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

francesco oteri francesco.oteri at gmail.com
Thu Jun 13 10:46:18 CEST 2013 

Hi Tianwu,
just to be sure, can you try to compile with CMAKE_BUILD_TYPE=Debug
and repeating again the runs?

Francesco


2013/6/13 Mark Abraham <mark.j.abraham at gmail.com>

>
>
>
> 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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