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

[francesco oteri]

Hi,
Marc said it is using -rerun and, as far as I know and basing on my
experience,
it gives exactly the same reults. Of course, also the seed has to be the
same :D

Francesco


2013/6/12 Berk Hess <hess at kth.se>

>  Hi,
>
> You haven't said at what step this happens.
> At step zero the forces should match, except for the last decimal(s).
> But since MD is chaotic, trajectories diverge exponentially, which is very
> fast.
> This usually means forces are significantly decorrelated after 100 to 1000
> steps.
>
> Cheers,
>
> Berk
>
>
> On 06/12/2013 01:50 PM, Mark Abraham wrote:
>
>
>
>
> 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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-- 
Cordiali saluti, Dr.Oteri Francesco
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