Re: [AMBER] GPU vs CPU test

From: Scott Le Grand <>
Date: Thu, 27 Jan 2011 13:12:48 -0800

Overall, I never expect quantitatively different calculations to produce the same result. Besides associative roundoff error (which can happen just by switching compilation modes on the same CPU), there is a difference in the precision model between GPU and CPU (remediable mostly by switching to use_DPDP compilation) and the random number generators between GPU and CPU are completely different, resulting in two different trajectories.

The last part is likely the most likely explanation for your divergence.

-----Original Message-----
From: Massimiliano Porrini []
Sent: Thursday, January 27, 2011 07:06
Subject: [AMBER] GPU vs CPU test

Dear all,

I had the possibility to run Amber11 across 2 Tesla C2050 GPUs and, in order to check the accuracy of the simulation, I ran exactly the same simulation on 4 CPUs, using the same Langevin random number ig generated from the GPU run.

Below there is the input file I used for my system (1561 atoms):

 imin = 0, irest = 1, ntx = 5,
 ntb = 0,
 igb = 5,
 cut = 999.0,
 temp0 = 343.0,
 ntt = 3, gamma_ln = 1.0, ig = -1,
 ntc = 2, ntf = 2,
 nstlim = 500000000, dt = 0.002,
 ntpr = 5000, ntwx = 1000, ntwr = 5000,

For the CPU run I used ig = 857210 .

I attached also a graph with RMSD values and a breakdown of energies calculated for both GPU and CPU runs.

Since I used the same random number for Langevin dynamics, should I expect exactly the same behavior of RMSD and energies?

Or the values in the graph compare anyway well and I am on the safe side with regard to the accuracy of my GPU simulation?
If so, I would guess Amber has another source to make the values unreproducible.

Thanks in advance.

All the best,

PS: I hope the graph is understandable.

Dr. Massimiliano Porrini
Institute for Condensed Matter and Complex Systems School of Physics & Astronomy The University of Edinburgh James Clerk Maxwell Building The King's Buildings Mayfield Road Edinburgh EH9 3JZ
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Received on Thu Jan 27 2011 - 14:00:08 PST
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