Re: [gmx-users] gromacs parallel problem

[Mark Abraham]

mario ciappy wrote:

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.


One can get what one pays for with network hardware. Search in the 
archives for posts by Carsten Kutzner with lots of comments here.


Mark
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[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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