[R] RAM Filling up

From: Thomas Allen <hedbag_at_gmail.com>
Date: Sat, 01 Mar 2008 11:44:01 +1300


Hi

I'm using Ubuntu 7.10 with 2GB RAM and a 2GB partition of the HDD set aside as a swap drive.

I'm trying to write programs which are quite RAM intensive and as such I sometimes run out of RAM and the process is killed.

At the moment I'm storing much data on disk, reading it in to a datastructure, processing it, then writing it out again. Finally the datastructure is removed with rm() in an effort to free up the RAM before reading in more data.

Unfortunately, memory still fills up over time. It seems R copies objects for various reasones and then doesn't release the memory later.
Do I need to call gctorture() or something?

There should be a more clever way to manage memory allocation and release in R (I just haven't found it yet).

Also, what's the best way to observe when R is releasing memory? Rprof only seems to record memory allocations and not memory release (or am I blind?)

What I'm really asking is what are some really informative memory management tools for observing and controlling memory usage in R on a unix based system?

Kind regards

Tom

-- 
Thomas Allen
Department of Biochemistry
University of Otago
email1: hedbag_at_gmail.com
email2: allth025_at_student.otago.ac.nz
Work: (+64)3 479 5123
Mobile: 027 321 4269

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Received on Fri 29 Feb 2008 - 23:00:23 GMT

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