[R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

[ivo welch]

dear R experts:

I am of course no R experts, but use it regularly.  I thought I would
share some experimentation  with memory use.  I run a linux machine
with about 4GB of memory, and R 2.5.0.

upon startup, gc() reports

         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 268755 14.4     407500 21.8   350000 18.7
Vcells 139137  1.1     786432  6.0   444750  3.4

This is my baseline.  linux 'top' reports 48MB as baseline.  This
includes some of my own routines that are always loaded.  Good..


Next, I created a s.csv file with 22 variables and 500,000
observations, taking up an uncompressed disk space of 115MB.  The
resulting object.size() after a read.csv() is 84,002,712 bytes (80MB).

> s= read.csv("s.csv");
> object.size(s);

[1] 84002712


here is where things get more interesting.  after the read.csv() is
finished, gc() reports

           used (Mb) gc trigger  (Mb) max used  (Mb)
Ncells   270505 14.5    8349948 446.0 11268682 601.9
Vcells 10639515 81.2   34345544 262.1 42834692 326.9

I was a big surprised by this---R had 928MB intermittent memory in
use.  More interestingly, this is also similar to what linux 'top'
reports as memory use of the R process (919MB, probably 1024 vs. 1000
B/MB), even after the read.csv() is finished and gc() has been run.
Nothing seems to have been released back to the OS.

Now,

> rm(s)
> gc()
         used (Mb) gc trigger  (Mb) max used  (Mb)
Ncells 270541 14.5    6679958 356.8 11268755 601.9
Vcells 139481  1.1   27476536 209.7 42807620 326.6

linux 'top' now reports 650MB of memory use (though R itself uses only
15.6Mb).  My guess is that It leaves the trigger memory of 567MB plus
the base 48MB.


There are two interesting observations for me here:  first, to read a
.csv file, I need to have at least 10-15 times as much memory as the
file that I want to read---a lot more than the factor of 3-4 that I
had expected.  The moral is that IF R can read a .csv file, one need
not worry too much about running into memory constraints lateron.  {R
Developers---reducing read.csv's memory requirement a little would be
nice.  of course, you have more than enough on your plate, already.}

Second, memory is not returned fully to the OS.  This is not
necessarily a bad thing, but good to know.

Hope this helps...

Sincerely,

/iaw