[R] help debugging segfaults
Liaw, Andy
andy_liaw@merck.com
Thu, 13 Jun 2002 08:38:32 -0400
Hi all,
Thanks to Prof. Ripley, Prof. Gentleman, and Simon Wood (did I miss
anyone?). The problem seemed to have gone away.
Everyone suggested using some malloc debugger (such as Electric Fence). All
I did was following half of what BDR suggested below, i.e., changing all the
S_alloc() calls to Calloc() and Free(). I didn't get to try efence, and the
problem seems to have disappeared!
As I read it from the R-exts manual, the difference between S_alloc and
Calloc is that S_alloc takes memory from the heap, whereas Calloc takes
memory addtional to the heap. So can anyone explain what's going on? It's
still kind of mysterious to me...
Again, thanks very, very much for the help!
(Some day I might try to use .Call rather than .C, but I think I need to get
a bit more familiarity with .Call on simpler things before I try it with
randomForest.)
Regards,
Andy
> -----Original Message-----
> From: Prof Brian D Ripley [mailto:ripley@stats.ox.ac.uk]
> Sent: Wednesday, June 12, 2002 10:02 AM
> To: Liaw, Andy
> Cc: 'r-devel@stat.math.ethz.ch'
> Subject: Re: [R] help debugging segfaults
>
>
> (Confined to R-devel).
>
> This almost always means that R's memory system (or malloc's) has been
> corrupted by array overruns.
>
> Sometimes gctorture(TRUE) helps. However in your case it's
> more likely
> those S_alloc calls, so try (temporarily) replacing them by
> calls to Calloc
> and then use something like Purify or `Electric Fence'. to test for
> overruns.
>
> On Wed, 12 Jun 2002, Liaw, Andy wrote:
>
> > (Sorry for the cross-post--- I wasn't sure which list is more
> > appropriate...)
>
> Only a few people read R-devel and not R-help.
>
> > 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):
>
> This is just saying it can't allocate the copies for the returned
> values of the .C arguments. I think you might want to consider .Call
> given that you are probably using quite large structures.
>
> > 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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> --
> Brian D. Ripley, ripley@stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272860 (secr)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
>
>
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