[R] Re: help debugging segfaults

[Luke Tierney]

These symptoms suggest that your code may be writing outside of the
data it allocates, which would trash internal data structures of the R
heap and result in a segfault at a GC.  I would try to find a malloc
debugging library, use malloc in place of S_alloc, and see if the
malloc debugging tools show any malloc heap corruption. The standard
malloc in Mac OS X has very good debugging support if you have access
to that.

luke

On Wed, Jun 12, 2002 at 09:26:07AM -0400, Liaw, Andy wrote:
> (Sorry for the cross-post--- I wasn't sure which list is more
> appropriate...)
> 
> Hi everyone,
> 
> I've run into segfaults when using my randomForest package on large dataset
> (e.g., 100 x 15200) and large number of trees (e.g., ntree=7000 and
> mtry=3000).  I'm wondering if anyone can give me some hints on where to look
> for the problem.
> 
> The randomForest package mainly consists of two things: rf.c contains rf(),
> a C wrapper function that calls the Fortran subroutines in rfsub.f that do
> most of the work (slightly altered from Breiman's original code).  All
> memory allocations are done in rf.c, using S_alloc().  When I run random
> forest with the data and setting as mentioned above, it was able to finish
> growing the 7000 trees, but segfault when returning from rf() to R.  GDB
> gave the following (gdb prompts removed):
> 
> do_dotCode (call=0x873aff4, op=0x8a5f620, args=0x8a5d010, env=0x86fd0a4)
>     at dotcode.c:1413
> 1413            break;
> 1845        PROTECT(ans = allocVector(VECSXP, nargs));
> 1846        havenames = 0;
> 1847        if (dup) {
> 1849            info.cargs = cargs;
> 1850            info.allArgs = args;
> 1851            info.nargs = nargs;
> 1852            info.functionName = buf;
> 1853            nargs = 0;
> 1854            for (pargs = args ; pargs != R_NilValue ; pargs =
> CDR(pargs)) {
> 1855                if(argConverters[nargs]) {
> 1864                    PROTECT(s = CPtrToRObj(cargs[nargs], CAR(pargs),
> which));
> 
> Program received signal SIGSEGV, Segmentation fault.
> 0x080ddc6a in RunGenCollect (size_needed=1515400) at memory.c:1133
> 1133                    SEXP next = NEXT_NODE(s);
> 
> This is obtained on Linux (Mandrake 8.2 w/enterprise kernel 2.4.8) running
> on dual P3-866 Xeon with 2GB RAM, using R-1.5.0 compiled from source.
> 
> Any help/hints/comments are greatly appreciated!
> 
> Regards,
> Andy
> 
> Andy I. Liaw, PhD
> Biometrics Research          Phone: (732) 594-0820
> Merck & Co., Inc.              Fax: (732) 594-1565
> P.O. Box 2000, RY70-38            Rahway, NJ 07065
> mailto:andy_liaw at merck.com
> 
> 
> 
> ------------------------------------------------------------------------------
> Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.
> 
> ==============================================================================
> 
> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> r-devel mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !)  To: r-devel-request at stat.math.ethz.ch
> _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._

-- 
Luke Tierney
University of Minnesota                      Phone:           612-625-7843
School of Statistics                         Fax:             612-624-8868
313 Ford Hall, 224 Church St. S.E.           email:      luke at stat.umn.edu
Minneapolis, MN 55455 USA                    WWW:  http://www.stat.umn.edu
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._