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

Berk Hess hess at kth.se
Fri May 13 12:10:35 CEST 2016


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.



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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