99ba31ba __cxxabiv1::__unexpected(void (*)()) + 0
7   libstdc++.6.dylib             	0x99ba32b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0
8   minqa.so                      	0x27c54f00 calfun_ + 688
9   minqa.so                      	0x27c5a61f prelim_ + 863
10  minqa.so                      	0x27c50cc0 bobyqb_ + 272
11  minqa.so                      	0x27c50b1b bobyqa_ + 731
12  minqa.so                      	0x27c55ff5 bobyqa_cpp + 1029
13  libR.dylib                    	0x00124811 do_dotcall + 1009 (dotcode.c:856)
14  libR.dylib                    	0x00152ef1 Rf_eval + 1777 (eval.c:495)
15  libR.dylib                    	0x00156066 do_set + 678 (eval.c:1709)
16  libR.dylib                    	0x00152cf2 Rf_eval + 1266 (eval.c:469)
17  libR.dylib                    	0x001549c7 do_begin + 327 (eval.c:1407)
18  libR.dylib                    	0x00152cf2 Rf_eval + 1266 (eval.c:469)
19  libR.dylib                    	0x00157d31 Rf_applyClosure + 833 (eval.c:825)
20  libR.dylib                    	0x00152bf2 Rf_eval + 1010 (eval.c:513)
21  libR.dylib                    	0x00156066 do_set + 678 (eval.c:1709)
22  libR.dylib                    	0x00152cf2 Rf_eval + 1266 (eval.c:469)
23  libR.dylib                    	0x001549c7 do_begin + 327 (eval.c:1407)
24  libR.dylib                    	0x00152cf2 Rf_eval + 1266 (eval.c:469)
25  libR.dylib                    	0x00157d31 Rf_applyClosure + 833 (eval.c:825)
26  libR.dylib                    	0x00152bf2 Rf_eval + 1010 (eval.c:513)
27  libR.dylib                    	0x001549c7 do_begin + 327 (eval.c:1407)
28  libR.dylib                    	0x00152cf2 Rf_eval + 1266 (eval.c:469)
29  libR.dylib                    	0x00157d31 Rf_applyClosure + 833 (eval.c:825)
30  libR.dylib                    	0x00152bf2 Rf_eval + 1010 (eval.c:513)
31  libR.dylib                    	0x00156066 do_set + 678 (eval.c:1709)
32  libR.dylib                    	0x00152cf2 Rf_eval + 1266 (eval.c:469)
33  libR.dylib                    	0x0018dd51 R_ReplDLLdo1 + 513 (main.c:358)
34  org.R-project.R               	0x0001f4ac run_REngineRmainloop + 252
35  org.R-project.R               	0x0001474c -[REngine runREPL] + 284
36  org.R-project.R               	0x00002600 main + 1024
37  org.R-project.R               	0x00002046 start + 54

Thread 1:  Dispatch queue: com.apple.libdispatch-manager
0   libSystem.B.dylib             	0x9237a382 kevent + 10
1   libSystem.B.dylib             	0x9237aa9c _dispatch_mgr_invoke + 215
2   libSystem.B.dylib             	0x92379f59 _dispatch_queue_invoke + 163
3   libSystem.B.dylib             	0x92379cfe _dispatch_worker_thread2 + 240
4   libSystem.B.dylib             	0x92379781 _pthread_wqthread + 390
5   libSystem.B.dylib             	0x923795c6 start_wqthread + 30

Thread 2:
0   libobjc.A.dylib               	0x99a27fa0 objc_msgSend + 48
1   com.apple.Foundation          	0x9046f352 -[NSDistantObject methodSignatureForSelector:] + 192
2   com.apple.CoreFoundation      	0x9194a9c0 ___forwarding___ + 320
3   com.apple.CoreFoundation      	0x9194a802 _CF_forwarding_prep_0 + 50
4   org.R-project.R               	0x00011465 -[RController readThread:] + 2181
5   com.apple.Foundation          	0x90417564 -[NSThread main] + 45
6   com.apple.Foundation          	0x90417514 __NSThread__main__ + 1499
7   libSystem.B.dylib             	0x92381259 _pthread_start + 345
8   libSystem.B.dylib             	0x923810de thread_start + 34

Thread 3:  com.apple.CFSocket.private
0   libSystem.B.dylib             	0x92372ac6 select$DARWIN_EXTSN + 10
1   com.apple.CoreFoundation      	0x9194cc83 __CFSocketManager + 1091
2   libSystem.B.dylib             	0x92381259 _pthread_start + 345
3   libSystem.B.dylib             	0x923810de thread_start + 34

Thread 4:
0   libSystem.B.dylib             	0x92353afa mach_msg_trap + 10
1   libSystem.B.dylib             	0x92354267 mach_msg + 68
2   com.apple.CoreFoundation      	0x9190d30f __CFRunLoopRun + 2079
3   com.apple.CoreFoundation      	0x9190c3f4 CFRunLoopRunSpecific + 452
4   com.apple.CoreFoundation      	0x9190c221 CFRunLoopRunInMode + 97
5   com.apple.Foundation          	0x904502c4 +[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] + 329
6   com.apple.Foundation          	0x90417564 -[NSThread main] + 45
7   com.apple.Foundation          	0x90417514 __NSThread__main__ + 1499
8   libSystem.B.dylib             	0x92381259 _pthread_start + 345
9   libSystem.B.dylib             	0x923810de thread_start + 34

Thread 5:
0   libSystem.B.dylib             	0x92379412 __workq_kernreturn + 10
1   libSystem.B.dylib             	0x923799a8 _pthread_wqthread + 941
2   libSystem.B.dylib             	0x923795c6 start_wqthread + 30

Thread 6:
0   libSystem.B.dylib             	0x92379412 __workq_kernreturn + 10
1   libSystem.B.dylib             	0x923799a8 _pthread_wqthread + 941
2   libSystem.B.dylib             	0x923795c6 start_wqthread + 30

Thread 7:
0   libSystem.B.dylib             	0x92379412 __workq_kernreturn + 10
1   libSystem.B.dylib             	0x923799a8 _pthread_wqthread + 941
2   libSystem.B.dylib             	0x923795c6 start_wqthread + 30

Thread 8:
0   libSystem.B.dylib             	0x92381aa2 __semwait_signal + 10
1   libSystem.B.dylib             	0x923ad9c5 nanosleep$UNIX2003 + 188
2   libSystem.B.dylib             	0x923ad903 usleep$UNIX2003 + 61
3   com.apple.AppKit              	0x95b52e2d -[NSUIHeartBeat _heartBeatThread:] + 2039
4   com.apple.Foundation          	0x90417564 -[NSThread main] + 45
5   com.apple.Foundation          	0x90417514 __NSThread__main__ + 1499
6   libSystem.B.dylib             	0x92381259 _pthread_start + 345
7   libSystem.B.dylib             	0x923810de thread_start + 34

Thread 0 crashed with X86 Thread State (32-bit):
  eax: 0x00000000  ebx: 0x9245d693  ecx: 0xbfffdd1c  edx: 0x923b4c5a
  edi: 0xa02d4b30  esi: 0x251b4b4c  ebp: 0xbfffdd38  esp: 0xbfffdd1c
   ss: 0x0000001f  efl: 0x00000282  eip: 0x923b4c5a   cs: 0x00000007
   ds: 0x0000001f   es: 0x0000001f   fs: 0x00000000   gs: 0x00000037
  cr2: 0xa02e6020

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0x99070000 - 0x9919efe7  com.apple.CoreData 102.1 (251) <E6A457F0-A0A3-32CD-6C69-6286E7C0F063> /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
0x9919f000 - 0x99321fe7  libicucore.A.dylib 40.0.0 (compatibility 1.0.0) <D5980817-6D19-9636-51C3-E82BAE26776B> /usr/lib/libicucore.A.dylib
0x99322000 - 0x993defff  com.apple.ColorSync 4.6.6 (4.6.6) <7CD8B191-039A-02C3-EA5E-4194EC59995B> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
0x993eb000 - 0x993ebff7  com.apple.Accelerate.vecLib 3.6 (vecLib 3.6) <1DEC639C-173D-F808-DE0D-4070CC6F5BC7> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x9943e000 - 0x9954aff7  libGLProgrammability.dylib ??? (???) <04D7E5C3-B0C3-054B-DF49-3B333DCDEE22> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x99553000 - 0x9977eff3  com.apple.QuartzComposer 4.2 ({156.30}) <2C88F8C3-7181-6B1D-B278-E0EE3F33A2AF> /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer
0x99877000 - 0x9987aff7  libCGXType.A.dylib 545.0.0 (compatibility 64.0.0) <4D766435-EB76-C384-0127-1D20ACD74076> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGXType.A.dylib
0x99894000 - 0x998ccfe7  libncurses.5.4.dylib 5.4.0 (compatibility 5.4.0) <8776C654-D54E-9756-A58D-74738A4E9497> /usr/lib/libncurses.5.4.dylib
0x998cd000 - 0x998daff7  com.apple.NetFS 3.2.2 (3.2.2) <DDC9C397-C35F-8D7A-BB24-3D1B42FA5FAB> /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
0x998db000 - 0x99978fe3  com.apple.LaunchServices 362.3 (362.3) <15B47388-16C8-97DA-EEBB-1709E136169E> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
0x99979000 - 0x99979ff7  com.apple.vecLib 3.6 (vecLib 3.6) <7362077A-890F-3AEF-A8AB-22247B10E106> /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib
0x9997a000 - 0x999bcff7  libvDSP.dylib 268.0.1 (compatibility 1.0.0) <3F0ED200-741B-4E27-B89F-634B131F5E9E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
0x999e4000 - 0x99a21ff7  com.apple.CoreMedia 0.484.52 (484.52) <62B0C876-A931-372F-8947-7CBA0379F427> /System/Library/PrivateFrameworks/CoreMedia.framework/Versions/A/CoreMedia
0x99a22000 - 0x99acffe7  libobjc.A.dylib 227.0.0 (compatibility 1.0.0) <9F8413A6-736D-37D9-8EB3-7986D4699957> /usr/lib/libobjc.A.dylib
0x99ad3000 - 0x99b09fff  libtidy.A.dylib ??? (???) <0FD72C68-4803-4C5B-3A63-05D7394BFD71> /usr/lib/libtidy.A.dylib
0x99b59000 - 0x99bc3fe7  libstdc++.6.dylib 7.9.0 (compatibility 7.0.0) <411D87F4-B7E1-44EB-F201-F8B4F9227213> /usr/lib/libstdc++.6.dylib
0x99cc1000 - 0x99d53fe7  com.apple.print.framework.PrintCore 6.3 (312.7) <7410D1B2-655D-68DA-D4B9-2C65747B6817> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
0xbb100000 - 0xbb103fe7  libLatinSuppConverter.dylib 49.0.0 (compatibility 1.0.0) <80CA35C5-AFBF-DD2D-B47B-9CE773B9CAEF> /System/Library/CoreServices/Encodings/libLatinSuppConverter.dylib
0xffff0000 - 0xffff1fff  libSystem.B.dylib ??? (???) <2DCD13E3-1BD1-6F25-119A-3863A3848B90> /usr/lib/libSystem.B.dylib

Model: iMac8,1, BootROM IM81.00C1.B00, 2 processors, Intel Core 2 Duo, 3.06 GHz, 2 GB, SMC 1.30f1
Graphics: NVIDIA GeForce 8800 GS, NVIDIA GeForce 8800 GS, PCIe, 512 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8C), Broadcom BCM43xx 1.0 (5.10.131.42.4)
Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Serial ATA Device: WDC WD5000AAKS-40YGA1, 465.76 GB
Parallel ATA Device: MATSHITADVD-R   UJ-875
USB Device: Built-in iSight, 0x05ac  (Apple Inc.), 0x8502, 0xfd400000 / 2
USB Device: Keyboard Hub, 0x05ac  (Apple Inc.), 0x1006, 0xfa200000 / 2
USB Device: Apple Keyboard, 0x05ac  (Apple Inc.), 0x0221, 0xfa220000 / 3
USB Device: BRCM2046 Hub, 0x0a5c  (Broadcom Corp.), 0x4500, 0x1a100000 / 2
USB Device: Bluetooth USB Host Controller, 0x05ac  (Apple Inc.), 0x820f, 0x1a110000 / 3
USB Device: IR Receiver, 0x05ac  (Apple Inc.), 0x8242, 0x5d100000 / 2
FireWire Device: Rugged FW/USB, LaCie, Up to 800 Mb/sec
On 26 Jun 2011, at 21:59, Ben Bolker wrote:

            

      
      
      
    

        

      
      
    

        
Dr. Christopher Philipson
Institute of Evolutionary Biology and Environmental Studies,
Winterthuerstrasse 190,
CH-8057,
Zurich
Tel:  00 41 44 635 61 29
Fax: 00 41 44 635 57 11
christopher.philipson at ieu.uzh.ch

  
  


  


      

    

    

      
      

        


  

        

      Ben Bolker
    

    

      
      #
    

  


  

      
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On 06/29/2011 03:24 AM, Christopher Philipson wrote:

            

      
      
      
    

        
Thanks.

  The core dump is not so useful (although perhaps one of the other lme4
authors will find it so), but bandwidth is cheap.

  Just for general information: we have had trouble, for some time now,
managing to set up the lme4a code (which has lots of shiny Rcpp stuff
under the surface) so that errors emanating from inside C++ code are
caught correctly and passed back to the R "surface" rather than crashing
R.  As in your case, the results seem to be platform-dependent.

   We have some examples to work on (and just lack time, and in my case
knowledge, to spend tracking down and fixing the problems), but another
example would still be welcome.

  Of course, even if the program "only" stops with an error rather than
crashing you will still have a problem (albeit a less annoying one), in
that the optimization heads to a point that produces NaNs.  In the
spirit of working around that problem, here are a couple of thoughts:

  * can you specify "better" starting values, e.g. by starting with the
fixed-effect analogue of the model above?  (Perhaps you are already
doing this.)
  * your model is very complicated.  I hope you have a big data set ...
does it work if you eliminate one or more of the random effects?  Can
you use that approach to sneak up on better starting values?
  * there doesn't seem to be anything in your model that wouldn't work
with nlme (i.e. no crossed random effects -- although if your data set
is big nlmer will probably be faster than nlme).  Have you tried it in
nlme, perhaps with a subset of the data to start?

            

      
      
      
    

        
_______________________________________________
R-sig-mixed-models at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

            

      
      
      
    

        
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