Re: [igraph] Memory usage

[Tamas Nepusz]

Hello Russell,

> I have been benchmarking igraph to see if it might be possible to use it
> for building de Bruijn graphs for genome sequence assembly. I've hacked
> together a very simple implementation using the python bindings, and to
> my dismay, I seem to be getting memory usage of more than 6KB per
> vertex! 
I've did some similar measurements on OS X and the results are as follows:

Memory consumption right after starting igraph: 15.2 MB (real), 27.4 MB 
(virtual)
Memory consumption after constructing a random graph with 791954 vertices and 
792545 edges: 153.8 MB (real), 158.4 (virtual)

Memory consumed by the graph: 138.6 MB (real), 131.0 MB (virtual)
Memory consumed per vertex: 183.5 bytes (real), 173.4 bytes (virtual)

The graph I've constructed was not a de Bruijn graph but an Erdos-Renyi graph 
with similar # of vertices and edges, but that shouldn't matter.

By the way, there's a constructor in igraph for de Bruijn graphs, see 
help(Graph.De_Bruijn).

-- 
Tamas