R help - Nov 2010 - improve R memory under 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
(http://tolstoy.newcastle.edu.au/R/help/05/06/7565.html#7627qlink2).  However I
did not find yet the solution to improve my memory issue in Linux.  Somebody
cold please give some instruction how to improve my memory under linux?
> gc()
         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 170934  4.6     350000  9.4   350000  9.4
Vcells 195920  1.5     786432  6.0   781384  6.0

INCREASING THE R MEMORY FOLLOWING THE INSTRUCTION IN  ?Memory

I started R with:

R --min-vsize=10M --max-vsize=4G --min-nsize=500k
--max-nsize=900M
> gc()
         used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 130433  3.5     500000 13.4      25200   500000 13.4
Vcells  81138  0.7    1310720 10.0         NA   499143  3.9

It increased but not so much! 

Please, please let me know.  I have read all r-help about this matter, but not
solution. Thanks for your attention!

Ricardo


      
	[[alternative HTML version deleted]]

A "very small script" should fit just fine in an email: what are you 
trying to do?

Likely, you are assigning many small variables in some loop. Even if you 
have 4GB of RAM available, if R assigns 3.99 GB of it and then then a call 
comes in to assign something of size .02, it will tell you it can't 
allocate an object of size .02.
--------------------------------------
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
"Is the room still a room when its empty? Does the room,
 the thing itself have purpose? Or do we, what's the word... imbue it."
     - Jubal Early, Firefly



From:
ricardo souza <ricsouzabh@yahoo.com.br>
To:
r-help@r-project.org
Date:
11/05/2010 11:29 AM
Subject:
[R] improve R memory under linux
Sent by:
r-help-bounces@r-project.org



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 (
http://tolstoy.newcastle.edu.au/R/help/05/06/7565.html#7627qlink2).  
However I did not find yet the solution to improve my memory issue in 
Linux.  Somebody cold please give some instruction how to improve my 
memory under linux? 
> gc()
         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 170934  4.6     350000  9.4   350000  9.4
Vcells 195920  1.5     786432  6.0   781384  6.0

INCREASING THE R MEMORY FOLLOWING THE INSTRUCTION IN  ?Memory

I started R with:

R --min-vsize=10M --max-vsize=4G --min-nsize=500k
--max-nsize=900M
> gc()
         used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 130433  3.5     500000 13.4      25200   500000 13.4
Vcells  81138  0.7    1310720 10.0         NA   499143  3.9

It increased but not so much! 

Please, please let me know.  I have read all r-help about this matter, but 
not solution. Thanks for your attention!

Ricardo


 
                 [[alternative HTML version deleted]]

______________________________________________
R-help@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.



	[[alternative HTML version deleted]]