Hi Matt,
what's your sessionInfo()? Can you try installing bigmemory as follows:
install.packages("bigmemory", repos="http://R-Forge.R-project.org";)
it'll get you the latest version, in which I cannot reproduce the
problem you're reporting (ie, after gc(), I get all the RAM back)
b
On Sat, Feb 6, 2010 at 7:37 PM, Matthew Keller <mckellerc...@gmail.com> wrote:
> Hi Steve and other R folks,
>
> Thanks for the suggestion. No - that doesn't work. I meant to put that
> into my original email. To recap
>
> x <-
> big.matrix(nrow=20000,ncol=500000,type='short',init=0,dimnames=list(1:20000,1:500000))
> #Gets around the 2^31 issue - yay!
> #R takes 18 Gb RAM, so says top
>
> rm(x) #top says R still takes 18Gb RAM
> gc() #top says R still takes 18Gb RAM
>
> How do I flush the memory? I thought maybe R/bigmemory would give up
> the RAM if it was needed elsewhere, but apparently not:
>
> y <-
> big.matrix(nrow=20000,ncol=500000,type='short',init=0,dimnames=list(1:20000,1:500000))
> #takes *another* 18Gb RAM, and takes it away from several other
> processes I had running - OUCH!
>
> Any help would be appreciated.
>
> As an aside, I just want to say "thank you" to the teams developing
> bigmemory, ff, and other packages meant to allow users of large
> datasets to still use R.
>
> Matt
>
>
>
> On Fri, Feb 5, 2010 at 9:27 PM, Steve Lianoglou
> <mailinglist.honey...@gmail.com> wrote:
>> Hi,
>>
>> On Fri, Feb 5, 2010 at 9:24 PM, Matthew Keller <mckellerc...@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
>>
>
>
>
> --
> Matthew C Keller
> Asst. Professor of Psychology
> University of Colorado at Boulder
> www.matthewckeller.com
>
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