Hi Emmanuel, Try the following:
1) removing unnecessary programs from memory, this might give u a larger contiguous memory block for R 2) remove unnecessary data from R's memory, so many of the preceding data sets U no longer need can be removed. use the rm() command. U might need to run gc() after this to insure the new memory is available 3) make sure U've assigned as much memory to R as possible using memory.size() And make sure u have r's Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling, and Training (mobile) 0410 689 945 ch...@trickysolutions.com.au -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Emmanuel Bellity Sent: Monday, 17 January 2011 4:53 AM To: r-help@r-project.org Subject: [R] Memory issues Hi, I have read several threads about memory issues in R and I can't seem to find a solution to my problem. I am running a sort of LASSO regression on several subsets of a big dataset. For some subsets it works well, and for some bigger subsets it does not work, with errors of type "cannot allocate vector of size 1.6Gb". The error occurs at this line of the code: example <- cv.glmnet(x=bigmatrix, y=price, nfolds=3) It also depends on the number of variables that were included in "bigmatrix". I tried on R and R64 for both Mac and R for PC but recently went onto a faster virtual machine on Linux thinking I would avoid any memory issues. It was better but still had some limits, even though memory.limit indicates "Inf". Is there anyway to make this work or do I have to cut a few variables in the matrix or take a smaller subset of data ? I have read that R is looking for some contiguous bits of memory and that maybe I should pre-allocate the matrix ? Any idea ? Many thanks Emmanuel [[alternative HTML version deleted]] ______________________________________________ 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.
