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Re: [igraph] Saving Graphs

From: Matthew Walker
Subject: Re: [igraph] Saving Graphs
Date: Thu, 03 Dec 2009 10:10:29 -0500
User-agent: Thunderbird (X11/20090812)

Hi Marco,

I am no igraph nor python expert, but maybe you could try writing your graphs into one large XML file. You can easily compress such a file once you've finished adding graphs. I would even suspect that python would have the ability to compress the file on the fly.

I think GraphML (an XML format) would be ideal for this. You could write out a graph to a temporary file (using igraph_write_graph_graphml(), or its python equivalent) and then merge the temporary file into a main multi-graph file (also in GraphML). Just how to best do this, I am not sure. I imagine python already has strong abilities to manipulate XML files. If that's not for you, then there is a useful command-line utility called xmlstar [1] that could help you do such a merge.

I note that igraph already has the ability to select which graph to read given such a multi-graph file (see the documentation for the "index" parameter for igraph_read_graph_graphml()).

I hope that helps,

[1] http://xmlstar.sourceforge.net/



Marco wrote:
Hi all!

In the simulations I write I have to save very often the graph, with
all the attributes.
If I save it using gml or something like this, I end up with many
(say: thousands) of very small files, which are not very practical to
carry around and tend to full the filesystem very quickly.

I am looking for a way to save graphs (even not single graphs, but
rather more graphs in the same file) which is a little more clever.

So far I have been looking at pickling the whole thing, but I find it
rather unsatisfactory.
I have heard of hdf (or something like this). Looks to me that the
overhead to use it is rather big.

Someone has highlights, remarks, advice?

Thank you in advance,


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