[gmx-developers] gromacs 2016 beta1 bug somewhere in the new simd for bonded/LJ/lincs

Carlo Camilloni carlo.camilloni at gmail.com
Tue May 17 09:58:58 CEST 2016


The x must be identical because I used -rerun to parse the trr file, while
I don’t know if the velocities are recalculated by rerun.
What I am sure about is that the differences observed with metadynamics
are highly significant. 
Right now I don’t have more time to investigate this, I will definitely
do it as soon as I can, but if you have time i would have a further
look into it..


> Message: 1
> Date: Fri, 13 May 2016 12:10:52 +0200
> From: Berk Hess <hess at kth.se>
> To: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] gromacs 2016 beta1 bug somewhere in the
> 	new simd for bonded/LJ/lincs
> Message-ID: <5735A82C.7080508 at kth.se>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
> Hi,
> In the files you sent I see that x and v are identical for all versions 
> and f has a few components that differ up to 0.002 kJ/mol/nm. This is 
> fully within the variation I would expect from different codes.
> We need more evidence to judge if there is a bug present here. I can't 
> judge if the differences in your metadynamics results are significant 
> compared to the statistical accuracy.
> Cheers,
> Berk
> On 2016-05-13 11:59, Carlo Camilloni wrote:
>> Dear GMX developers,
>> First of all thanks for your continuos efforts in making gromacs better.
>> I have done a very basic calculation with the new gromacs-2016-beta1 
>> and I think there is a bug somewhere
>> in the force calculation. (all calculations are run using 1 processor, 
>> no mpi, no openmp, no gpus)
>> I have run a calculation on alanine dipeptide:
>> 1) GMX507: 2 steps using 1 processor (avx2 simd and nothing else, the 
>> tpr is generated with gromacs 507)
>> 2) rerun with GMX512 on the trr file
>> 3) rerun with GMX2016 on the trr file
>> and then I compared forces, velocities and energies, and while they 
>> are essentially the same for the step 0
>> in the case of GMX507 and 512 they are not the same anymore for GMX2016b1.
>> The differences are not huge, even if from a rerun I would expect no 
>> differences at all, in particular on the
>> forces, so I have run a metadynamics calculation from the same tpr 
>> file and using the three codes
>> patched with plumed to see the effect on the free energy along the phi 
>> torsion angle, and unfortunately the
>> difference is quite significant.
>> to be sure I repeated the same tests on a linux workstation (the first 
>> test was on my macbook), so different
>> compilers and so on, but always avx2 simd)
>> here you can find everything (all the files I have generated):
>> https://dl.dropboxusercontent.com/u/1349402/bug-report-aladip-2016.tgz
>> I hope this helps.
>> Best,
>> Carlo
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