can't find array overruns (was: help debugging segfaults)
Liaw, Andy
andy_liaw@merck.com
Tue, 18 Jun 2002 09:25:02 -0400
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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