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POPython networkx memory error on small dataset
 

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  1. POPython networkx memory error on small dataset
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    <p>I have a relatively small dataset consisting of ~100k edges and ~7000 nodes. I am trying to use two algorithms to find communities within my dataset. I added the edges and proceeded to run an algorithm that was implemented here: <a href="http://perso.crans.org/aynaud/communities/#as-python-module" rel="nofollow">http://perso.crans.org/aynaud/communities/#as-python-module</a></p> <p>Data is basically as follows:</p> <p>Node1,Node2 </p> <p>Node1 is connected to node2 and the graph is undirected. </p> <p>But the program just runs for a bit then gives me a memory error. I know it works because I tested it on a small dataset and it works properly but it's giving me a memory error. I don't know a lot about these algorithms but I was under the impression that the dataset I have is really small and I am running it on my personal home computer. Is this just a problem with the implementation itself or due to my machine's limitations? </p> <p>Would any of you have an idea as to how to get this to work (i.e. another piece of software or algorithm) besides running it on a server with a lot more memory?</p> <p>Thanks!</p> <p>traceback:</p> <pre><code>Traceback (most recent call last): File "&lt;wingdb_compile&gt;", line 65, in &lt;module&gt; File "C:\Python27\lib\site-packages\networkx\drawing\layout.py", line 242, in fruchterman_reingold_layout pos=_fruchterman_reingold(A,dim,pos_arr,fixed,iterations) File "C:\Python27\lib\site-packages\networkx\drawing\layout.py", line 280, in _fruchterman_reingold delta = np.zeros((pos.shape[0],pos.shape[0],pos.shape[1]),dtype=A.dtype) MemoryError </code></pre>
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    1. PTQuestion
    1. USPaul
    1. USPaul
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    1. COTraceback, please.
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      1. POPython networkx memory error on small dataset
      1. USkristaps
    2. COOk added traceback
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      1. POPython networkx memory error on small dataset
      1. USPaul
    3. CO@Paul: Error seems to happen while trying to draw the network. If you don't need to draw, then remove those part, try again and see if you get an error.
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      1. POPython networkx memory error on small dataset
      1. USAvaris
 

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