If the -reprod option works fine and we can get complete reproducability on one machine, then I would think there must be a way of at least minimizing differences on two machines.
I was hoping to pick on the experience with precision, whether it is worth having a go with a double precision compilation? Igor On Sun, Nov 20, 2011 at 9:16 AM, Mark Abraham <[email protected]>wrote: > On 20/11/2011 7:31 PM, Igor Druz wrote: > > I recompiled gromacs, lam, fftw3 on both PCs with the same version of > intel compilers (before they were different, v. 10 & 12), set gen_vel=no > and optimize_fft=no. > > With these changes I am getting agreement between two PCs within ~5% (was > ~20% before). Ignore the nsteps value from the pasted mdp file. The actual > run with ~20% difference was for the 30 ns run. I will test longer runs. > > Is there anything else to consider for better reproducability on two PCs? > Hardware is the same, but OSes are RedHat and OpenSuse. > > > So far, you don't even know that the variation attributable to the > difference in machines is significant compared to the intrinsic variation > observed over replicates of the same kind of simulation on the same machine > (e.g. different starting velocities). It's just not worth doing the work to > study those effects... > > Mark > > > > On Sat, Nov 19, 2011 at 11:31 AM, Mark Abraham > <[email protected]>wrote: > >> On 19/11/2011 10:10 PM, Igor Druz wrote: >> >> Hello, >> >> I am running MDs on a linux PC with OpenSuse, using: >> >> mpirun -np 4 mdrun -v -dlb auto -reprod .... >> >> If I repeat the calculation on the same PC, I get the same result. If I >> change to another PC with RedHat I get a different result. >> >> >> Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility >> >> >> More specifically, I am calculating a deviation from experiment, which >> varies by ~20 % on changing operating systems (pretty much the same >> hardware on both PCs). Is there any way to avoid such variations? I guess I >> am missing something in the mdp file, which is: >> >> >> Change your gen_vel seed and I bet you observe a similar variation on >> the same machine. There are rather few systems that will have equilibrated >> in 2ns, never mind converged. >> >> Mark >> >> >> >> cpp = /usr/bin/cpp -traditional >> integrator = sd >> tinit = 0 >> dt = 0.002 >> nsteps = 1000000 >> >> nstcomm = 1 >> nstcalcenergy = 1 >> nstxout = 5 >> nstvout = 100 >> nstlog = 100 >> nstenergy = 100 >> >> nstlist = 5 >> ns_type = grid >> >> pbc = xyz >> rlist = 0.9 >> >> optimize_fft = yes >> coulombtype = pme >> rcoulomb = 0.9 >> epsilon-r = 1 >> rvdw = 0.9 >> >> constraints = all-bonds >> constraint-algorithm = Lincs >> >> unconstrained-start = yes >> lincs-warnangle = 30 >> >> tc_grps = System >> tau_t = 0.1 >> ref_t = 300.0 >> >> Pcoupl = parrinello-rahman >> tau_p = 2 >> compressibility = 4.5e-05 >> ref_p = 1.0 >> >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = 173529 >> >> >> Many thanks for your help, >> Igor >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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