On Mon, 17 Jan 2011, Simon Urbanek wrote:
On Jan 16, 2011, at 10:41 PM, Simon Wotherspoon wrote:
I believe there is a memory leak in isoreg in the current version of R, as I
believe the following shows
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 120405 3.3 350000 9.4 350000 9.4
Vcells 78639 0.6 786432 6.0 392463 3.0
for(k in 1:100) {
+
+ y <- runif(10000)
+ isoreg(x,y)
+ }
rm(x)
rm(y)
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 121637 3.3 350000 9.4 350000 9.4
Vcells 578615 4.5 1300721 10.0 1300642 10.0
^^^
Looking at the C code, I believe the problem arises as a consequence of using
SETLENGTH to resize the result near the very end of isoreg.c,
and the solution is to make a copy of iKnots.
Using SETLENGTH in this way is definitely not intended -- only code in
memory.c should use it (and for now in envir.c). We should fix shis
use, and one other strange one in grevents.c, and probably should get
rid of it SETLENGTH altogether outside of memory.c.
Best,
luke
AFAICS this is more of a reporting issue than a memory leak -
ReleaseLargeFreeVectors() uses LENGTH() to determine the number by which to
reduce R_LargeVallocSize - and it will be smaller than the actually released
memory if SETLENGTH was used. I'm not sure how to fix it, because AFAICS the
real size is not recorded anywhere (unless we use truelength for that but I'm
not sure I know the implications). The good news is that it's not really a
memory leak - the bad news is that the memory usage stats are rather an upper
bound of the reality ;).
Cheers,
Simon
SEXP R_isoreg(SEXP y)
{
int n = LENGTH(y), i, ip, known, n_ip;
double tmp, slope;
SEXP yc, yf, iKnots, ans;
const char *anms[] = {"y", "yc", "yf", "iKnots", ""};
/* unneeded: y = coerceVector(y, REALSXP); */
PROTECT(ans = mkNamed(VECSXP, anms));
SET_VECTOR_ELT(ans, 0, y = y);
SET_VECTOR_ELT(ans, 1, yc = allocVector(REALSXP, n+1));
SET_VECTOR_ELT(ans, 2, yf = allocVector(REALSXP, n));
SET_VECTOR_ELT(ans, 3, iKnots= allocVector(INTSXP, n));
... calculation ...
SETLENGTH(iKnots, n_ip);
UNPROTECT(1);
return(ans);
}
But if this is the problem, I am at a bit of a loss as to what SETLENGTH is
actually for in general.
Clearly my understanding of how allocation/gc works is a bit off here, but I
can't see how else the leak may occur. Hope this is more use than nuisance.
Simon.
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Luke Tierney
Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
