Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent

From: Jason Swails <>
Date: Thu, 29 Jan 2015 12:42:32 -0500

On Thu, 2015-01-29 at 08:51 -0800, Scott Le Grand wrote:
> I think I found the problem. There's something I can fix that will make
> the manifestation disappear, but the underlying bad news is that I think
> your Born Radius parameters are invalid and that's triggering an
> uninitialized variable, the equivalent of a single threaded race condition
> because God only knows the order of computation and what ends up in that
> uninitialized variable.
> But the thing is that that variable should *never* see a situation where it
> doesn't get a value. It doing so is a sign there's something wrong with
> your Born Radii so I am somewhat tempted to leave the code as is because
> there's no way I'm putting a printf warning in an innermost loop on the GPU.
> David, Ross et al., is there a valid situation in the Born Radius
> calculation where dr should not get a value? Or should it *always* fall
> into one of the clauses as I previosuly believed?

Do any of the intrinsic RADII look bad? Do you know why none of the
clauses in kCalculateGBBornRadii.h are being hit?

Can you put the printf warning into the inner GB loop and see if that
warning is triggered for any of the CUDA tests? I *think* it should
always fall into one of the clauses you specify in that file, but I
haven't looked closely enough to tell for certain. (btw -- would this be
something along the line of adding a raw else clause ~line 171 of that

If you send me the prmtop, I can try and look to see if anything looks

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 29 2015 - 10:00:03 PST
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