[gmx-developers] Python interface for Gromacs

Sébastien Buchoux sebastien.buchoux at u-picardie.fr
Thu Sep 9 13:13:33 CEST 2010


On 09/09/2010 08:38 AM, David van der Spoel wrote:
> People in the Lindahl group are working on parallellizing analysis 
> tools because they are quickly becoming the bottleneck. We run 
> simulations of large systems on hundreds of processors, and due to 
> checkpointing this can be done largely unattended. Analysis can take a 
> lot of effort, both hardware (CPU, Disk) and organisational. I think 
> the prime advantage of a scripting languagae like Python could be 
> organisational.

 From my experience, Python is too slow to really make analysis tools 
(or any heavy computational work) on its own. But it can use C/C++ libs 
like a charm... hence a Python interface! :)

> @portability: I have tried compiling numpy a few times on mac & linux 
> without success. As long as numpy is not in the main python 
> distribution it will not be useful...

Numpy compilation can indeed be... troublesome. but I don't think it is 
 From my experience, Numpy is great for pure Python programming so it 
would be useful for a 100% Python analysis tool. But with the use of C 
to do the hard work, the advantage a Numpy is pretty slim and I think 
that new Python types defined within a C extension are more efficient 
since they allow Python users to access C objects directly (given the 
use of a descent interface).
This is specially true when dealing with already written C objects that 
are very different from C numarrays (i.e. they would need to be 
"translated" to Numpy arrays prior to use any of the Numpy routines).
IMHO, the #1 priority of Numpy is much more to ease life of pure Python 
programmers than to be useful to C extension programmers.


Sébastien Buchoux, MC
UMR 6022 - Génie Enzymatique et Cellulaire / Enzyme and Cell Engineering
Université Picardie Jules Verne (UPJV)
33, rue Saint Leu, 80000 Amiens, France
tel: +33(0)3 22 82 74 73 - email: sebastien.buchoux[at]u-picardie.fr

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