[gmx-users] Software Raid and low GROMACS performance

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Wed Jan 21 12:17:33 CET 2009

Hi Martin

Martin Höfling escreveu:
> Am Dienstag, den 20.01.2009, 17:07 -0200 schrieb Alexandre Suman de
> Araujo:
>> 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
> cases...).

In my experience, if you use a high output frequency in simulations, the 
scaling is affected. So I thought that a possible low writing 
performance of software RAID 1 should reflect in the GROMACS scaling 

>> 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
> scenarios.
Nothing related with system is using high CPU resources. The top utility 
gives me only 4 mdrun_mpi process using around 70% of each CPU and 
anything else related to OS using more than 5%.

>> 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
> disks.
> Best
> 	Martin
The problem is that the computer with low performance is much more 
powerful (more RAM and more CPU frequency) than the other one which 
gives me 100% of scaling! To turn off one HD is a good idea that I 
already had and I should try this ASAP.


Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman at gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *

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