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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.
--
Tamas
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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