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

Mark Abraham mark.j.abraham at gmail.com
Tue Aug 5 16:11:34 CEST 2014

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.


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