R help - Aug 2006 - Memory usage decreases drastically after save workspace, quit, restart, load workspace

Dear all,

I have the following problem:

  - I have written a program in R which runs out of physical memory  
on my MacBook Pro with 1.5 GB RAM

  - The memory usage is much higher then I would expect from the  
actual data in my global environment

  - When I save the workspace, quit R, restart R and load the  
workspace again, memory usage is much less then before
    (~50 MB instead of ~1.5 GB), although nothing seems to be missing.

  - It doesn't seem to be possible to reduce the amount of memory  
used by calling gc()

  - the behavior is independent of if I use R in command line or from  
GUI, so I can exclude a problem of the Mac GUI

Any suggestions what the problem might be or how I could debug this?

Thanks in advance for any help.

Best regards,
Klaus


platform       i386-apple-darwin8.6.1
arch           i386
os             darwin8.6.1
system         i386, darwin8.6.1
status
major          2
minor          3.1
year           2006
month          06
day            01
svn rev        38247
language       R
version.string Version 2.3.1 (2006-06-01)

On Sat, 26 Aug 2006, Klaus Thul wrote:
> Dear all,
> 
> I have the following problem:
> 
>   - I have written a program in R which runs out of physical memory  
> on my MacBook Pro with 1.5 GB RAM
How does R know about physical memory on a virtual-memory OS?  I presume 
the symptom is swapping by your OS, but how do you attribute that to R?
>   - The memory usage is much higher then I would expect from the  
> actual data in my global environment
> 
>   - When I save the workspace, quit R, restart R and load the  
> workspace again, memory usage is much less then before
>     (~50 MB instead of ~1.5 GB), although nothing seems to be missing.
> 
>   - It doesn't seem to be possible to reduce the amount of memory  
> used by calling gc()
> 
>   - the behavior is independent of if I use R in command line or from  
> GUI, so I can exclude a problem of the Mac GUI
> 
> Any suggestions what the problem might be or how I could debug this?
How are you measuring memory usage?

If this is by gc(), note that lazyloading is one-way, and memory increases 
after you use a lazyloaded object in a session.  This can be dramatic 
where datasets are involved.

If you are asking the OS about memory usage, return of memory to the OS is 
a rather haphazard and OS-specific issue.  On some OSes virtual memory is 
not actually reclaimed from applications until it is needed (or ever).

It is certainly possible that something you are using has a memory leak, 
but valgrind has been used to plug those on the most-used parts of R.


I at least need more precise indications of what you observed to be able 
to comment more.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595