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Re: [igraph] Memory usage

From: Tamas Nepusz
Subject: Re: [igraph] Memory usage
Date: Thu, 11 Nov 2010 10:17:57 +0000

Hi again,

I think what may have happened is that you used tons of string operations in 
your implementation to construct the graph. The Python interpreter may have 
interned some of the strings (i.e. it keeps the corresponding Python object 
around in memory in case you need that string later), and that's what could 
have caused the increased memory consumption.  Another thing that may have 
caused this is the fact that the Python interpreter never releases memory back 
to the OS on its own (again, for performance reasons), so if the peak memory 
consumption was larger than the final one, you can only measure the peak 
consumption and not the actual one.


On 11 Nov 2010, at 09:21, Russell Neches wrote:

> Greetings!
> I have been benchmarking igraph to see if it might be possible to use it
> for building de Bruijn graphs for genome sequence assembly. I've hacked
> together a very simple implementation using the python bindings, and to
> my dismay, I seem to be getting memory usage of more than 6KB per
> vertex! 
>        edges    : 791198
>        vertices : 791954
>        memory   : 5029084 kb
> Is this typical?
> Russell
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