[gmx-users] Software Raid and low GROMACS performance

Martin Höfling martin.hoefling at gmx.de
Tue Jan 20 20:20:33 CET 2009

Am Dienstag, den 20.01.2009, 17:07 -0200 schrieb Alexandre Suman de

> I have two machines with Intel Quad Core processors and Intel 
> motherboards. In the first one I'm running Open Suse with normal 
> partition scheme. In the second I'm running Ubuntu 8.04 with software 
> RAID 1.

Hard disk IO should not limit scaling and simulations at all (in most

> Running a simulations in parallel (4 process, one for each core) in the 
> first computer I have a scaling of almost 100%. The same simulation in 
> the second computer gives me a very worst scaling.

In principle, software RAID and RAID functions implemented in
chipsets/BIOS require the CPU. Although RAID 1 should be pretty
inexpensive and even RAID 5 should create high load in most MD

> Is it possible that the software RAID is the responsible for this lost 
> in GROMACS performance? Does anybody have experience with this?

Is the rest of the Hardware comparable? To further test impact of your
RAID, you can easily disable RAID 1 by (temporarily) remove one of the


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