[gmx-users] Slow Runs

[Justin A. Lemkul]

Denny Frost wrote:
> Here's what I've got:
> 
> M E G A - F L O P S   A C C O U N T I N G
> 
>    RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
>    T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
>    NF=No Forces
> 
>  Computing:                               M-Number         M-Flops  % Flops
> -----------------------------------------------------------------------------
>  Coul(T) + VdW(T)                   1219164.751609    82903203.109    80.6
>  Outer nonbonded loop                 25980.879385      259808.794     0.3
>  Calc Weights                         37138.271040     1336977.757     1.3
>  Spread Q Bspline                    792283.115520     1584566.231     1.5
>  Gather F Bspline                    792283.115520     4753698.693     4.6
>  3D-FFT                              119163.856212      953310.850     0.9
>  Solve PME                             2527.465668      161757.803     0.2
>  NS-Pairs                             47774.705001     1003268.805     1.0
>  Reset In Box                           371.386080        1114.158     0.0
>  Shift-X                              24758.847360      148553.084     0.1
>  CG-CoM                                1237.953600        3713.861     0.0
>  Angles                               18569.135520     3119614.767     3.0
>  Propers                              14855.308416     3401865.627     3.3
>  Impropers                             3094.855920      643730.031     0.6
>  Virial                                1242.417375       22363.513     0.0
>  Stop-CM                               1237.953600       12379.536     0.0
>  P-Coupling                           12379.423680       74276.542     0.1
>  Calc-Ekin                            12379.436160      334244.776     0.3
>  Lincs                                11760.476208      705628.572     0.7
>  Lincs-Mat                           245113.083072      980452.332     1.0
>  Constraint-V                         23520.928704      188167.430     0.2
>  Constraint-Vir                       11760.452496      282250.860     0.3
> -----------------------------------------------------------------------------
>  Total                                               102874947.133   100.0
> -----------------------------------------------------------------------------
> 
> 
>      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     %
> -----------------------------------------------------------------------
>  Neighbor search    1      99195     8779.027     3300.3       3.8
>  Force                   1     991941   188562.885    70886.8    81.7
>  PME mesh           1     991941    18012.830     6771.6      7.8
>  Write traj.             1            41     16.835          6.3         
>  0.0
>  Update                 1     991941     2272.379      854.3       1.0
>  Constraints           1     991941    11121.146     4180.8     4.8
>  Rest                     1                    2162.628      813.0      0.9
> -----------------------------------------------------------------------
>  Total                    1                  230927.730    86813.1   100.0
> -----------------------------------------------------------------------
> -----------------------------------------------------------------------
>  PME spread/gather      1    1983882      17065.384    6415.4   7.4
>  PME 3D-FFT               1    1983882      503.340       189.2     0.2
>  PME solve                  1     991941       427.136       160.6     0.2
> -----------------------------------------------------------------------
> 
> Does that mean it's only using 1 node?  That would explain the speed issues.
> 

That's what it looks like to me.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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