[gmx-users] parallel question!!!

Erik Lindahl lindahl at stanford.edu
Wed Apr 9 06:49:00 CEST 2003

Hi Venkat,

Download the benchmarks from www.gromacs.org and run the DPPC system -  
that should scale better (130000 atoms).

We're working on improving the parallelization for smaller systems too,  
but 100Mbit ethernet really won't do for small systems - the latency  
kills you!



On Tuesday, Apr 8, 2003, at 21:31 US/Pacific, Venkat Ramanan K wrote:

> Hi,
> facing the same problem, at present I have to standardize the speed of  
> my cluster (16 IBM's cluster running on LAM). Please suggest the type  
> and kind of system I should simulate in order to standardize the  
> cluster computing power.
> Presently I am running Candida Rugosa Lipase (1CRL) in spc216 water  
> generated box....please suggest.
> thanks
> Venkat
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Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464

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