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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