[gmx-users] Core i7 vs Core2Quad

[Sander Pronk]

Hi,

In Linux, one can apparently set processor affinity (or, in this case  
core affinity) with 'taskset'. The command is used like this:

taskset <bitmask> command

where <bitmask> is a hexadecimal bit mask with the cpus to use (in a  
format like 0xff, where 0xff enables the first 8 cpus on a system).  
For mdrun using MPI on a core i7, with 4 (or fewer) tasks each on  
their own real core it would be

mpirun -np 4 taskset 0x55 mdrun

I don't have access to a cpu with hyperthreading right now so I can't  
check whether it actually works, though.

Sander



On Sep 15, 2009, at 18:41 , Berk Hess wrote:

> That is incorrect.
>
> A Core I7 is about 40% faster with hyperthreading turned off.
> A Core I7 is about 65% faster with hyperthreading turned on
> and running 8 processes.
>
> What you should NOT do (but which can happen very easily)
> is running on a Core I7 with hyperthreading turned on and using
> only 4 processes. In that case the processes are distributed
> randomly over the 8 virtual and 4 real cores and the chance
> is very high that at least one real cores gets 2 mdrun processes
> and your simulation is nearly 50% slower than it could be.
>
> If somebody has a solution for this problem under Linux,
> that would be extremely useful.
>
> Berk
>
> > Date: Tue, 15 Sep 2009 14:20:09 +0200
> > From: Antoine.Fortune at ujf-grenoble.fr
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Core i7 vs Core2Quad
> >
> > I7 about 20% faster at same clock speed ...
> > Antoine
> >
> >
> >
> > marcos a écrit :
> > > Hi,
> > >
> > > I wander if somebody has compared Core i7 vs Core2Quad in Gromacs
> > > simulations.
> > > Is Core i7 faster in a per clock basis?
> > >
> > > Marcos.
> > >
> > >
> > > Marcos Villarreal
> > >
> > >
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