Fair enough, thanks for your time. I will wait for my Linux PCs! -----Original Message----- From: Duncan Murdoch [mailto:murd...@stats.uwo.ca] Sent: 16 September 2009 16:42 To: michael watson (IAH-C) Cc: r-help@r-project.org Subject: Re: [R] Memory in R on windows running 64bit XP
On 9/16/2009 10:54 AM, michael watson (IAH-C) wrote: > Hi Duncan > > Many thanks for the reply. Here are the results of the commands: > >> Rprofmem() > Error in Rprofmem() : memory profiling is not available on this system >> memory.size(NA) > [1] 3500 >> memory.size() > [1] 16.19 > > > Clearly Rprofmem() is a dead end, though if there is some way of enabling it, > I will be happy to. I forgot that you need to recompile R to enable it. Not impossible, but probably not worth the trouble just for this problem. Using gcinfo(TRUE) may give you enough information: it will report whenever there's a garbage collection. > I am only actually using 16.19Mb of memory, as all I do is open R and read in > some data (a 2.7Mb text file). I would guess that mclust does a lot of other allocations before it fails. > I am not sure how to guard against the memory fragmentation problem. The > machine has 16Gb of RAM and I am only running R and Internet Explorer, but I > don't know if that helps. Is there a way to deliver contiguous memory to R? R doesn't give you any real control over that. I would guess that R is getting 3.5 Gb in a contiguous chunk based on your memory.size report, but then it is fragmenting it. > Is 64bit R available for Windows? Sorry to bang on about Windows, I'm > waiting for my IT department to build Linux machines, and this is what I have > in the meantime. Revolution Computing sells one. There's no (reliable) 64 bit version of gcc for Windows, so we don't distribute one. Duncan Murdoch > > Thanks > Mick > > ________________________________________ > From: Duncan Murdoch [murd...@stats.uwo.ca] > Sent: 16 September 2009 15:43 > To: michael watson (IAH-C) > Cc: r-help@r-project.org > Subject: Re: [R] Memory in R on windows running 64bit XP > > On 9/16/2009 10:16 AM, michael watson (IAH-C) wrote: >> Hi >> I'm running 32-bit R on Windows XP 64bit and the machine has 16Gb of RAM. >> The help for memory.limit states: >> >> If 32-bit R is run on some 64-bit versions of Windows the maximum value of >> obtainable memory is just under 4GB. >> >> So, using the help which states the size parameter can go up to 4095: >> >> memory.limit(size=4095) >> >> When I run mclust I get: >> >> Error: cannot allocate vector of size 1.3 Gb >> >> So, now I set the max-mem-size flag: >> >> --max-mem-size=3500M >> >> Repeat and I still get the same error: >> >> Error: cannot allocate vector of size 1.3 Gb >> >> So, can anyone help? 32 bit R is reported to be able to use up to 4Gb of >> RAM on 64 bit windows, yet mine croaks at 1.3Gb. > > You are misreading things in a couple of places. The most important one > is the error message: it says allocation of a 1.3 Gb object failed. You > may have 4 Gb available in total, but have used so much of it already > that Windows won't allocate a 1.3 Gb piece to R. Using Rprofmem() might > show how the allocations are happening. > > Another possibility is that your particular version of Windows doesn't > support giving 4 Gb to R. Run memory.size(NA) to find out the limit, > memory.size() to find out the current amount in use. > > And even if the limit is close to 4 Gb and you have more than 1.3 Gb > free, the allocation may fail because there is no sufficiently large > contiguous block available. Once memory is allocated, that address is > in use and is unavailable. Since the 32 bit address space only covers 4 > Gb, you can fairly easily end up with allocations that are spread out > across it leaving no large blocks available. That's the advantage of > switching to 64 bit R: even if you still only had 4 Gb of memory > available, the address space is so much bigger that fragmentation > probably won't be a problem. > > Duncan Murdoch > >> >>> sessionInfo() >> R version 2.9.2 (2009-08-24) >> i386-pc-mingw32 >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >> Kingdom.1252;LC_MONETARY=English_United >> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] mclust_3.3.1 >> >> Thanks >> Mick >> >> ______________________________________________ >> 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. ______________________________________________ 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.
