Memory leak (igraph, watts.strogatz.game, get.all.shortest.paths)

Memory leak (igraph, watts.strogatz.game, get.all.shortest.paths)



I try to make a quite simple computation but I get an out of memory

message whose origin is not clear to me. Here is what I want: for the

small-world model (watts.strogatz.game) and several p-values I create

nsamp many graphs and compute the distance between the first node and the

opposite node at n/2. When nsamp = 1, everything works fine. Setting it to

100 or larger gives an "out of memory" error right in the first round

(i=1, j=5), i.e., for the smallest p-value (0.01). Setting nsamp=10 gives

no error (huh?? Shouldn't that include i=1, j=5?). I tried to explicitly

remove all the larger objects (graph, len) but to no avail. Any ideas

here? Here is the code:

require(igraph)

probs <- c(1:25)*0.01

n = 1000

target <- n/2

nsamp = 100

for(i in c(1:length(probs))){

for(j in c(1:nsamp)){

graph <- watts.strogatz.game(dim=1, size=n, p=probs[i], nei=4)

shortest.paths(graph, v=V(graph)[1], to=V(graph)[target])

len <- get.all.shortest.paths(graph, from=V(graph)[1])

rm(graph)

#The number of shortest paths between 1 and target can be found in

numbPathsBetw1AndTarget <- len$nrgeo[target]

#In len$res there are all shortest paths between node 1 and all other

#nodes. It comes as a list which at each point contains a vector of

#so we need to use lapply to find out which of

#the lists are of interest to us.

lengths <- unlist(lapply(len$res, function(x) length(x)))

rm(len)

}

}

I am aware that I can increase the memory, but it bugs me that for nsamp

being small everything is fine. It seems to be a memory leak but I do not

there where it comes into play.

Edit: it is so unreproducible that I suspect it is not a memory leak but

rather a bad configuration of the graph. It always happens for i=1 but for

different j. Thus: is there an intrinsic, upper limit on the diameter of

the graph to apply get.all.shortest.paths or on the number of shortest

paths?