[gmx-users] Reproducable MD runs on two PCs
Mark.Abraham at anu.edu.au
Sun Nov 20 10:16:46 CET 2011
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...
> On Sat, Nov 19, 2011 at 11:31 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
> On 19/11/2011 10:10 PM, Igor Druz wrote:
>> 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
> 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
> 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.
>> 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,
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