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

[Mark Abraham]

On Wed, Jun 12, 2013 at 3:28 AM, Mark Tianwu Zang <zangtw at gmail.com> wrote:

> 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
>

That's better, but the advice here is worth following:
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy


> 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..
>

Describing in words what your system is doing would be a good start ;-)

Mark


> -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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>
>
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