Re: [igraph] Problems calculating shortest paths for sparse large graph

[Tamás Nepusz]

> I am trying to calculate the shortest paths for a large sparse graph
> (48000 nodes and 2000 edges). [...]
> shortest_paths<-shortest.paths(net,weights=E(net)$weight);
> Error in .Call("R_igraph_shortest_paths", graph, v - 1, to - 1,
> as.numeric(mode),  :
>  negative length vectors are not allowed
Oh, hang on. If you have 48K nodes, the resulting shortest path matrix would 
have 48K * 48K elements. That's pretty big. I'm guessing that although you have 
32GB of memory, you hit some kind of internal limit within R and it simply 
cannot allocate the matrix it would require to return the result. The solution 
is to calculate the shortest paths for each start vertex separately in a for 
loop (use the v=... argument to specify the start vertex). You can also use 
smaller batches, say, 1000 vertices at the same time.

Best,
Tamas