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

[Justin A. Lemkul]

Itamar Kass wrote:
> Hi,
> 
> 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?
> 

Sorry I can't help with the above problem, but the old search interface is 
indeed still functional:

http://oldwww.gromacs.org/swish-e/search/search2.php

-Justin

> All the Best,
> Itamar
> 
> ---
> 
>  "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 
> <mailto:Itamar.Kass at med.monash.edu.au>
> ============================================
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================