[gmx-users] Poor parallel performance in Ubuntu 8.04

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Wed Feb 4 18:59:14 CET 2009

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.

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%

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

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.

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

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