[gmx-users] Help improving multi core processor's speed

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 10 03:44:25 CEST 2008

fabracht sdf wrote:
> Hello. I was reading the Gromacs manual in order to see if how I can 
> improve my processor's performance. I am using an intel core 2 quad 
> processor to run dynamics. On page 194 of the manual 

It's the 194th page, but it's numbered 178 in manual version 3.3... 
referring also to the section number/name would be a good idea.

> ther is something 
> written about using multiple core processors and modifying parameters in 
> mdrun so that you can actually take advantage of those extra processors.
> I would like some information on how to (if it is actually possible) 
> really improve my dynamic's calculation.
> Please remember that i am not used to many of the programming language I 
> usually see here, so if you can suggest any further reading that is 
> newbie compatible, i would really appreciate that.

With versions prior to GROMACS 4.0, in order to take advantages of your 
multiple cores, you will need to have an MPI library installed, and 
configure it to use those cores. That topic is outside the scope of this 
list. Once you've got that sorted out, further instructions for 
configuring GROMACS for MPI usage are on the GROMACS webpage.


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