[gmx-developers] Inconsistent force calculating result between generic kernel and interaction-specific kernel?

[Mark Tianwu Zang]

Hi Francesco and Mark,
Thanks for your precious advice. Now this time I didn't insert any code but
use the .mdp options instead. I used the following steps: first set the
environment variable GMX_NB_GENERIC=1, run the GROMACS, and run again with
the same input but GMX_NB_GENERIC unset. Next, compare two force.xvg
generated from two traj.trr using g_traj. However, I still found the
results different from each other.. My gcc version is 4.6.3(almost the
newest), my fftw version is 3.3.3(double precision, and GROMACS is also
build in double-precision) and I use the argument --reprod to make sure the
calculation of PME is reproducible.
My running command for GROMACS is
mpirun -np 2 mdrun_mpi -s test.tpr -v -reprod
I tried to attach my test tpr and mdp file in this email but my attempt was
not approved by administrator because the email would be oversized..

-Mark


On Sat, Jun 8, 2013 at 7:25 AM, francesco oteri
<francesco.oteri at gmail.com>wrote:

> In my case the excuse was that the system administrator never updated the
> compiler.
> So I after a couple of days I installed the new compiler.
> In any case, I noticed that the problem disappeared using the "Debug"
> version so  I guess
> it is something related either to the optimized kernel or the optimization
> strategy used by the compiler.
>
>
> Francesco
>
>
> 2013/6/8 Mark Abraham <mark.j.abraham at gmail.com>
>
>>
>>
>>
>> On Sat, Jun 8, 2013 at 12:59 PM, francesco oteri <
>> francesco.oteri at gmail.com> wrote:
>>
>>> H Mark,
>>> I had a similar problem recently and, eventually, I figured out the
>>> cause was the compiler version.
>>> I was using gcc4.1 and my problem got solved using a more recent
>>> version. Actually, this issue
>>> in the website is clearly stated. So, which compiler are you using?
>>> Could you report an example of inconsistency?
>>>
>>
>> That warning has been there many years, but AFAIK nobody ever identified
>> the real problem (if it exists). Nevertheless, there is no excuse for using
>> both GROMACS and such an old compiler! :-)
>>
>> Mark
>>
>>
>>> Francesco
>>>
>>>
>>> 2013/6/8 Mark Abraham <mark.j.abraham at gmail.com>
>>>
>>>>
>>>>
>>>>
>>>> On Sat, Jun 8, 2013 at 1:44 AM, Mark Tianwu Zang <zangtw at gmail.com>wrote:
>>>>
>>>>> Dear all,
>>>>> I have inserted only a few lines after update() in md.c to monitor how
>>>>> forces change after every step. My codes are very simple, just like:
>>>>>
>>>>> for i=0 to md->nalloc
>>>>>  fprintf f[i][0], f[i][1], f[i][2]
>>>>>
>>>>
>>>> That seems like the hard way to do it, with nstfout available in the
>>>> .mdp file.
>>>>
>>>> However, I found the results of my output become quite different after
>>>>> exporting GMX_NB_GENERIC=1, which means the forces calculated by generic
>>>>> kernel and interaction-specific kernel are not the same. I am a little
>>>>> confused now.. It this phenomena quite normal or I ignored something
>>>>> important?
>>>>>
>>>>
>>>> AFAIK the generic kernel should serve as a reference for the
>>>> interaction-specific kernels. If not, there might a problem to fix. Hard to
>>>> say without context.
>>>>
>>>> Mark
>>>>
>>>> Thanks a lot!
>>>>> -Mark
>>>>>
>>>>>
>>>>>
>>>>> --
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>>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> Cordiali saluti, Dr.Oteri Francesco
>>>
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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
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