[Rsiena-help] problem running Rsiena

[Ruth M. Ripley]

Dear Maarten,

It seems you do not have enough memory. You are using a 32 bit version of 
R: if you computer is 64-bit, try running 64-bit R. It might also help a 
little if you got the latest version of RSiena (you may need to upgrade to 
R 2.13.1 to get a binary for this), as I recently removed some arrays 
which were always allocated and seldom used.

(Recent versions do not produce the message about xtable!)

If your computer is short of memory, I would run fewer processes. Although 
this tends to produce very slow execution due to swapping rather than a 
failure.

Regards,

Ruth


On Wed, 31 Aug 2011, maarten van zalk wrote:

> Dear all,
>
> I'm trying to run a model on large networks (n = around 2500) and get the 
> following error:
>
> Last login: Tue Aug 30 16:36:37 on ttys000
> maarten-van-zalks-mac-pro:~ maartenselfhout$ r
>
> R version 2.12.1 (2010-12-16)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> setwd("/Users/maartenselfhout/Desktop/Datfiles")
> Error in setwd("/Users/maartenselfhout/Desktop/Datfiles") :
> cannot change working directory
>> library(RSiena)
> Loading required package: xtable
>> library(snow)
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>> library(rlecuyer)
>> library(xtable)
>> setwd("/Users/maartenselfhout/Desktop/Dat files")
>> net.w1 <- as.matrix(read.table("nw3.dat"))
>> net.w2 <- as.matrix(read.table("nw4.dat"))
>> net.w3 <- as.matrix(read.table("nw5.dat"))
>> net.w1[net.w1 %in% c(6,9)] <- NA
>> net.w2[net.w2 %in% c(6,9)] <- NA
>> net.w3[net.w3 %in% c(6,9)] <- NA
>> friend <- sienaNet(array(c(net.w1, net.w2, net.w3), dim=c(2529, 2529, 3)))
>> soc <- as.matrix(read.table("Shyness.dat"))
>> soc[soc %in% c(99)] <- NA
>> soc <- sienaNet(soc, type="behavior")
>> mydata <- sienaDataCreate(friend, soc, peer, dad, mum)
> Error in sienaDataCreate(friend, soc, peer, dad, mum) :
> object 'peer' not found
>> mydata <- sienaDataCreate(friend, soc)
>> myeff <- getEffects(mydata)
>> fix(myeff)
>> mymodel <- sienaModelCreate(useStdInits = FALSE, projname = 'soctot')
>> ans <- siena07(mymodel, data=mydata, effects=myeff, 
>> batch=FALSE,verbose=TRUE, nbrNodes=8, useCluster=TRUE, initC=TRUE)
> Loading Tcl/Tk interface ... done
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>   enquote
>
> R(29941) malloc: *** mmap(size=76750848) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(29941) malloc: *** mmap(size=76750848) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Error: cannot allocate vector of size 73.2 Mb
>
> Does anyone know how to fix this?
>
> Kind regards,
>
> Maarten
>