Jim,
On Sep 14, 2011, at 5:21 PM, 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()
>
This seems a little optimistic to me - at least on the machines most mortals
have - since it will allocate ~93GB of memory - before rm/gc:
vmmap:
VIRTUAL ALLOCATION BYTES
MALLOC ZONE SIZE COUNT ALLOCATED % FULL
=========== ======= ========= ========= ======
DefaultMallocZone_0x1004cf000 62.8M 120044 93.5G 152363%
environ_0x100601000 1024K 27 1280 0%
=========== ======= ========= ========= ======
TOTAL 63.8M 120071 93.5G 149977%
ps:
UID PID PPID CPU PRI NI VSZ RSS WCHAN STAT TT TIME COMMAND
501 26287 26170 0 31 0 100511220 64864 - S+ s002 1:06.81
/Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R
fortunately it's never used, so it's actually possible (purely virtual). But as
Matt said, it gets released without problems - after rm/gc:
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 433341 23.2 667722 35.7 597831 32.0
Vcells 630031 4.9 1300721 10.0 1211088 9.3
VIRTUAL ALLOCATION BYTES
MALLOC ZONE SIZE COUNT ALLOCATED % FULL
=========== ======= ========= ========= ======
DefaultMallocZone_0x1004cf000 59.3M 19083 36.6M 61%
environ_0x100601000 1024K 27 1280 0%
=========== ======= ========= ========= ======
TOTAL 60.3M 19110 36.6M 60%
501 26287 26170 0 31 0 2522872 60880 - S+ s002 1:35.69
/Library/Frameworks/R.framework/Resources/bin/exec/x86_64/R
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
> 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.
>
You didn't mention your OS - some OSes do not release memory immediately (some
wait until you try to allocate new memory) and some can't release certain type
of memory at all. Also depending on your OS allocation library you can get more
info about the allocation pool to understand what is going on. But for that
you'd have to share with us the platform info ...
> thanks much in advance, to me it really resembles the connection.c code, but
> what am I missing?
>
Cheers,
Simon
PS: This has nothing to do with your question but I'd suggest checking the
result on malloc [e.g.,
if (!vector) Rf_error("unable to allocate %d bytes", i);
Also i = asInteger(size) is much more safe (and convenient) than i =
INTEGER(size)[0] and completely irrelevantly as.integer(1000000) is more
efficiently written as 1000000L.
> thanks, jim
>
>
> [[alternative HTML version deleted]]
>
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>
>
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