[gmx-users] Mac OS X setup for paralell gmx

Choon Peng cpchng at bii.a-star.edu.sg
Thu Sep 16 02:36:39 CEST 2004

Hi David,

   I recently received an email about installing Gromacs on G5 from Shreyas
Bhide, also from UNC.

I think my How-To might be still useful.
Also, the G5 benchmarks I got:

I find that the more MPI processes I start (or rather, the more machines I
use), the higher the CPU usage of the "kernel_tas" process, leaving less CPU
available for computation.
Hence, the parallel performance of our 4 PowerMac dual-G5s connected by
Gigabit Ethernet is low.
Anyone also face the same problem.
As a result, I didn't use the G5 cluster for our simulations.

We use LAM-MPI v7.0.6 with GROMACS 3.2.1 and GCC 3.3.

Mr Choon-Peng Chng
Research Associate
Computational Biology Group
Bioinformatics Institute, A*STAR
30 Biopolis Street, Level 7. Singapore 138671.
DID: +65 6478 8301 FAX: +65 6478 9047
WWW: http://www.bii.a-star.edu.sg/~cpchng

On 9/16/04 6:20 AM, "David L. Bostick" <dbostick at physics.unc.edu> wrote:

> Dear all,
> I have recently started using a dual processor Mac-G5 w/ OS 10.3.5. I wish
> to start using gmx on this machine and was wondering if anyone could tell
> me straight-up the best way to configure and run mpi and gmx.  I imagine
> there are many of you who have gone through the trials and tribulations of
> doing this, and was hoping that I could learn from your experiences.
> - What do you find is the best mpi to use? lam-mpi, mpich, mpich-gm .. etc.
> What are the benefits of each.
> - Are there any special things I must do to get it to work
> properly/optimally ... i.e. I noticed from the archives that someone
> recommends using an --with-rpi=tcp option when configuring lam-mpi
> installation.
> - Can one recommend alternative compilers like the IBM xlc or xlf
> compilers.
> - Are there options I should turn on or off in order to run optimally on
> such an operating system?
> The emails on this subject in the user-archive are a little fragmented,
> perhaps if I can gather suggestions from as many users/developers as
> possible, I can come up with a coherent user-friendly recipe for compiling
> and running on the Mac.
> I would really appreciate any help anyone could offer.
> Thanks,
> David Bostick
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