[gmx-users] Re: a tip to run gromacs from Fink in mac duo core

Carsten Kutzner ckutzne at gwdg.de
Wed Jul 23 13:05:40 CEST 2008

Alan wrote:
> Thanks vdSpoel,
> Just one more question.
> So, in a dual/quad core computer, do -sort -shuffle do any difference
> for better? I mean, is there use for 'sort and shuffle' in a
> multi-core computer (not cluster!)?
Definitely, because shuffle will enhance the load balancing (unless you
have just one protein in water) and sort the locality of the data.
This will enhance the performance on both shared and distributed memory.


> Cheers,
> Alan
> On Tue, Jul 22, 2008 at 4:26 PM, Alan <alanwilter at gmail.com> wrote:
>> Hi list!
>> I would like to know among mac intel users with Fink, which gromacs
>> with mpi to use:
>> gromacs-mpi-lammpi or
>> gromacs-mpi-openmpi
>> Or there's any easier way (multi-threads is still not working in GMX, right?)?
>> Many thanks in advance.
>> Alan
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>> http://www.bio.cam.ac.uk/~awd28<<

Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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