[gmx-users] gromacs parallel problem

[mario ciappy]

Dear All,
I configured gromacs 3.3.3 for parallel runs, using the precompiled packeges on ubuntu server 8.04, with LAM program 7.1.2 ( alreay present in server verison). I tried with d.villin benchmark but I detected an decrease of performance increasing the node's number.
The obtained results for 1 node are:
                       (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:      6.686      1.437      8.471      2.833
The obtained results for 7 nodes are:
                    (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:      5.169      1.112      6.545      3.667

I have a cluster of 7 nodes (pentium 4 3.2 Ghz with RAM 2Gb) connected on 10/100 Mbps dual speed up hub. 
I don't know if it is a configuration problem (because with precompiled packages I couldn't use the configuration parameters described on web) or an hardware problem due to hub. 
Please can you help me? 
Is possible to improve performance changing some other parameters or configuration settings?




	
	
	
	
	
		
Thank you in advance

Best regards

Mario




	
	
	
	
	
		
	
	


	
	
		
			

			

			

		
	






	
	
	
	
	
		



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