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

[Carlo Camilloni]

Hi Berk

Yes I confirm that this fixes the problem, the metadynamics calculated free energies are know 
in agreement within the statistical accuracy

Cheers,
Carlo

> 
> Message: 1
> Date: Mon, 23 May 2016 14:49:59 +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: <5742FC77.6080600 at kth.se>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> Hi,
> 
> I just found a bug in the 2016 beta that probably explains your 
> observations:
> http://redmine.gromacs.org/issues/1968
> Fix at:
> https://gerrit.gromacs.org/#/c/5885
> 
> Cheers,
> 
> Berk
> 
> On 2016-05-17 09:58, Carlo Camilloni wrote:
>> Hi
>> 
>> 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..
>> 
>> Cheers,
>> Carlo
>> 
>> 
>>> 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
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>> URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20160513/1ad1cd57/attachment-0001.html>
>>> 
>>> ------------------------------
>>> 
>>> -- 
>>> Gromacs Developers mailing list
>>> 
>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or send a mail to gmx-developers-request at gromacs.org.
>>> 
>>> End of gromacs.org_gmx-developers Digest, Vol 145, Issue 17
>>> ***********************************************************
>