[gmx-users] How do I get to know the meaning of the first column in log file?
Theodore Si
sjyzhxw at gmail.com
Mon Jul 28 13:46:26 CEST 2014
Hi all,
Could anyone explain all the meanings of these columns in log?
I'd appreciate your help.
Domain decomp.
DD comm. load
DD comm. bounds
Send X to PME
Neighbor search
Comm. coord.
Force
Wait + Comm. F
PME mesh
PME wait for PP
Wait + Recv. PME F
NB X/F buffer ops.
Write traj.
Update
Constraints
Comm. energies
Rest
------------------
Total
------------------
------------------
PME redist. X/F
PME spread/gather
PME 3D-FFT
PME 3D-FFT Comm.
PME solve
于2014年7月28日 15:51:15,Guillaume Chevrot写到:
> Hi,
>
> if you need 0.345 hour to get 1 ns, that means that you can simulate
> 1/0.345~2.9ns/hour, then in one day you will simulate 1/0.345*24~69.5 ns
>
> Guillaume
>
> On 07/28/2014 09:39 AM, Theodore Si wrote:
>> 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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