R help - Feb 2010 - question about bigmemory: releasing RAM from a big.matrix that isn't used anymore

Hi all,

I'm on a Linux server with 48Gb RAM. I did the following:

x <-
big.matrix(nrow=20000,ncol=500000,type='short',init=0,dimnames=list(1:20000,1:500000))
#Gets around the 2^31 issue - yeah!

in Unix, when I hit the "top" command, I see R is taking up about 18Gb
RAM, even though the object x is 0 bytes in R. That's fine: that's how
bigmemory is supposed to work I guess. My question is how do I return
that RAM to the system once I don't want to use x any more? E.g.,

rm(x)

then "top" in Unix, I expect that my RAM footprint is back ~0, but it
remains at 18Gb. How do I return RAM to the system?

Thanks,

Matt



-- 
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com

Hi,

On Fri, Feb 5, 2010 at 9:24 PM, Matthew Keller <mckellercran at gmail.com>
wrote:
> Hi all,
>
> I'm on a Linux server with 48Gb RAM. I did the following:
>
> x <-
big.matrix(nrow=20000,ncol=500000,type='short',init=0,dimnames=list(1:20000,1:500000))
> #Gets around the 2^31 issue - yeah!
>
> in Unix, when I hit the "top" command, I see R is taking up about
18Gb
> RAM, even though the object x is 0 bytes in R. That's fine: that's
how
> bigmemory is supposed to work I guess. My question is how do I return
> that RAM to the system once I don't want to use x any more? E.g.,
>
> rm(x)
>
> then "top" in Unix, I expect that my RAM footprint is back ~0,
but it
> remains at 18Gb. How do I return RAM to the system?
Maybe forcing R to do garbage collection might help?

Try calling `gc()` after your call to `rm(x)` and see what `top` tells you.

Did that do the trick?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

>>> See inline for responses.  But people are always welcome to contact
>>> us directly.
Hi all,

I'm on a Linux server with 48Gb RAM. I did the following:

x <-
big.matrix(nrow=20000,ncol=500000,type='short',init=0,dimnames=list(1:20000,1:500000))
#Gets around the 2^31 issue - yeah!
>>> We strongly discourage use of dimnames.
in Unix, when I hit the "top" command, I see R is taking up about 18Gb
RAM, even though the object x is 0 bytes in R. That's fine: that's how
bigmemory is supposed to work I guess. My question is how do I return
that RAM to the system once I don't want to use x any more? E.g.,

rm(x)

then "top" in Unix, I expect that my RAM footprint is back ~0, but it
remains at 18Gb. How do I return RAM to the system?
>>> It can take a while for the OS to free up memory, even after a
gc().
>>> But it's available for re-use; if you want to be really sure,
have a
look
>>> in /dev/shm to make sure the shared memory segments have been
>>> deleted.
Thanks,

Matt

-- 
John W. Emerson (Jay)
Associate Professor of Statistics
Department of Statistics
Yale University
http://www.stat.yale.edu/~jay <http://www.stat.yale.edu/%7Ejay>

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