[gmx-users] Some columns in log file.

Justin Lemkul 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
> (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


> Comm. coord.

Communicating coordinates.

> Force

Doing forces.

> 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.


> Update

Application of all relevant updating functions.

> Constraints


> Comm. energies

Communicating energy information.

> Rest

Everything else.

> -------------------
> Total
> -------------------
> -------------------
> PME redist. X/F
> PME spread/gather
> 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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