[gmx-users] Selecting Nodes While Running Parallel Mdrun

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Tue Apr 25 08:47:12 CEST 2006

On Tuesday 25 April 2006 07:44, Shankar Prasad Kanaujia wrote:
> Dear Gromacs Users,
> I am installing parallel version of gromacs on linux cluster, but I do not
> want to use all the nodes for my simulation. Is there any way to select
> some specific nodes for simulation ?
> Will I have to specify the nodes while installing or I would be able to
> select the nodes after installation according to my requirement ?
> What are the necessary files to be edited for the same ?

You have to install a batch processing and resource management system, there 
are several around like openpbs (http://www-unix.mcs.anl.gov/openpbs/), maui 
and torque ... also there s a solution from sun/ sgi 

afaik the only free solution is openpbs and it will work for small 
installations without high requirements.

if you want to run it parallel you have to install mpich and lam.
Also a shared filesystem for all this nodes would be nice (easiest nfs also 
afs or any other shared filesystem like clusterfs).
> Thanks,
> Shankar Prasad Kanaujia
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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