[R] .Call and to reclaim the memory by allocVector

Yongchao Ge Yongchao.Ge at mssm.edu
Thu Aug 23 20:36:08 CEST 2007


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
cp <- function(a, b) .Call("crossprod2", a, b)
gc() #i

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 



> 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

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