similar to: R memory allocation in Linux

Dear all, I am using ubuntu linux 32 with 4 Gb.  I am running a very small script and I always got the same error message:  CAN NOT ALLOCATE A VECTOR OF SIZE 231.8 Mb. I have reading carefully the instruction in ?Memory.  Using the function gc() I got very low numbers of memory (please sea below).  I know that it has been posted several times at r-help

Dear all, I am using ubuntu linux 32 with 4 Gb.  I am running a very small script and I always got the same error message:  CAN NOT ALLOCATE A VECTOR OF SIZE 231.8 Mb. I have reading carefully the instruction in ?Memory.  Using the function gc() I got very low numbers of memory (please sea below).  I know that it has been posted several times at r-help

Dear all, I am using ubuntu linux 32 with 4 Gb.  I am running a very small script and I always got the same error message:  CAN NOT ALLOCATE A VECTOR OF SIZE 231.8 Mb. I have reading carefully the instruction in ?Memory.  Using the function gc() I got very low numbers of memory (please sea below).  I know that it has been posted several times at r-help

Dear R-ers, somehow it is not possible to increase nsize to more than 20000k. When I specify e.g. > R --vsize=10M --nsize=21000K the result is: free total (Mb) Ncells 99658 350000 6.7 Vcells 1219173 1310720 10.0 Maybe I have overlooked s.th.... Marcus -- +------------------------------------------------------- | Marcus Eger | E-Mail: eger.m at gmx.de (NEW) |

I have a question concerning memory. I understood that R takes a fixed amount of memory at startup (which I can influence with --vsize --nsize) and that gc() shows the memory still free of the total memory reserved for R. However, if I create a long vector of character data, gc() only seem to reflect the space needed for a vector of pointers to char, the space used for the character data itself

Dear Group I'm still trying to bring many data into R (see older postings). After solving some troubles with the database I do most of the work in MySQL. But still I could be nice to work on some data using R. Therefore I can use a dedicated Server with Gentoo Linux as OS hosting only R. This Server is a nice machine with two CPU and 4GB RAM which should do the job: Dual Intel XEON 3.06 GHz

Hello everyone - I have a couple of questions about memory management of large objects. Thanks in advance for your response. I'm running R version 1.9.1 on solaris 8, compiled as a 32 bit app. My system has 12.0 GB of memory, with usually ~ 11GB free. I checked system limits using ulimit, and there is nothing set that would limit the maximum amount of memory for a process (with the

Hi, I am trying to minimize a rather complex function of 5 parameters with gafit and nlm. Besides some problems with both optimization algorithms (with respect to consistantly generating similar results), I tried to run this optimization about a hundred times for yet two other parameters. Unfortunately, as the log below shows, during that batch process R starts to eat up all my RAM,

I am running R version ??? under Redhat 5.2. It seems as though the --nsize object has no effct on the size of the allocated Ncells as determined using gc(). Yes, I have that much data.... That is if I envoke R with R --vsize 100 --nsize 5000000 then type gc() I get free total Ncells 92202 200000 Vcells 12928414 13107200 Thanks Tony Long Ecology and Evolutionary Biology Steinhaus

Just wanted to start a discussion on whether R could ship with more appropriate GC parameters. Right now, loading the recommended package Matrix leads to: > library(Matrix) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1076796 57.6 1368491 73.1 1198505 64.1 Vcells 1671329 12.8 2685683 20.5 1932418 14.8 Results may vary, but here R needed 64MB of N cells and 15MB

Martin Morgan discussed this a year or so ago and as I recall bumped up these values to the current defaults. I don't recall details about why we didn't go higher -- maybe Martin does. I suspect the main concern would be with small memory machines in student labs and less developed countries. If there was a way on all platforms to identify how much memory is available that might help to

I don't know whether this belongs to r-devel or rather r-help. Under RW1.11 --nsize=8M --vsize=512M I could n <- 500000 m <- 20 x <- matrix(rnorm(n*m), ncol=m, nrow=n) gc() > n <- 500000 > m <- 20 > x <- matrix(rnorm(n*m), ncol=m, nrow=n) > gc() free total (Mb) Ncells 8190509 8388608 160 Vcells 57033698 67108864 512 # under RW1.20 --vanilla

I am trying to upload into R 143 Affymetrix chips onto using R on the NIH Nimbus server. I can load 10 chips without a problem, however, when I try to load 143 I receive a error message: cannot create a vector of 523263 KB. I have expanded the memory of R as follows: R --min-vsize=10M --max-vsize=2500M --min-nsize=10M -max-nsize=50M (as specified in help in R). After running this command the

Dear all, I am working on a 64 bits Linux system. I issue the following R commands: > rm(list=ls()) # To remove all objects in the workspace. > gc() # To free memory. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124250 6.7 350000 18.7 350000 18.7 Vcells 124547 1.0 786432 6.0 476934 3.7 > gc() # I had to do it again, don't know why! used (Mb) gc trigger (Mb) max used (Mb) Ncells

Full_Name: Viktor Moravetski Version: Version 1.2.0 (2000-12-13) OS: Win-NT 4.0 SP5 Submission from: (NULL) (209.128.81.199) I've started R (v.1.20) with command: rgui --vsize 450M --nsize 40M Then at the command prompt: > gc() used (Mb) gc trigger (Mb) Ncells 358534 9.6 41943040 1120 Vcells 3469306 26.5 58982400 450 >df <- data.frame(x=1:30000,y=2,z=3)

Hi, when doing as.double() on an object that is already a double, the object seems to be copied internally, doubling the memory requirement. See example below. Same for as.character() etc. Is this intended? Example: % R --vanilla > x <- double(1e7) > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 234019 6.3 467875 12.5 350000 9.4 Vcells 10103774 77.1

No. But it has not been posted either. You got that message because you sent your message to the wrong address. You should have sent it to r-help at r-project.org You had probably sent it to r-help-request at r-project.org which would have had the effect that the server would have tried to interpret the contents of you message as commands (e.g. to unsubscribe, change your subscription

Windows users note: the rw-faq says |1.8) Can I use rw0xx with ESS and emacs? | |Yes. Some time soon versions of ESS (5.1.3 has a `somewhat rough' |prototype for rw0632) will come with support for this version of R. If |yours does not, edit essd-r.el to have | | (inferior-ess-start-args . "--ess")) | |and make sure you give the full path to Rterm.exe as the R executable.

I am using ESS on a unix system for my analysis. My R environment contains a 90118 by 94 dataframe. I am trying to calculate the mean of a column in this data frame and I am getting the following error: Error: can not allocate a vector of size 704 Kb I have tried options(memory=1000000000000000000) and this does not help. when I call gc() this is what is returned > gc() used

I've looked through all of the posts about this issue (and there are plenty!) but I am still unable to solve the error. ERROR: cannot allocate vector of size 455 Mb I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am randomly assigned to a x86_64 node. I am using package GenABEL. My data (~ 650,000