Admin
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I need advice for rendering an undirected graph with 178,000 nodes and 500,000 edges. I've tried Neato, Tulip, and Cytoscape. Neato doesn't even come remotely close, and Tulip and Cytoscape claim they can handle it but don't seem to be able to. (Tulip does nothing and Cytoscape claims to be working, and then just stops.)
I'd just like a vector format file (ps or pdf) with a remotely reasonable layout of the nodes.
I suggest that you first do some preprocessing of the data, for example collapsing nodes to clusters and then visualizing the clusters. Collapsing will reduce the number of nodes and makes it easier for algorithms such as Kamada-Kawai or Fruchterman-Reingold to render the resulting graph.
If you really need to visualize 500.000 nodes then can you consider using a simple circular layout. This will be easy to render without the issues that force-based algorithms have. Take a look at Circos: http://mkweb.bcgsc.ca/circos/
Circos is graph visualization developed by bio-informatics people which is tailored to visualize genomes and other extremely large and complex data-sets.
It's a PERL based package, I hope that's not problematic.
Mathematica could very likely handle it, but I have to admit my first reaction was along the lines of the comment that said "take a piece of paper and color it black." Is there no way to reduce the density of the graph?
A possible issue is that you seem to be looking for layout, not just rendering. I have no knowledge about the Big O characteristics of the layouts implemented by various tools, but intuitively I would guess that it might take a long time to lay out that much data.
Does it need to be truly accurate?
Depending on what you're trying to accomplish it might be good enough to just graph 10% or 1% of the data volume. (of course, it might also be completely useless, but it all depends on what the visualization is for)
