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memory problem in handling large dataset

2 messages · Weiwei Shi, Bert Gunter

Original
Weiwei Shi
# 
Dear Listers:
I have a question on handling large dataset. I searched R-Search and I
hope I can get more information as to my specific case.

First, my dataset has 1.7 billion observations and 350 variables,
among which, 300 are float and 50 are integers.
My system has 8 G memory, 64bit CPU, linux box. (currently, we don't
plan to buy more memory).
_
platform i686-redhat-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    2
minor    1.1
year     2005
month    06
day      20
language R


If I want to do some analysis for example like randomForest on a
dataset, how many max observations can I load to get the machine run
smoothly?

After figuring out that number, I want to do some sampling first, but
I did not find read.table or scan can do this. I guess I can load it
into mysql and then use RMySQL do the sampling or use python to subset
the data first. My question is, is there a way I can subsample
directly from file just using R?

Thanks,
--
Weiwei Shi, Ph.D

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III
Bert Gunter
# 
I think the general advice is that around 1/4 or 1/3 of your available
memory is about the largest data set that R can handle -- and often
considerably less depending upon what you do and how you do it (because R's
semantics require explicitly copying objects rather than passing pointers).
Fancy tricks using environments might enable you to do better, but that
requires advice from a true guru, which I ain't.

See ?connections, ?scan, ?seek  for reading in a file a chunk at a time from
a connection, thus enabling you to sample one line of data from each chunk,
say.

I suppose you could do this directly with repeated calls to scan() or
read.table() by skipping more and more lines at the beginning at each call,
but I assume that is horridly inefficient and would take forever.

HTH.

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box