[gmx-users] How do I get to know the meaning of the first column in log file?

[Mark Abraham]

On Jul 28, 2014 4:53 AM, "Theodore Si" <sjyzhxw at gmail.com> wrote:
>
> For example, in the following form, what does Wait + Comm. F mean? Is
> there a webpage that explains the forms in log file?

Unfortunately not (yet), but they correspond in a more-or-less clear way to
the segments in manual figure 3.16. In this case, to the three boxes below
"Evaluate potential/forces." Significant time spent here would indicate
poor balance of compute load.

Mark

>
> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>
> Computing: Nodes Th. Count Wall t (s) G-Cycles %
>
-----------------------------------------------------------------------------
> Domain decomp. 24 2 801 2.827 351.962 5.7
> DD comm. load 24 2 800 0.077 9.604 0.2
> DD comm. bounds 24 2 800 0.354 44.014 0.7
> Neighbor search 24 2 801 1.077 134.117 2.2
> Launch GPU ops. 24 2 40002 1.518 189.021 3.1
> Comm. coord. 24 2 19200 2.009 250.121 4.0
> Force 24 2 20001 8.478 1055.405 17.0
> Wait + Comm. F 24 2 20001 1.967 244.901 4.0
> PME mesh 24 2 20001 24.064 2995.784 48.4
> Wait GPU nonlocal 24 2 20001 0.170 21.212 0.3
> Wait GPU local 24 2 20001 0.072 8.935 0.1
> NB X/F buffer ops. 24 2 78402 0.627 78.050 1.3
> Write traj. 24 2 2 0.037 4.569 0.1
> Update 24 2 20001 0.497 61.874 1.0
> Constraints 24 2 20001 4.198 522.645 8.4
> Comm. energies 24 2 801 0.293 36.500 0.6
> Rest 24 1.478 184.033 3.0
>
-----------------------------------------------------------------------------
> Total 24 49.744 6192.746 100.0
>
-----------------------------------------------------------------------------
>
-----------------------------------------------------------------------------
> PME redist. X/F 24 2 40002 6.199 771.670 12.5
> PME spread/gather 24 2 40002 7.194 895.557 14.5
> PME 3D-FFT 24 2 40002 2.727 339.480 5.5
> PME 3D-FFT Comm. 24 2 80004 7.460 928.742 15.0
> PME solve 24 2 20001 0.434 53.968 0.9
>
-----------------------------------------------------------------------------
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