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 <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> 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/ReproducibilityMore 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. Markcpp = /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 gmx-users@gromacs.org <mailto: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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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