[R] memory problem

Huntsinger, Reid reid_huntsinger at merck.com
Wed Dec 8 18:06:29 CET 2004

OK, I would do the following:

1. Watch memory usage as the program runs, both within R and at the OS level
for the R process. I suppose your code allocates memory (eg with "new")
within the R process but the R memory manager knows nothing about it. So you
can tell where memory is leaking, if at all.

2. write a dummy .so to return constant values, doing no computation, but
using the same interface. If you still have the problem then you have a
problem with the R code.

If this got me nowhere I would start R under gdb and look around. The
"Writing R Extensions" has a section on this.


-----Original Message-----
From: Samuel Kemp [mailto:sam.kemp2 at ntlworld.com] 
Sent: Wednesday, December 08, 2004 11:46 AM
To: Huntsinger, Reid
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] memory problem


Here is some more information.....

My platform is a Linux desktop.

The C++ code implements a Gamma test which is calculated by constructing 
near neighbour lists (kd-tree) - the C++ code returns the deltas and 
gammas, the R code gets the noise estimate of the data by doing a linear 
regression on these deltas and gammas. However, at the end of my C++ 
code I do delete all objects on the free store.

This Gamma test code should be called 16,000 times but R crashes after 
about 14,000, with "killed".

Huntsinger, Reid wrote:

>Some additional details would help. What platform? What does the C++ code
>that might cause a memory leak? How are you calling it? 
>I don't see why unloading the library would free memory even if it were
>allocated outside R's memory management. Unless you're using Windows you
>don't need to worry about allocating memory for R, just check that there
>no limits on memory allocation set by the administrator. 
>Reid Huntsinger 
>-----Original Message-----
>From: r-help-bounces at stat.math.ethz.ch
>[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Samuel Kemp
>Sent: Wednesday, December 08, 2004 6:29 AM
>To: r-help at stat.math.ethz.ch
>Subject: [R] memory problem
>I am trying to run a very computationally expensive procedure in 
>R-2.0.0. and the process always gets killed after approx 8 minutes. This 
>procedure calls some of my own C++ code - in case it was this code 
>causing a memory leak I unload and then reload the .so file every time, 
>however I still get the same problem. The procedure is run 16000 times 
>and always calls the lm() function. My believe at the moment is that I 
>need to allocate more memory for R - is this correct? I did try envoking 
>R from the command line using R --min-vsize=1000M, however still no luck.
>I have googled around and looked at the help files, but I am still 
>confused about how to fix this problem.
>Any insight would be greatly appeciated.
>Kind Regards,
>R-help at stat.math.ethz.ch mailing list
>PLEASE do read the posting guide!
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