[gmx-users] please guide me through the confusing gromacs results!!!

[Justin Lemkul]

On 2/26/14, 4:31 AM, delara aghaie wrote:
> Dear Gromacs users,
> we want to simulateHSA protein using8 processors. Usually with our available system 10ns simulation on 8 processors lasts 2-3 days.
> This time we submitted 10 ns simulation, after almost 6 days it has finished but when we look at md.log file, only 179411 steps has been completed and all the averages are over this time, although we have submitted the run 5000000 steps=10ns
> 1) First I want to know how the log file shows the end of simulation, although only 0.35 ns of simulation is done and if we draw RDF the time again shows completing of 0.35 ns.
> you can see the ending part of log file below:
> 2) the second point is that the average load imbalance is shown as 110.3% while for previous runs we had this as 3-4 %.
> what can be the reason for this high load imbalance?
> and is this responsible for the lower simulation efficiency and higher time?

Something is unhealthy with the nodes you ran on; either they had other jobs 
running that competed with yours or something is simply wrong with one or more 
of them.

> and the most important that why the log file is written in the way that the simulation has been completed while only 0.3 ns has passes?

Something caused the run to end, and when that happens, mdrun writes the 
statistics to the .log file.  Presumably you hit a wallclock limit or something 
that told mdrun to stop.

-Justin

> Thanks for your time
> **********************************************************
>   D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
>
>   av. #atoms communicated per step for force:  2 x 97992.1
>   av. #atoms communicated per step for LINCS:  2 x 2373.8
>
>   Average load imbalance: 110.3 %
>   Part of the total run time spent waiting due to load imbalance: 1.4 %
>
>
>       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     Number     G-Cycles    Seconds     %
> -----------------------------------------------------------------------
>   Domain decomp.         8      35882   556174.638   209101.4     5.1
>   DD comm. load          8        359      235.791       88.6     0.0
>   Comm. coord.           8     179411   407595.614   153241.1     3.7
>   Neighbor search        8      35883    39333.698    14788.0     0.4
>   Force                  8     179411   205203.393    77149.0     1.9
>   Wait + Comm. F         8     179411   471040.171   177093.9     4.3
>   PME mesh               8     179411  8699277.459  3270611.0    79.1
>   Write traj.            8        752    15563.463     5851.3     0.1
>   Update                 8     179411    12991.140     4884.2     0.1
>   Constraints            8     179411   438837.169   164986.8     4.0
>   Comm. energies         8      35884   149298.111    56130.6     1.4
>   Rest                   8                6090.776     2289.9     0.1
> -----------------------------------------------------------------------
>   Total                  8            11001641.424  4136215.9   100.0
> -----------------------------------------------------------------------
> -----------------------------------------------------------------------
>   PME redist. X/F        8     358822  1446552.180   543850.9    13.1
>   PME spread/gather      8     358822   820940.059   308643.5     7.5
>   PME 3D-FFT             8     358822  6426689.995  2416201.0    58.4
>   PME solve              8     179411     5033.523     1892.4     0.0
> -----------------------------------------------------------------------
>
>          Parallel run - timing based on wallclock.
>
>                 NODE (s)   Real (s)      (%)
>         Time: 517026.991 517026.991    100.0
>                        5d23h37:06
>                 (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
> Performance:      9.634    506.361      0.060    400.250
> Finished mdrun on node 0 Tue Feb 25 13:34:48 2014
>

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================