On 20/11/2011 9:11 PM, Igor Druz wrote:
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.
Sure. Make as many things as similar as you can. Just don't bother
trying too hard. The first tiny difference sees the simulations diverge,
and you likely cannot prevent such a difference occurring, even if the
difference is just a different OS on identical hardware. Chaos is
inescapable here.
I was hoping to pick on the experience with precision, whether it is
worth having a go with a double precision compilation?
That will reduce the effect of differences that affect numerical
accuracy but make things more than twice as slow.
Mark
Igor
On Sun, Nov 20, 2011 at 9:16 AM, Mark Abraham <[email protected]
<mailto:[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] <mailto:[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
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