[gmx-users] Reproducable MD runs on two PCs

[Igor Druz]

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 <Mark.Abraham at anu.edu.au>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 <Mark.Abraham at 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/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
>>
>>
>>
>>
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>
>
>
>
>
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