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

Mon Jul 28 09:40:00 CEST 2014

I thought that 69.479 ns/day means I can simulate 69.479 ns per day. But 
if as you said, I need 0.345 hour to get a simulated nanosecond, then I 
can only get 0.345 * 24 = 8.28 simulated nanosecond per day? Then what 
does 69.479 mean? And the Core t(s)?

于 2014/7/28 15:29, Mark Abraham 写道:
> 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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