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

[Mark Abraham]

I plan to put some more of this kind of documentation in the upcoming User
Guide, but it isn't done yet.

Number of times that section was entered, the total wall time spent in that
section, and the total number of processor gigacycles spent in that
section, and percentage of same. Some columns are useful for only some
kinds of comparisons.

Mark


On Mon, Jul 28, 2014 at 5:35 AM, Theodore Si <sjyzhxw at gmail.com> wrote:

> Thanks a lot!
> But I am still confused about other things.
> For instance, what do count, wall t(s) G-Cycles mean? It seems that the
> last column is the percentage of G-Cycles.
> I really hope there is a place where I can find all relative information
> of the log file.
>
> 于 2014/7/28 11:12, Mark Abraham 写道:
>
>  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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