[gmx-users] strategy of clustering 10nodes ?

Erik Lindahl lindahl at stanford.edu
Thu May 22 20:01:01 CEST 2003

Hi Taeho,

The best way to manage the nodes is to use a batch system like PBS - 
have a look at www.openpbs.org. That way you can keep them running 
24/7, and there are also advanced features like fair-share scheduling 

When it comes to interconnects there are two options: Either using 
something expensive (but fast) like myrinet, or use cheap ethernet with 
a central switch.

Gigabit ethernet can provide slightly better performance if you find 
the price acceptable - Dell Computer sells pretty cheap switches 



On Thursday, May 22, 2003, at 10:12  AM, Taeho Kim wrote:

> Hi
> We'd like to set up our own cluster, none commercial products, firstly 
> 10 nodes and go large later.  If you are in a situation with 2users 
> and 10nodes cluster, how could you split jobs / nodes?   i.e. 
> clustering nodes for multi-jobs like 2jobs (4nodes-6nodes, 8-2), 3jobs 
> (4-4-2), or 4jobs(3-3-2-2) ?  Is there anyone have similar 
> system/situation?
> And I wonder how important the network topology of cluster is to get 
> the best performance.  Do I need to optimize the hardware 
> interconnectivities of nodes? For example, one group of 4nodes need to 
> be connected each other, like ring topology.  If so, do I need to 
> compile Lam-mpi/fftw/Gromacs with a specific option to enable that 
> cluster group configuration ?
> Even though the size of simulation box will be another factor to 
> answer to this question, I'd be happy for any reference data.  I 
> appreciate any help or suggestions in advance.
> Taeho
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