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I have the following problem: I created ~100 MB file using R by exporting as a graph (hence I can re-export if necessary) I would need to open it in gephi (0.8.2) the file includes ~2.6k nodes, ~170k edges and every node has several attributes.

I have reduced all the attributes to only the necessary ones, but Gephi still won't open. I am running a laptop with 4 GB memory (I have shutdown everything unnecessary) and I have Java 64bit. Yet, I still get the following problem:

java.lang.RuntimeException: java.lang.IndexOutOfBoundsException: Index5, Size: 5

I do not think it is a memory issue like I had before, I still have plenty (at least ~600 MB) free memory even at the most problematic point. The config file is set to : Xmx2827m

The file currently is exported as GML, but I can use any format igraph can export to. So any solution that would allow me to open the file in gephi including the nodes, edges and attributes would be welcome. I picked GML because it seemed smallest file format that supports attributes.

Any ideas?

Thank you very much for your time!

Jakub Langr
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    shouldn't be a problem. i've done 100k nodes and 10m edges on my mbp (www.twittercensus.com/graph). Which plattform are you running? – Hampus Brynolf Apr 21 '13 at 20:44
  • Oh I eventually managed to avoid the problem (by reducing the number of attributes even further) but I did not find a solution. Windows 7 64bit; 64bit Java; 32bit Gephi (the 64 one does not work, but I do not think it would be constrained by that) – Jakub Langr Apr 22 '13 at 21:20

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