[gmx-users] MPICH or LAM/MPI

Carsten Kutzner ckutzne at gwdg.de
Mon Jun 19 10:28:51 CEST 2006

Hello Hector,

since it does not take long to install lam and mpich, I would install 
both MPI implementations and then benchmark with a typical MD system 
which one performs better.

I would suggest LAM 7.1.2 which is the newest version, and MPICH-2 
1.0.3, which works well, at least on our cluster. Many users (including 
myself) found that GROMACS on top of MPICH-1.2.x hangs when executed on 
more than 4 CPUs.

My guess is that LAM-GROMACS outperforms MPICH-GROMACS on a smaller 
number of CPUs, but on 6 or more CPUs MPICH-GROMACS might be faster, 
since it provides optimized collective communication routines.

If you only want to install a single MPI implementation, I would choose 
LAM for a start.

Hope that helps,

hseara at netscape.net wrote:
> Dear Gmx-Users,
> I'm configuring a small cluster of 5 Dell Power Edge 1800 with dual xeon 
> conected by a gigabit dell switch. I was wondering which MPI 
> distribution, LAM/MPI or MPICH(which version), on this platform has 
> better performance for gromacs 3.3.1 on a  fedora 5 linux distribution. 
> I will try to combine that with SGEgrid as a queue manager. Also I will 
> like to know if I can expect for big systems, 200.000 atoms, good 
> parallelitzarion in the 5 nodes ( 10 processors).
> Thank you
> Hector Martínez-Seara Monné
> University of Barcelona
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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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