Dear Yanbin, On Dec 30, 2010, at 9:20 PM, WU Yanbin wrote: > I'm simulating a SPC/E water box with the size of 4nm by 4nm by 4nm. The > command "g_tune_pme" was used to find the optimal PME node numbers, Coulomb > cutoff radius and grid spacing size. > > The following command is used: > g_tune_pme -np 24 -steps 5000 -resetstep 500 ... > rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 > > The simulation is done with no error. Below is the output: > --------------------------- > Line tpr PME nodes Gcycles Av. Std.dev. ns/day PME/f DD > grid > 0 0 12 2813.762 187.115 9.604 0.361 4 > 3 1 > 1 0 11 2969.826 251.210 9.112 0.510 13 > 1 1 > 2 0 10 2373.469 154.005 11.385 0.445 2 > 7 1 > 3 0 9 2129.519 58.132 12.665 0.601 5 > 3 1 > 4 0 8 2411.653 265.233 11.248 0.570 4 > 4 1 > 5 0 7 2062.770 514.023 13.490 0.616 17 > 1 1 > 6 0 6 1539.237 89.189 17.547 0.748 6 > 3 1 > 7 0 0 1633.318 113.037 16.548 - 6 > 4 1 > 8 0 -1( 4) 1330.146 32.362 20.276 1.050 4 > 5 1 > --------------------------- > > The optimal -npme is 4. > > It seems to me that the "Std. dev" is too huge. This is the standard deviation resulting from multiple runs with the same settings. If you do not specify "-r" for the number of repeats explicitly to g_tune_pme, it will do two tests for each setting. For the optimum of 4 PME nodes the standard deviation is 2.4 percent of the mean, thus not large at all.
> Can anyone tell me the meaning of "Gcycles Av." and "Std. dev" and their > relations to the accuracy of "ns/day"? Both the number of CPU cycles as the ns/day values are determined from the md.log output file of the respective runs. g_tune_pme does the averaging for you, but you can also look at the individual results, these log files are still there after the tuning run. The standard deviation is printed only for the Gcycles - maybe it is a good idea to also print the standard deviation for the ns/day values. If the standard dev is X percent of the mean for the cycles, then it is also X percent of the mean ns/day. > > Another question: > I tried > g_tune_pme -np 24 -steps 1000 -resetstep 100 ... (the default value of > g_tune_pme) > rcoul=1.5nm, rvdw=1.5nm, fourierspacing=0.12 > > The optimal -npme is 6, different from "-npme=4" as obtained with big > "-nsteps". > Should I increase "-nsteps" even more to get better estimate, or what else > parameters should I try? > In principle the results will become more exact, the longer the test runs are. For your system it seems that the load between the processes is not yet optimally balanced after the default 100 steps so that -resetstep 500 gives you a more accurate value. I think the -steps 5000 value is large enough, but another test with a higher resetstep value would answer your question. Since you already know that 7-12 PME nodes will not perform well, I would try g_tune_pme -np 24 -steps 5000 -resetstep 5000 -min 0.16 -max 0.25 ... Regards, Carsten > Do let me know if the questions are not made clear. > Thank you. > > Best, > Yanbin > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
