[gmx-users] Slow Runs
Denny Frost
dsfrost at cableone.net
Fri Jan 28 21:17:14 CET 2011
all 8 nodes are running at full capacity, though
On Fri, Jan 28, 2011 at 1:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ========================================
>
> 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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