Re: [R] Memory Management under Linux
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 ricsouz...@yahoo.com.br 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?
__
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.
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 jholt...@gmail.com
Assunto: Re: [R] Memory Management under Linux
Para: ricardo souza ricsouz...@yahoo.com.br
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 ricsouz...@yahoo.com.br 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.
Re: [R] Memory Management under Linux
I would do some monitoring (debugging) of the script by placing some 'gc()'
calls in the sequence of statements leading to the problem to see what the
memory usage is at that point. Take a close look at the sizes of your
objects. If it is happening in some function you have called, you may have
to take a look and understand if multiple copies are being made. Most
problems of this type may require that you put hooks in your code (most of
the stuff that I write has it in so I can isolate performance problems) to
gain an understanding of what is happening when. To improve memory
allocation, you first have to understand what is causing the problem, and
enough information has not been provided so that I could make a comment on
it. There are lots of rules of thumb that can be used, but many depend on
exactly what you are trying to do.
On Fri, Nov 5, 2010 at 2:59 PM, ricardo souza ricsouz...@yahoo.com.brwrote:
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 jholt...@gmail.com
Assunto: Re: [R] Memory Management under Linux
Para: ricardo souza ricsouz...@yahoo.com.br
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
ricsouz...@yahoo.com.brhttp://mc/compose?to=ricsouz...@yahoo.com.br
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 0.71310720 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 http://mc/compose?to=r-h...@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.htmlhttp://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?
--
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.
