[gmx-users] [gmx-users]Strange statistics when running parallel Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 25 17:39:15 CEST 2002

On Wed, 2002-09-25 at 18:21, Paulo S. L. de Oliveira wrote:
> Hi GMXers
>          I've started to use Gromacs and I'm trying to put the program to run 
> in my PC cluster using MPI. I started to test the program in an Dual Athlon 
> XP 1800+ using a system protein+water (4180 atoms) by 1000ps . For that I 
> used:
> grompp -np 2 -shuffle -sort -s -f complex -o full -c after_pr  -p MUT_R167Q
> mpirun -np 2 -s n0 mdrun_mpi -v -s full  
>          It worked fine. Both CPU on Dual Athlon reached about 99% and 
> performance was 8.75 NODE hours/ns. After that, I (LAM)booted the system 
> using nine CPU (two Dual Athlon and five single Athlon). I repeated the 
> command above changing -np 2 by -np 9 and for my surprise the performance 
> became worse: 9.85 NODE hours/ns).  CPU loading for first dual machine show 
> 80 and 60% and for another dual 70 and 55%. For all single CPU machines the 
> CPU loading got about 20%. All machines are dedicated to run molecular 
> dynamics aplication and there  wasn't other application consuming CPU that 
> justified the low performance.
>          Please, I would like to know if someone had a similar problem  and 
> appreciated any suggestion.
you are probably using PME which is not very well parallellized.
Otherwise, 4000 water molecules is too small to scale very well on a
normal network. See the benchmarks on gromacs.org for a 120000 atom

>          Thanks in advance!
>                                  Paulo
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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