Re: [R] Memory Management under Linux
Dear Jim,
Thanks for your attention. I am running a geostatistic analysis with geoR that
is computational intense. At the end my analysis I call the function
krige.control and krige.conv. Do you have any idea how to improve the memory
allocation in Linux?
Thanks,
Ricardo
De: jim holtman
Assunto: Re: [R] Memory Management under Linux
Para: "ricardo souza"
Cc: r-help@r-project.org
Data: Sexta-feira, 5 de Novembro de 2010, 10:21
It would be very useful if you would post some information about what
exactly you are doing. There si something with the size of the data
object you are processing ('str' would help us understand it) and then
a portion of the script (both before and after the error message) so
we can understand the transformation that you are doing. It is very
easy to generate a similar message:
> x <- matrix(0,2, 2)
Error: cannot allocate vector of size 3.0 Gb
but unless you know the context, it is almost impossible to give
advice. It also depends on if you are in some function calls were
copies of objects may have been made, etc.
On Thu, Nov 4, 2010 at 7:52 PM, ricardo souza wrote:
> 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 35 9.4 35 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 50 13.4 25200 50 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.
>
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[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.
[R] improve R memory under linux
Dear Jonathan, It is not small, I passed the wrong information. I am running a geostatistic analysis with geoR that is computational intense. At the end my analysis I call the function krige.control and krige.conv. However, what call my attention is that I have a friend that was able to run the same code with his MAC 5 years old (OS 32 with 4 Gb of memory). Reading several email list I discovered that MAC has better library than repository in linux, but we can in increase the memory allocation in linux. I do not know how Below is the memory allocation for a MAC 32 of 4 Gb Ran. I know that it depends of the machine but it is far way better than in linux. Why? How to improve it in linux? Memory allocation in a laptop 4 years old MAC: > gc() used (Mb) gc trigger ( Mb) max used (Mb) Ncells 481875 25.8 984024 52.6 984024 52.6 Vcells 481512 3.7 140511341 1072.1 641928461 4897.6 Memory allocation in a new laptop Linux 4Gb 32 Ubuntu: >gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 170934 4.6 35 9.4 35 9.4 Vcells 195920 1.5 786432 6.0 781384 6.0 Thanks for your attention, Ricardo De: Jonathan P Daily Assunto: Re: [R] improve R memory under linux Para: "ricardo souza" Cc: r-help@r-project.org, r-help-boun...@r-project.org Data: Sexta-feira, 5 de Novembro de 2010, 13:36 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: To: r-help@r-project.org Date: 11/05/2010 11:29 AM Subject: [R] improve R memory under linux Sent by: r-help-boun...@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 35 9.4 35 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 50 13.4 25200 50 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, [[elided Yahoo spam]] 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]] __ 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.
[R] 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 35 9.4 35 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 50 13.4 25200 50 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.
[R] Memory Management 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 35 9.4 35 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 50 13.4 25200 50 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.
