[gmx-users] strategy of clustering 10nodes ?

Taeho Kim taeho.kim at utoronto.ca
Thu May 22 19:29:01 CEST 2003

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.


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