Le lundi 29 octobre 2012 à 12:01 +0530, Purna chander a écrit : > Dear Milan, > > Thank you for telling about gc(). > > I'm using R 2.15.1. It's session info is displayed below: > > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: i686-redhat-linux-gnu (32-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > ** I'm working with 3GB RAM. How can I use the available memory to > optimize my goal. Well, I gave you one idea, but for us to tell you more you need to give us the code you are using. A better solution would be to spend some money to buy more RAM, given it's quite cheap these days, and to install a 64-bit version of Linux and R, if your computer supports it.
Regards > On 10/26/12, Milan Bouchet-Valat <nalimi...@club.fr> wrote: > > Le jeudi 25 octobre 2012 à 15:02 +0530, Purna chander a écrit : > >> Dear All, > >> > >> > >> My main objective was to compute the distance of 100000 vectors from a > >> set having 900 other vectors. I've a file named "seq_vec" containing > >> 100000 records and 256 columns. > >> While computing, the memory was not sufficient and resulted in error > >> "cannot allocate vector of size 152.1Mb" > >> > >> So I've approached the problem in the following: > >> Rather than reading the data completely at a time, I read the data in > >> chunks of 20000 records using scan() function. After reading each > >> chunk, I've computed distance of each of these vectors with a set of > >> another vectors. > >> > >> Even though I was successful in computing the distances for first 3 > >> chunks, I obtained similar error (cannot allocate vector of size > >> 102.3Mb). > >> > >> Q) Here what I could not understand is, how come memory become > >> insufficient when dealing with 4th chunk? > >> Q) Suppose if i computed a matrix 'm' during calculation associated > >> with chunk1, then is this matrix not replaced when I again compute 'm' > >> when dealing with chunk 2? > > R's memory management is relatively complex, i.e. objects are not always > > replaced in memory, they are only garbage collected from time to time. > > You may try to call gc() after each chunk to limit memory fragmentation, > > which help reducing allocation problems a little. > > > > But please tell us how many RAM you have on the machine you're using, > > and post the output of sessionInfo(). > > > > > > Regards > > ______________________________________________ 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.
