From luke@stat.umn.edu  Wed Jun 12 15:07:57 2002
From: luke@stat.umn.edu (Luke Tierney)
Date: Wed, 12 Jun 2002 09:07:57 -0500
Subject: help debugging segfaults
In-Reply-To: <51F9C42DA15CD311BD220008C707D81906FFC351@usrymx10.merck.com>; from andy_liaw@merck.com on Wed, Jun 12, 2002 at 09:26:07AM -0400
References: <51F9C42DA15CD311BD220008C707D81906FFC351@usrymx10.merck.com>
Message-ID: <20020612090756.C12694@nokomis.stat.umn.edu>

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@merck.com
> 
> 
> 
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-- 
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@stat.umn.edu
Minneapolis, MN 55455 USA                    WWW:  http://www.stat.umn.edu
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help debugging segfaults
Luke Tierney