From ross at biostat.ucsf.edu  Mon Feb 26 07:43:36 2007
From: ross at biostat.ucsf.edu (Ross Boylan)
Date: Sun, 25 Feb 2007 22:43:36 -0800
Subject: [Rd] R/C++/memory leaks
In-Reply-To: <F3C922F3-4B4C-4DA9-84E1-F17B52302BCB@ic.ac.uk>
References: <39CFDB8F-918C-48FB-9A6D-D8055D828C13@ic.ac.uk>
	<20070225222144.GA16188@wheat.betterworld.us>
	<F3C922F3-4B4C-4DA9-84E1-F17B52302BCB@ic.ac.uk>
Message-ID: <20070226064336.GL5871@wheat.betterworld.us>

Here are a few small follow-up comments:
On Sun, Feb 25, 2007 at 11:18:56PM +0000, Ernest Turro wrote:
> 
> On 25 Feb 2007, at 22:21, Ross Boylan wrote:
> 
> >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.
> >
> 
> " 'on.exit' records the expression given as its argument as needing
>      to be executed when the current function exits (either naturally
>      or as the result of an error)."
> 
> 
> This means you call on.exit() somewhere at the top of the function.  
> You are guaranteed the expression you pass to on.exit() will be  
> executed before the function returns. So, even though you call on.exit 
> () before .C(), the expression you pass it will actually be called  
> after .C().
> 
> This means you can be sure that freeMemory() is called even if an  
> interrupt or other error occurs.
> 
> 
> >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.
[details snipped]
> 
> Since this is a standalone C++ program too, I'd rather use the R API  
> as little as possible... But I will look at your solution if I find  
> it is really necessary.. Thanks

The use of the R api can be confined to a wrapper function.  But I can
think of no reason that a change to the alternate approach I outlined
would solve the apparent leaking you describe.

> 
> >>
> >>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?
> 
> This is called thanks to on.exit()
> 
> >>4) Just after freeing memory [288MB]
> >There are at least 3 possibilities:
> >  * your C++ code is leaking
> 
> The number of news and deletes are the same, and so is their  
> branching... I don't think it is this.
> 
> >  * 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.
> 
> OK, but the memory should be freed after the process completes,
> surely?

Most OS's I know will free memory when a process finishes, except for
shared memory.  But is that relevant?  I assume the process doesn't
complete until you exit R.  Your puzzle seems to involve different
stages within the life of a single process.

> 
> >  * 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.
> 
> Yep, I do stuff before .C and that accounts for the increase  
> before .C. But all the objects created before .C go out of scope by  
> 4) and so, after gc(), we should be back to 122MB. As I mentioned, ls 
> () after 5) returns only the data loaded in 1).

In principle (and according to ?on.exit) the expression registered by
on.exit is evaluated when the relevant function is exited.  In
principle garbage collection reclaims all unused space (though with no
guarantee of when).

It may be that the practice is looser than the principle.  For example,
Python always nominally managed memory for you, but I think for
quite awhile it didn't really reclaim the memory (because garbage
collection didn't exist or had been turned off).


> 
> >>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.
> >
> 
> That sounds rather dangerous!
At least tedious to get right.  My statements weren't intended as a
recommendation of this approach; I was just pointing out R_alloc and
C++ allocation could probably be fit together.  If your C++ program
isn't doing anything exotic with memory management there are probably
4 operators to redefine ( [singleton and array allocation] x
[exception specification present or absent]).  Oops, you'd need to get
the delete's as well...

> 
> Thanks very much for your thoughts, though.
> 
You could also try some memory leak detector on the problem to narrow
it down.

> >Ross Boylan
> >
> 
> 
> Ernest



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