[gmx-users] Why is there a NxN VdW [F] on a separate line?

[Theodore Si]

  Computing:                                           M-Number         
           M-Flops                      % Flops
----------------------------------------------------------------------------------------------------------------------------
  NxN Ewald Elec. + VdW [F]                  1254121.354624   
82772009.405            95.1
  NxN Ewald Elec. + VdW [V&F]            178.171584           
19064.359                 0.0

This is extracted from a log file. I don't understand it's meaning. Why 
the flops of  [V&F] (V&F=Potential and force)is 0.0% while [F](force 
only ) is 95.1%?

On 8/6/2014 10:24 AM, Theodore Si wrote:
> Please compare the file 8.log 
> <https://onedrive.live.com/redir?resid=990FCE59E48164A4%212481&authkey=%21AI9ThbRY_7ZgAg8&ithint=file%2clog> 
> and 512.log 
> <https://onedrive.live.com/redir?resid=990FCE59E48164A4%212482&authkey=%21APLkizOBzXtPHxs&ithint=file%2clog>.Their 
> M E G A - F L O P S   A C C O U N T I N  part are different as 8.log 
> has no standalone NxN VdW [F] and NxN VdW [V&F]. 512.log has the 
> following lines.
>
> NxN VdW [F]                             17.077648 563.562     0.0
> NxN VdW [V&F]                            0.002592 0.111     0.0
>
> Why the difference?
>
> And the both have
>
>  NxN Ewald Elec. + VdW [F]
>  NxN Ewald Elec. + VdW [V&F]
>
> Does  NxN Ewald Elec. + VdW [F] mean  NxN Ewald Elec.  and NxN VdW 
> [F]? If it is the case, why 512.log has both  NxN Ewald Elec. + VdW 
> [F] and NxN VdW [F]?
>
> On 8/5/2014 10:11 PM, Mark Abraham wrote:
>> On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si<sjyzhxw at gmail.com>  wrote:
>>
>>> This is extracted from a log file
>> There's no data. The list cannot accept attachments, so you need to
>> copy-paste a relevant chunk, or upload a log file to a file-sharing service.
>>
>>
>>> of a mdrun of 512 openMP threads without GPU acceleration.
>> mdrun will refuse to run with 512 OpenMP threads - please report your mdrun
>> command line rather than your mental model of it.
>>
>>
>>> Since the first line and third line both have N*N Vdw [F], does the former
>>> include the latter?
>>>
>> No, but there is no line with "N*N Vdw [F]". Please be precise if you are
>> asking for detailed information.
>>
>> As we can see, in the log file of a mdrun of 8 openMP threads without GPU
>>> acceleration, there is no standalone N*N Vdw [F], why the difference?
>> Can't tell, don't know what is different between the two runs. My guess is
>> that the former run is actually running on 64 MPI ranks, each of 8 OpenMP
>> threads, in which case you have domain decomposition per MPI rank, and in
>> that case there are separate calls to kernels that are aimed at computing
>> the interactions associated with atoms whose home is in different domains.
>> You should see the ratio vary as the number of ranks varies.
>>
>> Mark
>>
>>
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>