[gmx-users] Core i7 vs Core2Quad

[Berk Hess]

That is nearly correct.
For a single 4-core Intel Core I7 cpu, the first 4 cpu's (as well as the last 4)
cover all 4 physical cores.
Therefore the command line (under Linux) is:
mpirun -np 4 taskset 0xf mdrun
But you get 15% more performance using 8 processes (if your system is not too small):
mpirun -np 8 mdrun

It hope (but don't know) that newer Linux kernels would handle this issue better.
I am running 2.6.27.29.

Berk

From: pronk at cbr.su.se
Subject: Re: [gmx-users] Core i7 vs Core2Quad
Date: Wed, 16 Sep 2009 21:19:55 +0200
To: gmx-users at gromacs.org



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
> > 
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
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