[gmx-users] topol.tpr made for 2 nodes while mdrun expected 8

Stéphane Téletchéa steletch at jouy.inra.fr
Thu Apr 27 18:00:25 CEST 2006

Guillem Plasencia a écrit :
> Hello gmxers,
> i've been struggling to make gromacs be able to use my 2 Dual CPU 
> machines, without success.
> I'd like to know exactly how to configure lam and how to preprocess with 
> grompp (and then execute with mpirun) in order to be able to run as many 
> parallel processes in my 2 Dual CPU machines that sum 4 CPUs (8 with 
> hyperthreading).
> My lam configuration file content is:
> lead7 cpu=4
> cpu=4
> As a short brief, i've been able to run the same lisozyme cutoff 
> benchmark in 4 parallel processes in only one node by commenting out the 
> first line (the one which begins ..lead7) in my lam configuration file, 
> and then
> preprocessing as:
> grompp -f cutoff.mdp -c conf.gro -p topol.top -np 4 -shuffle -sort

It won't help much for your specific problem, but if you are the only 
one to use these computers, i'd suggest turning off HT (in the bios) and 
considering your dual-cpu for what they are dual CPUs.

You'd get better calculations figures and better scalability.

Use therefore -np 2.

My 0.02 cents.


Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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