[R] auditing R's memory usage

[jim holtman]

Here is a function I use to look at the size of objects:

######################start
my.ls <- function (pos = 1, sorted = FALSE, envir = as.environment(pos))
{
    .result <- sapply(ls(envir = envir, all.names = TRUE),
function(..x) object.size(eval(as.symbol(..x),
        envir = envir)))
    if (sorted) {
        .result <- rev(sort(.result))
    }
    .ls <- as.data.frame(rbind(as.matrix(.result), `**Total` = sum(.result)))
    names(.ls) <- "Size"
    .ls$Size <- formatC(.ls$Size, big.mark = ",", digits = 0,
        format = "f")
    .ls$Mode <- c(unlist(lapply(rownames(.ls)[-nrow(.ls)], function(x)
mode(eval(as.symbol(x),
        envir = envir)))), "-------")
    .ls
}
#########################end







> # create some large objects
> x <- matrix(0, 3000, 3000)
> my.ls()
              Size    Mode
x       72,000,112 numeric
**Total 72,000,112 -------
> gc()
           used (Mb) gc trigger (Mb) max used (Mb)
Ncells   684078 18.3    1368491 36.6  1368491 36.6
Vcells 10198339 77.9   11581078 88.4 10200979 77.9
> # make another one
> y <- matrix(0, 5000, 5000)
> my.ls()
               Size    Mode
x        72,000,112 numeric
y       200,000,112 numeric
**Total 272,000,224 -------
> gc()
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells   684087  18.3    1368491  36.6  1368491  36.6
Vcells 35198359 268.6   39143593 298.7 35201440 268.6
>




On Fri, May 4, 2012 at 12:49 PM, Alexander Shenkin <ashenkin at ufl.edu> wrote:
> Hi Folks,
>
> I'm running 32-bit R 2.14 in RStudio on my Win 7 x64 system with 8GB
> RAM.  I'm getting memory problems as R wants to swallow more than the
> 4GB limit.
>
> I think I'm stuck at 4GB as I have to use 32-bit R for a number of
> packages (ODBC, etc).  However, I doubt I really need to be using that
> much memory - I'm probably being very sloppy in my memory management,
> leaving lots of temporary dataframes around, etc.
>
> I'm looking for suggestions about how to audit R's memory usage.  Yes, I
> could go around my code and tie up every loose end.  But in the interest
> of efficiency, I'm wondering about ways I might more intelligently audit
> R's memory usage.  Are there any tools that can tell me what objects are
> swallowing what amounts of memory?  Armed with that information, I can
> go track down the worst culprits.
>
> Thanks,
> Allie
>
> ______________________________________________
> R-help at 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.



-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.