R help - Oct 2009 - Memory Problems with CSV and Survey Objects

I'm working with a 350MB CSV file on a server that has 3GB of RAM, yet
I'm
hitting a memory error when I try to store the data frame into a survey
design object, the R object that stores data for complex sample survey data.

When I launch R, I execute the following line from Windows:
"C:\Program Files\R\R-2.9.1\bin\Rgui.exe" --max-mem-size=2047M
Anything higher, and I get an error message saying the maximum has been set
to 2047M.

Here are the commands:
> library(survey)
#this step takes more than five minutes
> data08<-read.csv("data08.csv",header=TRUE,nrows=210437)
> object.size(data08)
#329877112 bytes

#Looking at Windows Task Manager, Mem Usage for Rgui.exe is already 659,632K
> brr.dsgn <-svrepdesign( data = data08 , repweights = data08[, grep(
"^repwgt" , colnames( data08)) ], type = "BRR" ,
combined.weights = TRUE ,
weights = data08$mainwgt )
#Error: cannot allocate vector of size 254.5 Mb

#The survey design object does not get created.

#This also causes Windows Task Manager, Mem Usage to spike to 1,748,136K

#And here are some memory diagnostics
> memory.limit()
[1] 2047
> memory.size()
[1] 1449.06
> gc()
           used  (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells   131148   3.6     593642   15.9  15680924  418.8
Vcells 45479988 347.0  173526492 1324.0 220358611 1681.3

A description of the survey package can be found here:
http://faculty.washington.edu/tlumley/survey/

I tried creating a work-around by using the database-backed survey objects
(DB SO), included in the survey package to conserve memory on larger
datasets like this one.  Unfortunately, I don't think the survey package
supports database connections for replicate weight designs yet, since I've
only been able to get a database connection working after creating a
svydesign object and not a svrepdesign object - and also because neither the
DB SO website nor the svrepdesign help page make any mention of those
parameters.

The DB SOs are described in detail here:
http://faculty.washington.edu/tlumley/survey/svy-dbi.html

Any advice would be truly appreciated.

Thanks,
 Anthony Damico

	[[alternative HTML version deleted]]

Yes, a 350Mb data frame is a bit big for 32-bit R to handle conveniently.

As you note, the survey package doesn't yet do database-backed
replicate-weight designs. You can get the same effect yourself without too much
work.

First, put the data into a database, such as SQLite.  If you have the data frame
read in then dbWriteTable will do it.

Now, drop most of the variables, keeping the sampling weights, replicate
weights, and a couple of other variables.

Create a svrepdesign() with the reduced data set.

When you want to do an analysis, use dbGetQuery() to load the variables you need
for the analysis, and put them in the $variables component of the svrepdesign.

That's exactly what the database-backed functions do for svydesign objects.

[If you only ever want to use a small subset of the variables, it's even
easier: drop all the extraneous variables and create a svrepdesign with the
variables you want]

        -thomas

On Fri, 23 Oct 2009, Anthony Damico wrote:
> I'm working with a 350MB CSV file on a server that has 3GB of RAM, yet
I'm
> hitting a memory error when I try to store the data frame into a survey
> design object, the R object that stores data for complex sample survey
data.
>
> When I launch R, I execute the following line from Windows:
> "C:\Program Files\R\R-2.9.1\bin\Rgui.exe" --max-mem-size=2047M
> Anything higher, and I get an error message saying the maximum has been set
> to 2047M.
>
> Here are the commands:
>> library(survey)
>
> #this step takes more than five minutes
>> data08<-read.csv("data08.csv",header=TRUE,nrows=210437)
>
>> object.size(data08)
> #329877112 bytes
>
> #Looking at Windows Task Manager, Mem Usage for Rgui.exe is already
659,632K
>
>> brr.dsgn <-svrepdesign( data = data08 , repweights = data08[, grep(
> "^repwgt" , colnames( data08)) ], type = "BRR" ,
combined.weights = TRUE ,
> weights = data08$mainwgt )
> #Error: cannot allocate vector of size 254.5 Mb
>
> #The survey design object does not get created.
>
> #This also causes Windows Task Manager, Mem Usage to spike to 1,748,136K
>
> #And here are some memory diagnostics
>> memory.limit()
> [1] 2047
>> memory.size()
> [1] 1449.06
>> gc()
>           used  (Mb) gc trigger   (Mb)  max used   (Mb)
> Ncells   131148   3.6     593642   15.9  15680924  418.8
> Vcells 45479988 347.0  173526492 1324.0 220358611 1681.3
>
> A description of the survey package can be found here:
> http://faculty.washington.edu/tlumley/survey/
>
> I tried creating a work-around by using the database-backed survey objects
> (DB SO), included in the survey package to conserve memory on larger
> datasets like this one.  Unfortunately, I don't think the survey
package
> supports database connections for replicate weight designs yet, since
I've
> only been able to get a database connection working after creating a
> svydesign object and not a svrepdesign object - and also because neither
the
> DB SO website nor the svrepdesign help page make any mention of those
> parameters.
>
> The DB SOs are described in detail here:
> http://faculty.washington.edu/tlumley/survey/svy-dbi.html
>
> Any advice would be truly appreciated.
>
> Thanks,
> Anthony Damico
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.
>
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

Hello,

Adding to Thomas' email, you could also use package colbycol which
allows you to load into R files that a simple read.table cannot cope
with, study columns independently, select those you are more interested
in and, finally, set up a dataframe with just the columns you are
interested in.

It is just the same strategy Thomas suggested, only that without the
requirement of an external tool and using almost the same syntax as you
would use in case you had no memory problems.

Best regards,

Carlos J. Gil Bellosta
http://www.datanalytics.com



On Fri, 2009-10-23 at 09:36 -0400, Anthony Damico wrote:
> I'm working with a 350MB CSV file on a server that has 3GB of RAM, yet
I'm
> hitting a memory error when I try to store the data frame into a survey
> design object, the R object that stores data for complex sample survey
data.
> 
> When I launch R, I execute the following line from Windows:
> "C:\Program Files\R\R-2.9.1\bin\Rgui.exe" --max-mem-size=2047M
> Anything higher, and I get an error message saying the maximum has been set
> to 2047M.
> 
> Here are the commands:
> > library(survey)
> 
> #this step takes more than five minutes
> > data08<-read.csv("data08.csv",header=TRUE,nrows=210437)
> 
> > object.size(data08)
> #329877112 bytes
> 
> #Looking at Windows Task Manager, Mem Usage for Rgui.exe is already
659,632K
> 
> > brr.dsgn <-svrepdesign( data = data08 , repweights = data08[, grep(
> "^repwgt" , colnames( data08)) ], type = "BRR" ,
combined.weights = TRUE ,
> weights = data08$mainwgt )
> #Error: cannot allocate vector of size 254.5 Mb
> 
> #The survey design object does not get created.
> 
> #This also causes Windows Task Manager, Mem Usage to spike to 1,748,136K
> 
> #And here are some memory diagnostics
> > memory.limit()
> [1] 2047
> > memory.size()
> [1] 1449.06
> > gc()
>            used  (Mb) gc trigger   (Mb)  max used   (Mb)
> Ncells   131148   3.6     593642   15.9  15680924  418.8
> Vcells 45479988 347.0  173526492 1324.0 220358611 1681.3
> 
> A description of the survey package can be found here:
> http://faculty.washington.edu/tlumley/survey/
> 
> I tried creating a work-around by using the database-backed survey objects
> (DB SO), included in the survey package to conserve memory on larger
> datasets like this one.  Unfortunately, I don't think the survey
package
> supports database connections for replicate weight designs yet, since
I've
> only been able to get a database connection working after creating a
> svydesign object and not a svrepdesign object - and also because neither
the
> DB SO website nor the svrepdesign help page make any mention of those
> parameters.
> 
> The DB SOs are described in detail here:
> http://faculty.washington.edu/tlumley/survey/svy-dbi.html
> 
> Any advice would be truly appreciated.
> 
> Thanks,
>  Anthony Damico
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at 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.