[gmx-users] Reproducable MD runs on two PCs
idruz512 at gmail.com
Sun Nov 20 09:31:36 CET 2011
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
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.
On Sat, Nov 19, 2011 at 11:31 AM, Mark Abraham <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 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.
> 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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