[gmx-users] paralleling problems

[Dallas Warren]

>I have a litlle problem with my cluster of 6 pcs running gromacs, When the 
>job starts the md run well but then the job is very slow, using only 4% of 
>each procesors, so my question is. Is there any command to use at the best 
>performance the procesors? I am using lammpi, maybe there is a comand to 
>indicate that.

It may just be a scaling issue.  The smaller the system size, the worse the 
scaling as you go to more CPUs.  It is also very important how the boxes 
are communicating with each other, the faster the hardware you are using, 
the better the scaling will be.

Have you tested how the system you have and run scales over the 1, 2, 4 etc 
CPUs?

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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When the only tool you own is a hammer, every problem begins to resemble a nail.
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