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

From: Ross Walker <>
Date: Tue, 27 Jan 2015 10:54:32 -0800

Hi Rosemary,

Okay, this definitely looks like a bug - although a weird one. Can you send me the input files you used for the EGB energies you list below (the structure with a low RMS force?) and I'll test this.

One quick question - does this only happen with GB simulations - or have you seen such behavior with PME simulations as well?

All the best

> On Jan 27, 2015, at 10:13 AM, Rosemary Mantell <> wrote:
> Hi Ross,
> I should probably mention that I first saw this problem when using the
> AMBER 12 DPDP model, so it's not just a problem with fixed precision.
> I've set a longer CPU minimisation running today as you suggested,
> though it will be a little while until it finishes. I will let you know
> what I find when it's done. However, I also have an L-BFGS minimiser
> written in CUDA that I have interfaced with the AMBER 12 DPDP potential
> and I have been using this to run minimisations with this system.
> Although the minimisations don't converge properly (the linesearch in
> the minimiser is not tolerant of the fluctuating energies that are being
> produced), I was able to generate some structures with a much lower RMS
> force and put these back into pmemd.cuda. I am still seeing the same
> problem with DPFP and not with SPFP for a variety of different structures.
> I also tried 'imin=0, nstlim=1, ntpr=1' and the EGB energies I got for
> 10 tests with DPFP are: -119767.0113, -119763.2412, -119764.3177,
> -119764.4183, -119763.3771, -119765.8321, -119765.3539, -119764.3328,
> -119764.1440, -119764.9855.
> Thanks,
> Rosie
> On 26/01/2015 15:48, Ross Walker wrote:
>> Hi Rosie,
>> This does indeed look concerning. Although is not surprising if your structure is highly strained. The fixed precision model is such that if energies or forces are too large they will overflow the fixed precision accumulators. This should never happen during MD since the forces would be so large as to cause the system to explode. But it can happen in minimization - but given minimization is designed just to clean up highly strained structures it should not be a concern. The first thing we should do though is establish if this is the case here or if this is a more deeply rooted bug.
>> Can you first run a few thousand steps of minimization of your structure using the CPU and then from the restart files you get from that repeat your tests (just pick a single GPU model and CUDA version as that should not be relevant unless the GPU is faulty but that's unlikely given what you describe) - try it 10 times or so with SPFP and DPFP and see what you get. This will give us an idea of where to start looking.
>> Could you also try, instead of imin=1 setting:
>> imin=0, nstlim=1, ntpr=1 and see what you get reported there for the energies. This does the same calculation but throuhg the MD routines rather than the minimization routines.
>> When I get a chance later today I'll also try it on my own machine with the input you provided.
>> All the best
>> Ross
>>> On Jan 26, 2015, at 7:34 AM, R.G. Mantell <> wrote:
>>> I'm not doing a full minimisation. I am using imin = 1, maxcyc = 0, ncyc
>>> = 0, so would hope to get the same energy if I ran this same
>>> calculation using DPFP several times. Running five times I get: EGB
>>> =-119080.5069, EGB = -119072.8449, EGB = -119079.8208, EGB =
>>> -119076.1230, EGB = -119073.7929
>>> If I do this same test with another system, I get the same EGB energy
>>> every time.
>>> Thanks,
>>> Rosie
>>> On 2015-01-26 15:09, David A Case wrote:
>>>> On Mon, Jan 26, 2015, R.G. Mantell wrote:
>>>>> I am having some problems with pmemd.cuda_DPFP in AMBER 14 and also
>>>>> seeing the same problems in AMBER 12 with DPDP and SPDP precision
>>>>> models. I have some input for which a single energy calculation does
>>>>> not
>>>>> yield the same energy each time I run it. Looking at min.out, it seems
>>>>> that it is the EGB component which gives a different value each time.
>>>>> This does not occur when using SPFP or the CPU version of AMBER. I do
>>>>> not see this problem when using input for other systems. I have tried
>>>>> the calculation on a Tesla K20m GPU and a GeForce GTX TITAN Black GPU
>>>>> using several different versions of the CUDA toolkit. I see the same
>>>>> problem with both igb=1 and igb=2. The input which causes the problem
>>>>> can be found here:
>>>> Can you say how different the values are on each run? What you
>>>> describe is
>>>> exactly what should be expected: parallel runs (and all GPU runs are
>>>> highly
>>>> parallel) with DPDP or SPDP are not deterministic, whereas Amber's SPFP
>>>> is.
>>>> On the other hand, if you are seeing significant differences between
>>>> runs for
>>>> DPDP, that might indicate a bug that needs to be examined.
>>>> ...thx...dac
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Received on Tue Jan 27 2015 - 11:00:02 PST
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