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 119775301.795 20.2 > 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 2332800.466560 27993605.599 4.7 > 3D-FFT 47185929.437184 377487435.497 63.6 > Solve PME 675840.135168 43253768.651 7.3 > NS-Pairs 823453.927656 17292532.481 2.9 > Reset In Box 2160.002160 6480.006 0.0 > CG-CoM 2160.004320 6480.013 0.0 > Virial 11700.002340 210600.042 0.0 > Ext.ens. Update 10800.002160 583200.117 0.1 > Stop-CM 10800.002160 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-Cycles Seconds % > ----------------------------------------------------------------------- > Domain decomp. 4 1000001 3859.416 1488.1 0.6 > Comm. coord. 4 5000001 1874.635 722.8 0.3 > Neighbor search 4 1000001 78640.722 30322.2 11.2 > Force 4 5000001 180659.902 69658.5 25.8 > Wait + Comm. F 4 5000001 2578.994 994.4 0.4 > PME mesh 4 5000001 422268.834 162817.7 60.4 > Write traj. 4 10001 17.526 6.8 0.0 > Update 4 5000001 2981.794 1149.7 0.4 > Comm. energies 4 5000001 2633.176 1015.3 0.4 > Rest 4 3580.341 1380.5 0.5 > ----------------------------------------------------------------------- > Total 4 699095.342 269556.0 100.0 > ----------------------------------------------------------------------- > > Thanks, > Gaurav > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
