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
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