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

[Stéphane Téletchéa]

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
> 192.168.1.9 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

-- 
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