[gmx-users] Using Myrinet, openmpi 1.3.3 and GROMACS 3.3.2

Itamar Kass itamar.kass at gmail.com
Sun Aug 23 13:30:24 CEST 2009


We have bought new cluster with Myrinet, and I have install GROMACS  
3.3.2 and openmpi 1.3.3. Now, in order to run my gromacs I am using  
'mpirun -np 32 mdrun_mpi -np 32 ...' (each node has 8 CPUs). my  
question is, are there any flags used with openmpi which will make it  
use Myrinet better? I am aware to the options '--mca btl sm,self,mx'  
and '--mca btl self,sm --mca mtl mx --mca pml cm' but some benchmarks  
I did show no improvement, on the contrary. So I will be happy to try  
some ideas in order to utilize the system better.

Now, I am quite sure that there is an answer to my question somewhere  
in the mailing list, but I can't check it 'cause I can search it.  
Someone knows how I can do it?

All the Best,


  "In theory, there is no difference between theory and practice. But,  
in practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at med.monash.edu.au

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