[gmx-users] Selecting Nodes While Running Parallel Mdrun

Erik Lindahl lindahl at sbc.su.se
Tue Apr 25 08:59:06 CEST 2006


On Apr 25, 2006, at 8:47 AM, Florian Haberl wrote:

> hi,
> 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.

Cluster resources provide great free tools in Maui (scheduler) and  
Torque (batch system build on OpenPBS). They are distributed with the  
(also free) Rocks linux cluster distribution, and we're using them  
quite successfully on a 600-CPU cluster in Stanford :-)



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