I got a long list of error message repeating with the following 3
lines when running the loop at the end of this mail:
R(580,0xa000ed88) malloc: *** vm_allocate(size=327680) failed (error
code=3)
R(580,0xa000ed88) malloc: *** error: can't allocate region
R(580,0xa000ed88) malloc: *** set a
It seems the problem lies in this line:
try(fit.lme - lme(Beta ~ group*session*difficulty+FTND, random =
~1|Subj, Model), tag - 1);
As lme fails for most iterations in the loop, the 'try' function
catches one error message for each failed iteration. But the puzzling
part is, why does the
Hi,
My computer has 2GB of ram and I also request 2GB of virtual ram from c
drive, therefore totally I have 4GB of ram. Before I open R workshop, I
also add C:\Program Files\R\R-2.5.0\bin\Rgui.exe
--max-mem-size=3000Mb--max-vsize=3000Mb into the target of R by right
clicking the R
Unfortunatelly, i have to fill all the cells, with numbers..., so I need a
better machine, or i have to split the data for smaller
parts, but that way is much slower, but i see i dont have other alternative
way.
But thanx for your help, because i work with big networks too (1
vertex), and
On Sat, 6 Jan 2007, Zoltan Kmetty wrote:
Hi!
I had some memory problem with R - hope somebody could tell me a solution.
I work with very large datasets, but R cannot allocate enough memoty to
handle these datasets.
You haven't said what you want to do with these datasets.
-thomas
UweL == Uwe Ligges [EMAIL PROTECTED]
on Sun, 07 Jan 2007 09:42:08 +0100 writes:
UweL Zoltan Kmetty wrote:
Hi!
I had some memory problem with R - hope somebody could
tell me a solution.
I work with very large datasets, but R cannot allocate
enough
Zoltan Kmetty wrote:
Hi!
I had some memory problem with R - hope somebody could tell me a solution.
I work with very large datasets, but R cannot allocate enough memoty to
handle these datasets.
I want work a matrix with row= 100 000 000 and column=10
A know this is 1 milliard
: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Uwe Ligges
Sent: Sunday, January 07, 2007 3:42 AM
To: Zoltan Kmetty
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] memory problem
Zoltan Kmetty wrote:
Hi!
I had some memory problem with R - hope somebody could tell me a
solution.
I work
Hi!
I had some memory problem with R - hope somebody could tell me a solution.
I work with very large datasets, but R cannot allocate enough memoty to
handle these datasets.
I want work a matrix with row= 100 000 000 and column=10
A know this is 1 milliard cases, but i thought R could handle
Kolder [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch; N.C. Onland-moret [EMAIL PROTECTED]
Sent: Monday, December 18, 2006 7:48:23 PM
Subject: RE: [R] Memory problem on a linux cluster using a large data set
[Broadcast]
In addition to my off-list reply to Iris (pointing her to an old post
On Thu, 21 Dec 2006, Iris Kolder wrote:
Thank you all for your help!
So with all your suggestions we will try to run it on a computer with a
64 bits proccesor. But i've been told that the new R versions all work
on a 32bits processor. I read in other posts that only the old R
versions
Section 8 of the Installation and Administration guide says that on
64-bit architectures the 'size of a block of memory allocated is
limited to 2^32-1 (8 GB) bytes'.
The wording 'a block of memory' here is important, because this sets a
limit on a single allocation rather than the memory consumed
Hello,
I have a large data set 320.000 rows and 1000 columns. All the data has the
values 0,1,2.
I wrote a script to remove all the rows with more than 46 missing values. This
works perfect on a smaller dataset. But the problem arises when I try to run it
on the larger data set I get an error
Iris --
I hope the following helps; I think you have too much data for a
32-bit machine.
Martin
Iris Kolder [EMAIL PROTECTED] writes:
Hello,
I have a large data set 320.000 rows and 1000 columns. All the data
has the values 0,1,2.
It seems like a single copy of this data set will be at
In addition to my off-list reply to Iris (pointing her to an old post of
mine that detailed the memory requirement of RF in R), she might
consider the following:
- Use larger nodesize
- Use sampsize to control the size of bootstrap samples
Both of these have the effect of reducing sizes of trees
Roger == Roger Bivand [EMAIL PROTECTED]
on Sat, 2 Dec 2006 22:11:12 +0100 (CET) writes:
Roger On Sat, 2 Dec 2006, Dylan Beaudette wrote:
Hi Stephano,
Roger Looks like you used my example verbatim
Roger (http://casoilresource.lawr.ucdavis.edu/drupal/node/221)
Roger :)
Hi Stephano,
Looks like you used my example verbatim
(http://casoilresource.lawr.ucdavis.edu/drupal/node/221)
:)
While my approach has not *yet* been published, the original source [4] by
Roger Bivand certainly has. Just a reminder.
That said, I would highly recommend reading up on the
On Sat, 2 Dec 2006, Dylan Beaudette wrote:
Hi Stephano,
Looks like you used my example verbatim
(http://casoilresource.lawr.ucdavis.edu/drupal/node/221)
:)
From exchanges on R-sig-geo, I believe the original questioner is feeding
NAs to clara, and the error message in clara() is overrunning
hi to all,
frustated for this error, to day i buy a 1 GB memory
slot for my laptop
now it have 1,28GB instead the old 512, but i've the
same error :-(
damn!damn!how can i do?
repeat for a little area (about 20X20 km and res=20m)
it work fine!
have you any suggestion?
is ther a method for look
Hi list,
I am analysing a large dataset using random coefficient (using nlme) and
fixed effects (using lm function) models. I have problem with my R version
2. 2. 1 due to memory allocation difficulties. When I try to expand the
memory I get the following error message.
R
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
is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Weiwei Shi
Sent: Thursday, October 27, 2005 9:28 AM
To: r-help
Subject: [R] memory problem in handling large dataset
Dear
the
scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Weiwei Shi
Sent: Thursday, October 27, 2005 9:28 AM
To: r-help
Subject: [R] memory problem in handling large dataset
Dear Listers
Hi, Jim:
Thanks for the calculation. I think you won't mind if I cc the reply
to r-help too so that I can get more info.
I assume you use 4 bytes for integer and 8 bytes for float, so
300x8+50x4=2600 bytes for each observation, right?
I wish I could have 500x8 G memory :) just kidding..
Of Weiwei Shi
Sent: Thursday, October 27, 2005 9:28 AM
To: r-help
Subject: [R] memory problem in handling large dataset
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
of the statistician is to catalyze the
scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Weiwei Shi
Sent: Thursday, October 27, 2005 9:28 AM
To: r-help
Subject: [R] memory problem in handling large
I'm a beginner in R and, therefore, I don't know how serious my trouble is.
After running a script:
**
*t**-c(14598417794,649693)*
*data**=data.frame(read.spss(C:\\Ginters\\Kalibracija\\cal_data.sav))*
*Xs=**as.matrix(data[,1:2])
*
On 7/14/2005 7:19 AM, Ginters wrote:
I'm a beginner in R and, therefore, I don't know how serious my trouble is.
After running a script:
**
*t**-c(14598417794,649693)*
*data**=data.frame(read.spss(C:\\Ginters\\Kalibracija\\cal_data.sav))*
*Xs=**as.matrix(data[,1:2])
*
On Thu, 14 Jul 2005, Duncan Murdoch wrote:
On 7/14/2005 7:19 AM, Ginters wrote:
Why does memory need so much (1.6 GB) space? How can I enlarge it? Is it
possible to allocate a part of memory used to the hard drive? Or, is the
trouble only with my script?
This sounds like a problem with the
@stat.math.ethz.ch
Subject: [R] memory problem with mac os X
Dear list,
I am using R.2.0.1 on a G5 biprocessor 2.5GHz with 2Go RAM (Mac OS X
10.3.8).
I'm trying to calculate an object of type dist. I am getting the
following memory error :
*** malloc: vm_allocate(size=1295929344) failed (error code=3
Dear list,
I am using R.2.0.1 on a G5 biprocessor 2.5GHz with 2Go RAM (Mac OS X
10.3.8).
I'm trying to calculate an object of type dist. I am getting the
following memory error :
*** malloc: vm_allocate(size=1295929344) failed (error code=3)
*** malloc[25960]: error: Can't allocate region
Hello,
I think we have a memory problem with em.mix.
We have done:
library(mix)
Manq - read.table(C:/.../file.txt)
attach(Manq)
Manq
V1 V2 V3 V4 .V27
1 1 1 1 1...
2 1 NA 3 6
3 1 2 6 2
...
...
300 2 NA 6 2...
Essaimanq
On 15-Feb-05 [EMAIL PROTECTED] wrote:
Hello,
I think we have a memory problem with em.mix.
We have done:
library(mix)
Manq - read.table(C:/.../file.txt)
attach(Manq)
Manq
V1 V2 V3 V4 .V27
1 1 1 1 1...
2 1 NA 3 6
3 1 2 6 2
...
...
300 2 NA 6
Happy new year to all;
A few days ago, I posted similar problem. At that time, I found out that our
R program had been 32-bit compiled, not 64-bit compiled. So the R program
has been re-installed in 64-bit and run the same job, reading in 150
Affymetrix U133A v2 CEL files and perform dChip
Have you checked whether there are limits set? What does `ulimit -a' say?
Do you know how much memory the R process is using when the error occurred?
We've had R jobs using upwards of 13GB on a box with 16GB of RAM (SLES8 on
dual Opterons) and never had problems.
Andy
From: Tae-Hoon Chung
Thanks Peter and Andy;
I just found it was not due to memory problem. It was false alarm ...
64-bit compiled program works fine!
On 1/3/05 3:39 PM, Peter Dalgaard [EMAIL PROTECTED] wrote:
Tae-Hoon Chung [EMAIL PROTECTED] writes:
Happy new year to all;
A few days ago, I posted similar
Hi
I have been creating very, very long jpeg images for the last two weeks
using jpeg(). All of a sudden, and I mean that, it's stopped working -
I've not changed a thing! The error message I get is:
jpeg(out.jpg,width=5,height=480, quality=100)
Error in devga(paste(jpeg:, quality, :,
michael watson (IAH-C) wrote:
Hi
I have been creating very, very long jpeg images for the last two weeks
using jpeg(). All of a sudden, and I mean that, it's stopped working -
I've not changed a thing! The error message I get is:
jpeg(out.jpg,width=5,height=480, quality=100)
Error in
It is also several times greater than the limit of human perception, being
several feet long at printing resolutions that need a magnifying glass
to see.
This is Windows and the limit is in the graphics card: mine is able to do
this but I suspect you need a 128Mb card (that jpeg is of itself
: Mon 12/20/2004 5:37 PM
To: Uwe Ligges
Cc: michael watson (IAH-C); [EMAIL PROTECTED]
Subject:Re: [R] Memory problem with jpeg() and wide jpegs
It is also several times greater than the limit of human perception, being
several feet long at printing resolutions that need a magnifying
Hi,
I am trying to run a very computationally expensive procedure in
R-2.0.0. and the process always gets killed after approx 8 minutes. This
procedure calls some of my own C++ code - in case it was this code
causing a memory leak I unload and then reload the .so file every time,
however I
PROTECTED]
Subject: [R] memory problem
Hi,
I am trying to run a very computationally expensive procedure in
R-2.0.0. and the process always gets killed after approx 8 minutes. This
procedure calls some of my own C++ code - in case it was this code
causing a memory leak I unload and then reload the .so
that there are
no limits on memory allocation set by the administrator.
Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Samuel Kemp
Sent: Wednesday, December 08, 2004 6:29 AM
To: [EMAIL PROTECTED]
Subject: [R] memory problem
Hi,
I am trying to run a very
-Original Message-
From: Samuel Kemp [mailto:[EMAIL PROTECTED]
Sent: Wednesday, December 08, 2004 11:46 AM
To: Huntsinger, Reid
Cc: [EMAIL PROTECTED]
Subject: Re: [R] memory problem
Thanks.
Here is some more information.
My platform is a Linux desktop.
The C++ code implements a Gamma
DeaR useRs:
I am working with 1 files at the same time. These files are in some
lists. When I begin to operate the memory size grows, but never exceeds the
computers RAM. And suddenly R reports:
Error: cannot allocate vector of size 23 Kb
Somebody know what can I do?
Perez Martin, Agustin wrote:
DeaR useRs:
I am working with 1 files at the same time. These files are in some
lists. When I begin to operate the memory size grows, but never exceeds the
computers RAM. And suddenly R reports:
Error: cannot allocate vector of size 23 Kb
Read the
I have (still) some memory problems, when trying to allocate a huge array:
WinXP pro, with 2G RAM
I start R by calling:
Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ)
R.Version(): i386-pc-mingw32, 9.1, 21.6.2004
## and here the problem
x.dim - 46
y.dim - 58
slices - 40
Christoph Lehmann wrote:
I have (still) some memory problems, when trying to allocate a huge array:
WinXP pro, with 2G RAM
I start R by calling:
Rgui.exe --max-mem-size=2Gb (as pointed out in R for windows FAQ)
Not sure that it actually says to use 2Gb there. You might try
Did you read the *rest* of what the rw-FAQ says?
Be aware though that Windows has (in most versions) a maximum amount of
user virtual memory of 2Gb, and parts of this can be reserved by
processes but not used. The version of the memory manager used from R
1.9.0 allocates large objects in
Hi everyone,
I'm running R1.9.1 on RedHat Linux. I'm trying to read in a matrix
file with 13956 by 858 dimensions. I realize this is pretty huge, though
I think the amount of memory I have should be able to handle it. R reads
the entire file and tells me Read in 11974247 values. This is
On Mon, 12 Jul 2004 21:53:34 -0400 (EDT), Tianyu Tom Wang
[EMAIL PROTECTED] wrote:
Hi everyone,
I'm running R1.9.1 on RedHat Linux. I'm trying to read in a matrix
file with 13956 by 858 dimensions. I realize this is pretty huge, though
I think the amount of memory I have should be able to
I doubt this is a memory problem, considering that R reported that it
read in the data! What exactly were the commands that you used to read
in the data?
-roger
Tianyu Tom Wang wrote:
Hi everyone,
I'm running R1.9.1 on RedHat Linux. I'm trying to read in a matrix
file with 13956 by 858
How many chips you can read is a function of how much RAM you have and
what chip it is. On a unix/linux box you will be able to read in and
process 143 of the HG-u95aV2 chips if you have about 2 Gb RAM. For the
larger U133A chips (RAE/MOE are about the same size), you will probably
need almost
Joshi, Nina (NIH/NCI) [EMAIL PROTECTED] writes:
I am trying to upload into R 143 Affymetrix chips onto using R on the NIH
Nimbus server. I can load 10 chips without a problem, however, when I try
to load 143 I receive a error message: cannot create a vector of 523263 KB.
I have expanded the
[EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Sent: Friday, January 30, 2004 11:44 AM
Subject: RE: [R] memory problem for R
You still have not read the posting guide, have you?
See more below.
From: Yun-Fang Juan
[...]
I tried 10% sample and it turned out the matrix became
singular after I
- Original Message -
From: Yun-Fang Juan [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, January 29, 2004 7:03 PM
Subject: [R] memory problem for R
Hi,
I try to use lm to fit a linear model with 600k rows and 70 attributes.
But I can't even load the data into the R
: Thursday, January 29, 2004 7:03 PM
Subject: [R] memory problem for R
Hi,
I try to use lm to fit a linear model with 600k rows and 70 attributes.
But I can't even load the data into the R environment.
The error message says the vector memory is used up.
Is there anyone having experience with large
: [R] memory problem for R
Hi,
I try to use lm to fit a linear model with 600k rows and 70
attributes.
But I can't even load the data into the R environment.
The error message says the vector memory is used up.
Is there anyone having experience with large datasets in R? (I bet
Hi,
I try to use lm to fit a linear model with 600k rows and 70 attributes.
But I can't even load the data into the R environment.
The error message says the vector memory is used up.
Is there anyone having experience with large datasets in R? (I bet)
Please advise.
thanks,
Yun-Fang
Have you read the posting guide for R-help?
You need to tell us more: What hardware/OS/version of R are you using?
A rough calculation on storage needed:
6e5 * 70 * 8 / 1024^2
[1] 320.4346
So you need 320+ MB of RAM just to store the data as a matrix of doubles in
R. You need enough RAM to
Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Thomas
W Blackwell
Sent: den 9 september 2003 01:28
To: array chip
Cc: [EMAIL PROTECTED]
Subject: Re: [R] memory problem in exporting data frame
Simplest is to save your workspace using save.image(),
then delete
Cc: [EMAIL PROTECTED]
Subject: Re: [R] memory problem in exporting data
frame
Simplest is to save your workspace using
save.image(),
then delete a bunch of large objects other than
the data
frame that you want to export, and run
write.table()
again, now that you've made
array chip [EMAIL PROTECTED] writes:
Hi all,
Thanks for all the suggestions. I was able to get the
data frame out by first deleting some other large
objects in the directory, and then changing the data
frame into matrix by as.matrix(), splitting the matrix
into 4 blocks and finally using
-Original Message-
From: array chip [mailto:[EMAIL PROTECTED]
Sent: den 9 september 2003 19:04
To: Henrik Bengtsson; 'Thomas W Blackwell'; Patrick Burns
Cc: [EMAIL PROTECTED]
Subject: RE: [R] memory problem in exporting data frame
Hi all,
Thanks for all the suggestions. I
I had a similar problem not long ago. My solution was to
look at the definition of write.table and essentially do it
by hand. The key steps are to create a matrix of characters
that includes the dimnames (if desired), and then use
writeLines to put that into a file.
My machine has 1G as well
Patrick,
Thanks for the suggestion. do you mean you need to
change each row of the data frame into a text string
using something like paste(data[1,],collapse='\t')
and then output the resulting character vector into a
file using writeLines?
It seems not working with my data mainly because my
Yes, you have the operation precisely right. What happens if
you coerce your data frame to a matrix:
data.mat - as.matrix(data)
and then do the paste and writeLines?
Pat
array chip wrote:
Patrick,
Thanks for the suggestion. do you mean you need to
change each row of the data frame into a
Hi,
I have a big problem with my R-script. It seems to be a memory problem, but I'm not
sure.
My script:
test.window - function(stat, some arguments){
several ifs and ifs in ifs (if(){...if(){...}})
}
...
for (ii in 1 : length(data)){ ## data is a vector of length 2500
stat -
On Mon, 11 Aug 2003, Unternährer Thomas, uth wrote:
test.window - function(stat, some arguments){
several ifs and ifs in ifs (if(){...if(){...}})
}
...
for (ii in 1 : length(data)){ ## data is a vector of length 2500
stat - test.window( some arguments )
## there are 15
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