From andy_liaw@merck.com  Tue Jun 18 14:25:02 2002
From: andy_liaw@merck.com (Liaw, Andy)
Date: Tue, 18 Jun 2002 09:25:02 -0400
Subject: can't find array overruns (was: help debugging segfaults)
Message-ID: <51F9C42DA15CD311BD220008C707D81906FFC389@usrymx10.merck.com>

Dear R-devel,

Last week I got several responses to my question about debugging segfaults
in my code (original post below).  After I changed the S_alloc() calls to
Calloc()/Free(), the symptom was gone, but I was told to keep looking.  So I
did:

o  Switched to Calloc/Free.  Electric Fence did not find any problem.

o  Put assert(index < bound); assert(index >=0); everywhere in the C routine
where arrays are accessed.  Everything ran fine.  (I did not (don't really
know easy way to) do the same thing for the Fortran subroutines (mostly
Breiman's original code) called by the C function.

o Changed to malloc()/free().  Still didn't find anything with Electric
Fence.

Can some one suggest how to proceed?  Is it still not save to assume the bug
is gone?

Regards,
Andy

> -----Original Message-----
> From: Liaw, Andy [mailto:andy_liaw@merck.com]
> Sent: Wednesday, June 12, 2002 9:26 AM
> To: 'r-devel@stat.math.ethz.ch'; 'r-help@stat.math.ethz.ch'
> Subject: [R] help debugging segfaults
> 
> 
> (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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can't find array overruns (was: help debugging segfaults)
Liaw, Andy