From ross at biostat.ucsf.edu  Sun Feb 25 23:21:44 2007
From: ross at biostat.ucsf.edu (Ross Boylan)
Date: Sun, 25 Feb 2007 14:21:44 -0800
Subject: [Rd] R/C++/memory leaks
In-Reply-To: <39CFDB8F-918C-48FB-9A6D-D8055D828C13@ic.ac.uk>
References: <39CFDB8F-918C-48FB-9A6D-D8055D828C13@ic.ac.uk>
Message-ID: <20070225222144.GA16188@wheat.betterworld.us>

On Sun, Feb 25, 2007 at 05:37:24PM +0000, Ernest Turro wrote:
> Dear all,
> 
> I have wrapped a C++ function in an R package. I allocate/deallocate  
> memory using C++ 'new' and 'delete'. In order to allow user  
> interrupts without memory leaks I've moved all the delete statements  
> required after an interrupt to a separate C++ function freeMemory(),  
> which is called using on.exit() just before the .C() call.

Do you mean that you call on.exit() before the .C, and the call to
on.exit() sets up the handler?  Your last sentence sounds as if you
invoke freeMemory() before the .C call.

Another approach is to associate your C objects with an R object, and
have them cleaned up when the R object gets garbage collected.
However, this requires switching to a .Call interface from the more
straightforward .C interface.

The finalizer call I used doesn't assure cleanup on exit. The optional
argument to R_RegisterCFinalizerEx might provide such assurance, but I
couldn't tell what it really does.  Since all memory should
be released by the OS, when the process ends, I wasn't so worried
about that.


Here's the pattern:
// I needed R_NO_REMAP to avoid name collisions.  You may not.
#define R_NO_REMAP 1
#include <R.h>
#include <Rinternals.h>

extern "C" {
// returns an |ExternalPtr|
SEXP makeManager(
	@<makeManager args@>);


// user should not need to call
// cleanup
void finalizeManager(SEXP ptr);

}

SEXP makeManager(
	@<makeManager args@>){
    // .... stuff

    Manager* pmanager = new Manager(pd, pm.release(), 
    	*INTEGER(stepNumerator), *INTEGER(stepDenominator),
    	(*INTEGER(isexact)) != 0);
    
    // one example didn't use |PROTECT()|
    SEXP ptr;
    Rf_protect(ptr = R_MakeExternalPtr(pmanager, R_NilValue, R_NilValue));
    R_RegisterCFinalizer(ptr, (R_CFinalizer_t) finalizeManager);
    Rf_unprotect(1);
    return ptr;

}

void finalizeManager(SEXP ptr){
  Manager *pmanager = static_cast<Manager *>(R_ExternalPtrAddr(ptr));
  delete pmanager;
  R_ClearExternalPtr(ptr);
}

I'd love to hear from those more knowledgeable about whether I did
that right, and whether the FinalizerEx call can assure cleanup on
exit.

Make manager needes to be called from R like this
      mgr <- .Call("makeManager", args)

> 
> I am concerned about the following. In square brackets you see R's  
> total virtual memory use (VIRT in `top`):
> 
> 1) Load library and data [178MB] (if I run gc(), then [122MB])
> 2) Just before .C [223MB]
> 3) Just before freeing memory [325MB]
So you explicitly call your freeMemory() function?
> 4) Just after freeing memory [288MB]
There are at least 3 possibilities:
  * your C++ code is leaking
  * C++ memory is never really returned (Commonly, at least in C, the
  amount of memory allocated to the process never goes down, even if
  you do a free.  This may depend on the OS and the specific calls the
  program makes.
  * You did other stuff in R  that's still around.  After all you went
  up +45MB between 1 and 2; maybe it's not so odd you went up +65MB
  between 2 and 4.
> 5) After running gc() [230MB]
> 
> So although the freeMemory function works (frees 37MB), R ends up  
> using 100MB more after the function call than before it. ls() only  
> returns the data object so no new objects have been added to the  
> workspace.
> 
> Do any of you have any idea what could be eating this memory?
> 
> Many thanks,
> 
> Ernest
> 
> PS: it is not practical to use R_alloc et al because C++ allocation/ 
> deallocation involves constructors/destructors and because the C++  
> code is also compiled into a standalone binary (I would rather avoid  
> maintaining two separate versions).

I use regular C++ new's too (except for the external pointer that's
returned).  However, you can override the operator new in C++ so that
it uses your own allocator, e.g., R_alloc.  I'm not sure about all the
implications that might make that dangerous (e.g., can the memory be
garbage collected?  can it be moved?).  Overriding new is a bit tricky
since there are several variants.  In particular, there is one with
and one without an exception.  Also, invdividual classes can define
their own new operators; if you have any, you'd need to change those
too.

Ross Boylan



[Rd] R/C++/memory leaks
Ross Boylan