Re: AMBER: amber8 parallel sander

From: yen li <>
Date: Wed, 12 Jan 2005 05:54:48 -0800 (PST)

Thanks Robert & Carlos for the clearifications.
I have one more related doubt. I also timed the same simulations for the 4 cases: namely 1, 4, 8 & 16 processors. I find that it's the fastest for 4 and slower for 1, 8 &16. I can understand for 1 but cannot understand it getting slower for increased number of processors.
All the processors are of the same make(Sun UltraSparc III+), same OS(Solaris 8), same amount of RAM(1GB each) and connected over 1GBps network.

Robert Duke <> wrote:
Yen -
As Carlos says, this is expected. The reason is that when you parallelize the job, the billions of calculations done occur in different orders, and this introduces different rounding errors. With pmemd, you will even see differences with the same number of processors, and this is because there is dynamic load balancing of direct force workload (ie., if one processor is taking more time to do the direct force calcs, it will be assigned fewer atoms to work on). You have to remember that the internal numbers used have way more precision than is justified by our knowledge of parameters, or for that matter how well the method represents reality, and that any one represents one of many possible trajectories.
Regards - Bob Duke
----- Original Message -----
From: yen li
Sent: Wednesday, January 12, 2005 5:57 AM
Subject: AMBER: amber8 parallel sander

Hello amber
I am testing the parallel version of amber8. I am running an md simulation over a small protein.
I am testing the calculations on four, eight and sixteen processors. My problem is that, initially the energy values in the output files are the same, but as the simulation proceeds, the values start to diverge making the differences large. Is this kind of behaviour ok or do i need to take care of some parameters.

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Received on Wed Jan 12 2005 - 14:53:00 PST
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