> dim(data)[1] 22283 19> dm=dist(data, method = "euclidean", diag = FALSE, upper = FALSE, p = 2)Error: cannot allocate vector of size 1.8 Gb Hi Guys, thank you in advance for helping. :-D Recently I ran into the "cannot allocate vector of size 1.8GB" error. I am pretty sure this is not a hardware limitation because it happens no matter I ran the R code in a 2.0Ghz Core Duo 2GB ram Mac or on a Intel Xeon 2x2.0Ghz quard-core 8GB ram Linux server. I also tried to clear the workspace before running the code too, but it didn't seem to help... Weird thing though is that once in a while it will work, but next when I run clustering on the above result>hc=hclust(dm, method = "complete", members=NULL)it give me the same error... I searched around already, but the memory.limit, memory.size method does not seem to help. May I know what can i do to resolve this problem? Thank you so much for your help. -- View this message in context: http://www.nabble.com/Error%3A-cannot-allocate-vector-of-size-1.8-Gb-tp21133949p21133949.html Sent from the R help mailing list archive at Nabble.com.
I hope the following info will help, thanks again!> sessionInfo()R version 2.7.1 (2008-06-23) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- View this message in context: http://www.nabble.com/Error%3A-cannot-allocate-vector-of-size-1.8-Gb-tp21133949p21137233.html Sent from the R help mailing list archive at Nabble.com.
On Mon, 22 Dec 2008, iamsilvermember wrote:> >> dim(data) > [1] 22283 19 > >> dm=dist(data, method = "euclidean", diag = FALSE, upper = FALSE, p = 2) > Error: cannot allocate vector of size 1.8 GbThat would be an object of size 1.8Gb. See ?"Memory-limits"> > > > Hi Guys, thank you in advance for helping. :-D > > Recently I ran into the "cannot allocate vector of size 1.8GB" error. I am > pretty sure this is not a hardware limitation because it happens no matter I > ran the R code in a 2.0Ghz Core Duo 2GB ram Mac or on a Intel Xeon 2x2.0Ghz > quard-core 8GB ram Linux server.Why? Both will have a 3GB address space limits unless the Xeon box is 64-bit. And this works on my 64-bit Linux boxes.> I also tried to clear the workspace before running the code too, but it > didn't seem to help... > > Weird thing though is that once in a while it will work, but next when I run > clustering on the above result >> hc=hclust(dm, method = "complete", members=NULL) > it give me the same error...See ?"Memory-limits" for the first part.> I searched around already, but the memory.limit, memory.size method does not > seem to help. May I know what can i do to resolve this problem?What are you going to do with an agglomerative hierarchical clustering of 22283 objects? It will not be interpretible.> Thank you so much for your help.-- 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
>What are you going to do with an agglomerative hierarchical clustering of22283 objects? It will not be interpretible. As a matter of fact I was ask to do a clustering analysis on gene expression. Something http://www.ncbi.nlm.nih.gov/projects/geo/gds/analyze/analyze.cgi?datadir=UCorrelationUPGMA&ID=GDS3254&myType=0 Like this>Why? Both will have a 3GB address space limits unless the Xeon box is64-bit. And this works on my 64-bit Linux boxes. I am pretty sure the linux server is 64bit. Sorry I am just a beginner in R. I read the "memory-limit" help you suggested, but I still cannot find a solution to my problem... May I know if there is any work around for this issue? Thank you so much again! -- View this message in context: http://www.nabble.com/Error%3A-cannot-allocate-vector-of-size-1.8-Gb-tp21133949p21149727.html Sent from the R help mailing list archive at Nabble.com.