[gmx-users] MPICH or LAM/MPI

[hseara at netscape.net]

Thank you very much you the advise, I will install fiors LAM and then 
MPICH. By the way you think can be interesting to invest in some low 
latenci network devices for this little clustter??. Or with the gigabit 
Can be enought

Thanks Hector

-----Original Message-----
From: Carsten Kutzner <ckutzne at gwdg.de>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Mon, 19 Jun 2006 10:28:51 +0200
Subject: Re: [gmx-users] MPICH or LAM/MPI

  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,
 Carsten

 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
 http://www.mpibpc.mpg.de/research/dep/grubmueller/
 http://www.gwdg.de/~ckutzne

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