[gmx-users] Some columns in log file.

[Theodore Si]

thnks a lot !

于2014年7月29日 19:53:19,Justin Lemkul写到:
>
>
> On 7/28/14, 10:11 PM, Theodore Si wrote:
>> For example, a form that explains the meanings of the all items in
>> the log file.
>> I found this page
>> (http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation,_%22What's_in_a_log_file%22,_basic_performance_improvements%3A_Mark_Abraham,_Session_1A)
>>
>> yesterday, it give some information about the log file, but I think it's
>> inadequate.
>>
>> Computing:
>> -------------------
>> Domain decomp.
>
> Doing DD.
>
>> DD comm. load
>> DD comm. bounds
>
> DD communication stuff.
>
>> Send X to PME
>
> Coordinate communication for PME.
>
>> Neighbor search
>
> Self-explanatory.
>
>> Comm. coord.
>
> Communicating coordinates.
>
>> Force
>
> Doing forces.
>
>> Wait + Comm. F
>
> Time spent waiting for, and communicating forces.
>
>> PME mesh
>
> Self-explanatory.
>
>> PME wait for PP
>
> Time spent on PME waiting for particle-particle interactions.
>
>> Wait + Recv. PME F
>
> Time spent waiting and receiving PME forces.
>
>> NB X/F buffer ops.
>
> Nonbonded forces and coordinate operations.
>
>> Write traj.
>
> Self-explanatory.
>
>> Update
>
> Application of all relevant updating functions.
>
>> Constraints
>
> Self-explanatory.
>
>> Comm. energies
>
> Communicating energy information.
>
>> Rest
>
> Everything else.
>
>> -------------------
>> Total
>> -------------------
>> -------------------
>> PME redist. X/F
>> PME spread/gather
>> PME 3D-FFT
>> PME 3D-FFT Comm.
>> PME solve
>> -------------------
>>
>
> A bunch of stuff related to how PME works, communicating data, etc.
>
>> Could you explain each of these items' meaning? Especially, what does
>> X mean?
>>
>
> X means coordinates.  F means forces.  Most of these terms are
> technical specs that determine how much time was spent doing what
> during the run.  Is there something in these terms that concerns you?
> Something indicative of bad performance?
>
> -Justin
>