From ripley@stats.ox.ac.uk  Wed Jun 12 15:01:56 2002
From: ripley@stats.ox.ac.uk (Prof Brian D Ripley)
Date: Wed, 12 Jun 2002 15:01:56 +0100 (BST)
Subject: [R] help debugging segfaults
In-Reply-To: <51F9C42DA15CD311BD220008C707D81906FFC351@usrymx10.merck.com>
Message-ID: <Pine.GSO.4.44.0206121453430.12434-100000@auk.stats>

(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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[R] help debugging segfaults
Prof Brian D Ripley