Re: [Boost-users] [BGL] visualizing large graphs

Subject: Re: [Boost-users] [BGL] visualizing large graphs
From: Cedric Laczny (cedric.laczny_at_[hidden])
Date: 2010-09-29 05:47:44

On Wednesday, 29. September 2010 11:36:03 Adam Spargo wrote:
> Hi Cedric,
> I have been trying to use a program called Tulip to visualise my graphs,
> it claims to work up to millions of nodes, but as yet I still get crashes
> for relatively small graphs. My main problem has been that all my machines
> with enough RAM are remote and the x-connection is too slow. I have put
> some more RAM in my desktop but now the graphics card seems to struggle.
> Waiting for a new graphics card ... Tulip does support batch mode, so I
> could run on a big memory machine and output hardcopy, but I haven't had a
> chance to really learn it interactively yet.
> 
> I'll let you know if I have any success.
>

Thank you, I will give it a try

> How big a graph can you look at with cytoscape? I haven't tried that.
>

If I remember correctly, you can load graphs with > 10k edges (no clue about 
the number of vertices, sorry) into cytoscape, but when you try to create an 
actual representation of that data, even with a "decent" 4GB RAM, it crashes. 
But I think that this is rather related due to the fact that cytoscape (at 
least my installation) is based on Java and I get an Buffer-overflow.
And I could imagine that for the special purposes in your case at the WTSI, 
you are handling way bigger graphs ;)

> Best,
> 
> Adam.

Best,

Cedric

> --
> Dr Adam Spargo
> High Performance Assembly Group   email: aws_at_[hidden]
> Wellcome Trust Sanger Institute   Tel: [phone] x7728
> Hinxton, Cambridge CB10 1SA       Fax: [phone]
> 
> On Wed, 29 Sep 2010, Cedric Laczny wrote:
> > Hi,
> > 
> > although this might seem a bit off-topic, I think it is an important
> > topic and might be very well interesting for some of us.
> > The boost graph library provides methods to export graphs e.g. for the
> > use with graphviz.
> > However, this is a rather "one-way" solution. Besides that, it is
> > difficult to handle large graphs with graphviz. Therefore, I was
> > wondering if there have been some recent developments here?
> > I would especially be interested in a solution that allows the direct
> > visualisation of a graph (even previously serialized), possibly
> > integrating ways to filter out some of the data in order to be able to
> > visualize the graph in some way. It is clear to me that visualizing
> > arbitrarily large graphs will be limited by physical limitations mostly
> > (RAM etc.). But I would find it very convenient to at least load the
> > graph, set some filters, so that I don't need to do this seperatly via a
> > C++-program. Actually, I am writing my graph to a format that can be
> > visualized by Cytoscape. Unfortunately, this suffers from large
> > limitations on the size of the graph (number of edges and nodes). I am
> > looking forward to hear your ideas about this and possible suggestions
> > about libraries or programs that might achieve this goal.
> > Thank you.
> > 
> > Best regards,
> > 
> > Cedric
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