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

[Mark Abraham]

Your run took nearly a minute, and did so at a rate that would take 0.345
hours to do a simulated nanosecond

Mark


On Mon, Jul 28, 2014 at 9:05 AM, Theodore Si <sjyzhxw at gmail.com> wrote:

>                Core t (s)   Wall t (s)        (%)
>        Time:     2345.800       49.744     4715.7
>                  (ns/day)    (hour/ns)
> Performance:       69.479        0.345
>
>
> What does 0.345 hour/ns stand for? and the Wall time 49.77s?
>
>
> 于 2014/7/28 14:53, Mark Abraham 写道:
>
>  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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