[gmx-users] Runtime on 8 processors

Mark Abraham Mark.Abraham at anu.edu.au
Fri Sep 23 08:48:07 CEST 2011

On 23/09/2011 4:37 PM, Sumanth M. Kumar wrote:
> Hi everyone,
> I did a simulation in an amazon cluster with 7.5 GB memory and 4 EC2 
> Compute Units (2 virtual cores with 2 EC2 Compute Units each) and it 
> was done with 0.5ns/day. Now Im running a simulation in another amazon 
> cluster of 7 GB of memory and 20 EC2 Compute Units (8 virtual cores 
> with 2.5 EC2 Compute Units each), but still the speed is same even if 
> i use "mpirun -np 8" with the mdrun, and finally its taking the same 
> time as 2core system, i.e. 0.5ns/day. I would like to know whether I 
> should make any changes during compilation?  I had enabled mpirun 
> while compiling GROMACS. Do I need to make any changes, so that it 
> will consider all the 8 processors?

Virtual cores are useless for GROMACS because it saturates the processor 
pipelines on its own (though Intel's hyperthreading from 5-6 years ago 
was an exception). You need real cores, and to configure MPI to assign 
processes 1-to-1 to real cores. The details will be up to you and your 
system admins. You don't need to do anything with GROMACS other than 
configure with MPI.


> Thank you very much.
> Sumanth
> -- 
> **
> *Sumanth Kumar.M
> *
> On-the-Job Trainee
> Plant Molecular Biology Lab.
> Plant Breeding, Genetics and Biotechnology
> International Rice Research Institute
> DAPO-7777, Metro Manila
> Philippines
> Tel : +63- 9163129718
> email :s.kumar at irri.org <mailto:s.kumar at irri.org>
> sumanthkumar07 at gmail.com <mailto:sumanthkumar07 at gmail.com>

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