[gmx-users] Some columns in log file.
jalemkul at vt.edu
Tue Jul 29 13:53:33 CEST 2014
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
> yesterday, it give some information about the log file, but I think it's
> Domain decomp.
> DD comm. load
> DD comm. bounds
DD communication stuff.
> Send X to PME
Coordinate communication for PME.
> Neighbor search
> Comm. coord.
> Wait + Comm. F
Time spent waiting for, and communicating forces.
> PME mesh
> 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.
Application of all relevant updating functions.
> Comm. energies
Communicating energy information.
> 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
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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