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

Theodore Si sjyzhxw at gmail.com
Wed Aug 6 04:24:44 CEST 2014

Please compare the file 8.log 
and 512.log 
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 

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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