[R] segfault -- address 0x29, cause 'memory not mapped'

[Uwe Ligges]

On 08.06.2013 15:38, mathias kuhnt wrote:
> Dear List,
>
> after a night of calculating, R says goodbye with a segmentation fault.
>
>   *** caught segfault ***
> address 0x29, cause 'memory not mapped'
>
> In my functions I subsequently read in network files of about 20KB using
> the IGraph package. Admittedly, I read in about 1 million files, in
> total 20GB. Still, the function saves the data to the same object and
> memory of the prior file should be freed.
>
> The crash occurs after some hours but not at the same time, last time
> after having read in 99% of the files. It probably depends on what I did
> before I started the function.
>
> Can anybody tell me if these are limitations of the program and I have
> to live with it or am I doing something wrong? Is it a general R problem
> or rather one of the IGraph package?

I guess igraph, butz cannot be sure without a reproducible example.
Perhaps the best idea is to find an example that generates the problem 
rather quickly and send it to the igraph maintainer.

Best,
Uwe Ligges



>
> Thanks in advance,
> Mathias
>
>
> here the code:
> #####################################################
> library(igraph)
>
> modnumber<-1200
> its<-1000
> seriespath<-"/daten/netgen_series/series_m1q2/"
> mylim<-200
> max<-100
> startval<-1
>
>
> sampledegcorr <- function (model, its, max)
> # I suppose it does not matter what I do here but as you see I read in
> 1000 network files and analyze them
> {
>      dc<-rep(NA,max)
>      for (i in 0:(its-1))
>      {
>          net<-read.graph(paste(seriespath,model,"/",i,".net", sep =
> ""),format="pajek")
>          net<-simplify(net)
>          ndeg <- sapply(V(net),function(x)
> mean(degree(net,neighbors(net,x))-1))
>          bo<-stats.bin(degree(net),ndeg,breaks=seq(-0.5,max ,1))
>          dc<-cbind(dc,bo$stats[2,])
>      }
>      dck<-as.vector(apply(dc,1,mean, na.rm=T))
>      return(cbind(seq(0,max-1,1),dck))
> }
>
>
> dc<-seq(0,max-1,1)
> for (i in startval:(modnumber))
> # here i start the function above with 1200 different networks
> {
>      print(paste("calculating model ", i, sep=""))
>      dc<-cbind(dc,sampledegcorr(paste("m", i, sep=""),its,mylim)[,2])
>      save(dc,file="series_m1q2_dc_results.RData")
> }
> ######################################################
>
> here my specs:
>
> R 3.0.1-3precise
> R crashed with SIGSEGV in Rf_StringTrue()
> Ubuntu 12.04.1
> 4 GB RAM
>
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