Hi Gaurav,
separate PME nodes usually pay off on a larger number of nodes
(16). In rare cases, you will see a performance benefit on a small number
of nodes as well. Just try it! Or use g_tune_pme ... ;)
Carsten
On Jun 25, 2010, at 3:32 PM, Gaurav Goel wrote:
I ran my simulation in parallel on 4 nodes (with zero separate PME
nodes). Below is the information printed in md.log.
I see that PME-Mesh calculations took 60% of CPU time. Any
recommendations on using 1 or more separate PME nodes to speed up?
Computing: M-Number M-Flops % Flops
---
Coul(T) + VdW(T) 1761401.496982 119775301.79520.2
Outer nonbonded loop 106414.135764 1064141.358 0.2
Calc Weights 32400.006480 1166400.233 0.2
Spread Q Bspline 2332800.466560 4665600.933 0.8
Gather F Bspline 2332800.46656027993605.599 4.7
3D-FFT 47185929.437184 377487435.49763.6
Solve PME 675840.13516843253768.651 7.3
NS-Pairs 823453.92765617292532.481 2.9
Reset In Box2160.0021606480.006 0.0
CG-CoM 2160.0043206480.013 0.0
Virial 11700.002340 210600.042 0.0
Ext.ens. Update10800.002160 583200.117 0.1
Stop-CM10800.002160 108000.022 0.0
Calc-Ekin 10800.004320 291600.117 0.0
---
Total 593905146.863 100.0
---
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-CyclesSeconds %
---
Domain decomp. 4101 3859.416 1488.1 0.6
Comm. coord. 4501 1874.635 722.8 0.3
Neighbor search410178640.72230322.211.2
Force 4501 180659.90269658.525.8
Wait + Comm. F 4501 2578.994 994.4 0.4
PME mesh 4501 422268.834 162817.760.4
Write traj.4 10001 17.5266.8 0.0
Update 4501 2981.794 1149.7 0.4
Comm. energies 4501 2633.176 1015.3 0.4
Rest 43580.341 1380.5 0.5
---
Total 4 699095.342 269556.0 100.0
---
Thanks,
Gaurav
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
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