Dongseok Choi
2005-Jul-13 00:29 UTC
[R] How to increase memory for R on Soliars 10 with 16GB and 64bit R
Dear all, My machine is SUN Java Workstation 2100 with 2 AMD Opteron CPUs and 16GB RAM. R is compiled as 64bit by using SUN compilers. I trying to fit quantile smoothing on my data and I got an message as below.> fit1<-rqss(z1~qss(cbind(x,y),lambda=la1),tau=t1)Error in as.matrix.csr(diag(n)) : cannot allocate memory block of size 2496135168 The lengths of vector x and y are both 17664. I tried and found that the same command ran with x[1:16008] and y[1:16008]. So, it looks to me a memory related problem, but I'm not sure how I can allocate memory block. I read the command line option but not sure what do to with it. Could you help me on this? Thank you very much, Dongseok Choi, Ph.D. Assistant Professor Division of Biostatistics Department of Public Health & Preventive Medicine Oregon Health & Science University 3181 SW Sam Jackson Park Road, CB-669 Portland, OR 97239-3098 TEL) 503-494-5336 FAX) 503-494-4981 choid at ohsu.edu
Prof Brian Ripley
2005-Jul-13 07:03 UTC
[R] How to increase memory for R on Soliars 10 with 16GB and 64bit R
On Tue, 12 Jul 2005, Dongseok Choi wrote:> My machine is SUN Java Workstation 2100 with 2 AMD Opteron CPUs and 16GB RAM. > R is compiled as 64bit by using SUN compilers. > I trying to fit quantile smoothing on my data and I got an message as below. > >> fit1<-rqss(z1~qss(cbind(x,y),lambda=la1),tau=t1) > Error in as.matrix.csr(diag(n)) :cannot allocate memory block of size 2496135168> > The lengths of vector x and y are both 17664. > I tried and found that the same command ran with x[1:16008] and y[1:16008]. > So, it looks to me a memory related problem, but I'm not sure how I can allocate memory block. > I read the command line option but not sure what do to with it. > Could you help me on this?It is trying to allocate a single memory block of size over 2^31-1 bytes. R internally uses ints for sizes of vectors and that is a limit (see help("Memory-limits") ). However, it is intended that on 64-bit systems that there is a limit here of 8*(2^31-1) but there was a typo. Please change line 1534 of src/main/memory.c to #if SIZEOF_LONG > 4 and re-compile. -- 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
Dongseok Choi
2005-Jul-13 18:34 UTC
[R] How to increase memory for R on Soliars 10 with 16GB and 64bit R
Thank you very much for your help!! Now, it runs without any problem. Is it going to be fixed in the next release? Thanks again, Dongseok Dongseok Choi, Ph.D. Assistant Professor Division of Biostatistics Department of Public Health & Preventive Medicine Oregon Health & Science University 3181 SW Sam Jackson Park Road, CB-669 Portland, OR 97239-3098 TEL) 503-494-5336 FAX) 503-494-4981 choid at ohsu.edu>>> "Prof Brian Ripley" <ripley at stats.ox.ac.uk> 07/13/05 12:03 AM >>>On Tue, 12 Jul 2005, Dongseok Choi wrote:> My machine is SUN Java Workstation 2100 with 2 AMD Opteron CPUs and 16GB RAM. > R is compiled as 64bit by using SUN compilers. > I trying to fit quantile smoothing on my data and I got an message as below. > >> fit1<-rqss(z1~qss(cbind(x,y),lambda=la1),tau=t1) > Error in as.matrix.csr(diag(n)) :cannot allocate memory block of size 2496135168> > The lengths of vector x and y are both 17664. > I tried and found that the same command ran with x[1:16008] and y[1:16008]. > So, it looks to me a memory related problem, but I'm not sure how I can allocate memory block. > I read the command line option but not sure what do to with it. > Could you help me on this?It is trying to allocate a single memory block of size over 2^31-1 bytes. R internally uses ints for sizes of vectors and that is a limit (see help("Memory-limits") ). However, it is intended that on 64-bit systems that there is a limit here of 8*(2^31-1) but there was a typo. Please change line 1534 of src/main/memory.c to #if SIZEOF_LONG > 4 and re-compile. -- 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
Liaw, Andy
2005-Jul-14 10:35 UTC
[R] How to increase memory for R on Soliars 10 with 16GB and 64bit R
> From: Uwe Ligges > > Uwe Ligges wrote: > > > Dongseok Choi wrote: > > > >> Thank you very much for your help!! > >> Now, it runs without any problem. > >> > >> Is it going to be fixed in the next release? > > > > > > Of course, Brian > > [hmmm, looks like some wrong shortcut has been used - and it > must have > been me who forgot to drink coffee before strating to post ...]Is this indication that R-help is more addictive than coffee? Andy> > I meant to say: Of course, Brian already did, see the svn log: > > -------------------------------------------------------------- > ---------- > r34947 | ripley | 2005-07-13 03:16:18 -0400 (Wed, 13 Jul > 2005) | 1 line > Changed paths: > M /trunk/NEWS > M /trunk/src/main/memory.c > > correct typo for R_alloc on 64-bit systems > > > > > Uwe Ligges > > > > > >> Thanks again, > >> Dongseok > >> > >> > >> > >> > >> Dongseok Choi, Ph.D. > >> Assistant Professor > >> Division of Biostatistics > >> Department of Public Health & Preventive Medicine > >> Oregon Health & Science University > >> 3181 SW Sam Jackson Park Road, CB-669 > >> Portland, OR 97239-3098 > >> TEL) 503-494-5336 > >> FAX) 503-494-4981 > >> choid at ohsu.edu > >> > >> > >>>>> "Prof Brian Ripley" <ripley at stats.ox.ac.uk> 07/13/05 > 12:03 AM >>> > >> > >> > >> On Tue, 12 Jul 2005, Dongseok Choi wrote: > >> > >> > >>> My machine is SUN Java Workstation 2100 with 2 AMD > Opteron CPUs and > >>> 16GB RAM. > >>> R is compiled as 64bit by using SUN compilers. > >>> I trying to fit quantile smoothing on my data and I got > an message as > >>> below. > >>> > >>> > >>>> fit1<-rqss(z1~qss(cbind(x,y),lambda=la1),tau=t1) > >>> > >>> > >>> Error in as.matrix.csr(diag(n)) : > >> > >> > >> cannot allocate memory block of size 2496135168 > >> > >>> The lengths of vector x and y are both 17664. > >>> I tried and found that the same command ran with x[1:16008] and > >>> y[1:16008]. > >>> So, it looks to me a memory related problem, but I'm not > sure how I > >>> can allocate memory block. > >>> I read the command line option but not sure what do to with it. > >>> Could you help me on this? > >> > >> > >> > >> It is trying to allocate a single memory block of size over 2^31-1 > >> bytes. R internally uses ints for sizes of vectors and > that is a limit > >> (see help("Memory-limits") ). However, it is intended > that on 64-bit > >> systems that there is a limit here of 8*(2^31-1) but there was a > >> typo. Please change line 1534 of src/main/memory.c to > >> > >> #if SIZEOF_LONG > 4 > >> > >> and re-compile. > >> > > > > > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > >