Hi,
I am not sure if this is a bug and I apologize if it is something I
didn't read carefully in the R extension manual. My initial search on the
R help and R devel list archive didn't find useful information.
I am using .Call (as written in the R extension manual) for the C code
and have found that the .Call didn't release the memory claimed by
allocVector. Even after applying gc() function and removing the R object
created by the .Call function, the memory was still not reclaimed back to
the operating system.
Here is an example. It was modified from the convolve2 example from the R
extension manual. Now I am computing the crossproduct of a and b, which
returns a vector of size length(a)*length(b).
The C code is at the end of this message with the modification commented.
The R code is here
----------------------------
dyn.load("crossprod2.so")
cp <- function(a, b) .Call("crossprod2", a, b)
gctorture()
a<-1:10000
b<-1:1000
gc() #i
c<-cp(a,b)
rm(c)
gc() #ii
--------------
When I run the above code in a fresh start R (version 2.5.0)
the gc() inforamation is below. I report the last column ("max
used (Mb)" ) here, which agrees the linux command "ps aux". Apparently
even after I removing the object "c", we still have un-reclaimed 70M bytes
of memory, which is approximately the memory size for the object "c".
If I run the command "c<-cp(a,b)" for three or four times and then remove the
object "c" and apply gc() function, the unclaimed memory can reach 150M
bytes. I tried gc(reset=TRUE), and it doesn't seem to make difference.
Can someone suggest what caused this problem and what the solution will
be? When you reply the email, please cc to me as I am not on the help
list.
Thanks,
Yongchao
------------------------------------------------
> dyn.load("crossprod2.so")
> cp <- function(a, b) .Call("crossprod2", a, b)
> gctorture()
> a<-1:10000
> b<-1:1000
> gc() #i
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 173527 4.7 467875 12.5 350000 9.4
Vcells 108850 0.9 786432 6.0 398019 3.1
>
> c<-cp(a,b)
> rm(c)
> gc() #ii
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 233998 6.3 467875 12.5 350000 9.4
Vcells 108866 0.9 12089861 92.3 10119856 77.3
>
-----------------------------------------------
--------------------------------------------
#include "R.h"
#include "Rinternals.h"
#include "Rdefines.h"
SEXP crossprod2(SEXP a, SEXP b);
//modified from convolve2 in the R extension
//R CMD SHLIB crossprod2.c
#include <R.h>
#include <Rinternals.h>
SEXP crossprod2(SEXP a, SEXP b)
{
R_len_t i, j, na, nb, nab;
double *xa, *xb, *xab;
SEXP ab;
PROTECT(a = coerceVector(a, REALSXP));
PROTECT(b = coerceVector(b, REALSXP));
na = length(a); nb = length(b);
//nab = na + nb - 1;
nab=na*nb;// we are doing the cross product
PROTECT(ab = allocVector(REALSXP, nab));
xa = REAL(a); xb = REAL(b);
xab = REAL(ab);
for(i = 0; i < nab; i++) xab[i] = 0.0;
for(i = 0; i < na; i++)
for(j = 0; j < nb; j++) //xab[i + j] += xa[i] * xb[j];
xab[i*nb + j] += xa[i] * xb[j];//we are computing crossproduct
UNPROTECT(3);
return(ab);
}
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