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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
