Simon Wood snw at st-and.ac.uk http://www.ruwpa.st-and.ac.uk/simon.html
The Mathematical Institute, North Haugh, St. Andrews, Fife KY16 9SS UK
Direct telephone: (0)1334 463799 Indirect fax: (0)1334 463748
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 at merck.com
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