[gmx-users] Poor parallel performance in Ubuntu 8.04

[Alexandre Suman de Araujo]

Hi GMXers

Some days ago I reported poor performance of GROMACS parallel runnings over
Ubuntu 8.04 and software RAID in a quad-core processor.
(http://www.gromacs.org/pipermail/gmx-users/2009-January/039088.html)

In a attempt to made some tests in non-raid systems running Ubuntu 8.04, I
performed simulations in a dual-quad Xeon box. I ran a simulations using the 8
CPUs (8 process) and the performance was also poor, with a behavior near that
observed in the quad-core (some cores with around 80% and the others with less
than 30%). If I ran 8 independent simulations, all CPUs show a 100%
performance.

Does anyone have any experience with this Gromacs+Ubuntu poor parallel
performance?

I think the problem is due to the use of the generic Ubuntu standard kernel.
Maybe if I recompile the kernel I can get a better performance system. However,
this is just a guess, and I would like to know if anyone already had this
problem and solved it.

Thanks
-- 
Alexandre Suman de Araujo
Instituto de Física de São Carlos
Universidade de São Paulo
São Carlos - Brasil





----------------------------------------------------------------
WEBMAIL - IFSC - Instituto de Física de São Carlos