James,
Works for me!
In a file, 'test.c', I have:
void h5R_allocate_finalizer(SEXP eptr) {
char* vector = (char*) R_ExternalPtrAddr(eptr);
free(vector);
printf("memory freed at address %lu\n", (long unsigned) vector);
R_ClearExternalPtr(eptr);
}
SEXP h5R_allocate(SEXP size) {
int i = INTEGER(size)[0];
char* vector = (char*) malloc(i*sizeof(char));
printf("memory allocated at address %lu\n", (long unsigned) vector);
SEXP e_ptr = R_MakeExternalPtr(vector, R_NilValue, R_NilValue);
R_RegisterCFinalizerEx(e_ptr, h5R_allocate_finalizer, TRUE);
return e_ptr;
}
I generated the shared library with R CMD SHLIB. Then, at the R prompt:
R> dyn.load('test.so')
R> system(paste('ps -eo pid,vsz | grep', Sys.getpid()))
10961 77160
R> v <- .Call('h5R_allocate', as.integer(2^24))
memory allocated at address 140127935406096
R> system(paste('ps -eo pid,vsz | grep', Sys.getpid()))
10961 93548
R> rm(v); gc()
memory freed at address 140127935406096
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 132769 7.1 350000 18.7 350000 18.7
Vcells 129312 1.0 786432 6.0 555216 4.3
R> system(paste('ps -eo pid,vsz | grep', Sys.getpid()))
10961 77160
It appears that the external pointer is behaving as expected. However, I
did find that gc() may not immediately collect the removed object 'v'.
Sometimes it took more than one call. In any case, the memory was freed
when R exits.
Best,
Matt
On Wed, 2011-09-14 at 21:21 +0000, James Bullard wrote:
> I'm using external pointers and seemingly leaking memory. My determination of
> a memory leak is that the R process continually creeps up in memory as seen
> by top while the usage as reported by gc() stays flat. I have isolated the C
> code:
>
> void h5R_allocate_finalizer(SEXP eptr) {
> Rprintf("Calling the finalizer\n");
> void* vector = R_ExternalPtrAddr(eptr);
> free(vector);
> R_ClearExternalPtr(eptr);
> }
>
> SEXP h5R_allocate(SEXP size) {
> int i = INTEGER(size)[0];
> char* vector = (char*) malloc(i*sizeof(char));
> SEXP e_ptr = R_MakeExternalPtr(vector, R_NilValue, R_NilValue);
> R_RegisterCFinalizerEx(e_ptr, h5R_allocate_finalizer, TRUE);
> return e_ptr;
> }
>
>
> If I run an R program like this:
>
> v <- replicate(100000, {
> .Call("h5R_allocate", as.integer(1000000))
> })
> rm(v)
> gc()
>
> Then you can see the problem (top reports that R still has a bunch of memory,
> but R doesn't think it does). I have tried using valgrind and it says I have
> memory left on the table at the end lest you think it is because top. Also, I
> have tried Free/Calloc as well and this doesn't make a difference. Finally, I
> see this in both R-2-12 (patched) and R-2-13 - I think it is more an
> understanding issue on my part.
>
> thanks much in advance, to me it really resembles the connection.c code, but
> what am I missing?
>
> thanks, jim
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> 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
