[gmx-users] link gromacs i7
gmx3 at hotmail.com
Wed Apr 7 10:16:47 CEST 2010
I am using openmpi 1.2.8 and it works fine.
You get 15% performance increase when going from 4 to 8 processes.
Note that with 4 processes you have to use:
mpirun -np 4 taskset 0xf mdrun ...
to avoid two processes running on the same physical core.
The only problem I can think of is that your system is so small
that it will anyhow not scale to more than 4 processes.
> From: x.periole at rug.nl
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] link gromacs i7
> Date: Wed, 7 Apr 2010 10:10:26 +0200
> We have been using gromacs-4.0.7 on I7 with up to 8 CPUs. The
> scaling is pretty good.
> Note that upgrading to openmpi-1.4.1 was necessary to be able
> to scale to up to 8 CPUs, if not the jobs where hanging ...
> Since you have it already, I do not see where the problem can
> come from. Are you sure you are using openmpi-1.4.1?
> On Apr 7, 2010, at 12:50 AM, Mark Abraham wrote:
> > On 7/04/2010 5:32 AM, Maurício Menegatti Rigo wrote:
> >> We are using an i7 920 processor to run Gromacs-4.0.7 with
> >> openmpi-1.4.1. The simulations run well using 4 threads (using
> >> "mpirun
> >> -np 4 mdrun...") but the performance is worse when we use 6 or 8
> >> threads.
> > Sure. You have four physical cores. If you're trying to get more
> > across a network, unless it is Infiniband you will take a big
> > performance hit. Intel's hyperthreading may work (it did 5 years ago
> > on different technology), but only if it is turned on, the MPI
> > processes are all on the same piece of processor, and you compile
> > with MPI and use mpirun -np x for x=1-8.
> > Even then, 8 virtual cores might over-saturate cache bandwidth, or
> > something. You'll need to provide a lot more information for more
> > help there.
> >> Looking for some way to improve our performance we found out
> >> this forum and then started to try use threads without openmpi. We
> >> compiled gromacs again and used the command line as described here
> >> ("mdrun -nt 8..."), but the following error appears:
> >> ------
> >> Program mdrun, VERSION 4.0.7
> >> Source code file: mdrun.c, line: 410
> >> Fatal error:
> >> GROMACS compiled without threads support - can only use one thread
> >> ------
> >> But in gromacs-4.0.7 threads are not supposed to be ON by default?
> > No post to this list has implied that threads work, because they
> > will not before GROMACS 4.1. The fact that the installation guides
> > on the website don't suggest using threads would also have guided
> > you here.
> > Mark
> > --
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