[gmx-users] Using Myrinet, openmpi 1.3.3 and GROMACS 3.3.2
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
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at med.monash.edu.au
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users