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

Thu Jun 13 09:53:11 CEST 2013

On Wed, Jun 12, 2013 at 10:58 PM, Tianwu Zang <tz4 at rice.edu> wrote:

> Hi all,
> I am using a very common system for testing, with only one protein (~1000+
> atoms) and ~7000+ water atoms with box size = 4.5
> When I tried rerun the simulation, results kept the same with the last run
> for the same kernel, but became quite different (even at step=0) for
> different kernel, like using generic kernel in the first run and specific
> kernel in the second run..
> In my case, for specific kernel, f[0]~884 and for generic kernel f[0]~337,
> which is a huge difference..
> I have already set the variable gen_seed in my .mdp file so there
> shouldn't be any problem of random seed.
> Now I am wondering if these force results should not differ from each
> other, where I am doing wrong?
>

OK. What's your .mdp file?

Mark

> Thanks again,
> -Mark
>
>
> On Wed, Jun 12, 2013 at 8:05 AM, francesco oteri <
> francesco.oteri at gmail.com> wrote:
>
>> 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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>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>>>> 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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