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On 20/11/2011 9:11 PM, Igor Druz wrote:
<blockquote
cite="mid:CAPEHq69DpySVgiRrh9gMoZZ9WR6Scy5-e3jwwox=wPxLK_bdhw@mail.gmail.com"
type="cite">
<div class="gmail_quote">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.</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAPEHq69DpySVgiRrh9gMoZZ9WR6Scy5-e3jwwox=wPxLK_bdhw@mail.gmail.com"
type="cite">
<div class="gmail_quote">
</div>
<div class="gmail_quote">I was hoping to pick on the experience
with precision, whether it is worth having a go with a double
precision compilation?</div>
</blockquote>
<br>
That will reduce the effect of differences that affect numerical
accuracy but make things more than twice as slow.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPEHq69DpySVgiRrh9gMoZZ9WR6Scy5-e3jwwox=wPxLK_bdhw@mail.gmail.com"
type="cite">
<div class="gmail_quote"> </div>
<div class="gmail_quote">Igor</div>
<div class="gmail_quote"> </div>
<div class="gmail_quote"> </div>
<div class="gmail_quote">On Sun, Nov 20, 2011 at 9:16 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
</div>
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<div> On 20/11/2011 7:31 PM, Igor Druz wrote:
<blockquote type="cite">
<div>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. </div>
<div> </div>
<div>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. </div>
<div> </div>
<div>Is there anything else to consider for better
reproducability on two PCs? Hardware is the same, but
OSes are RedHat and OpenSuse. <br>
</div>
</blockquote>
<br>
</div>
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...<span><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
<br>
<blockquote type="cite">
<div><br>
</div>
<div class="gmail_quote">On Sat, Nov 19, 2011 at 11:31
AM, Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote style="margin: 0px 0px 0px 0.8ex;
padding-left: 1ex; border-left-color: rgb(204, 204,
204); border-left-width: 1px; border-left-style:
solid;" class="gmail_quote">
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<div> On 19/11/2011 10:10 PM, Igor Druz wrote:
<blockquote type="cite">Hello,
<div><br>
</div>
<div>I am running MDs on a linux PC with
OpenSuse, using:</div>
<div><br>
</div>
<div>mpirun -np 4 mdrun -v -dlb auto -reprod
....</div>
<div><br>
</div>
<div>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.</div>
</blockquote>
<br>
</div>
Yep. <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Reproducibility"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a>
<div><br>
<br>
<blockquote type="cite">
<div> 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: <br>
</div>
</blockquote>
<br>
</div>
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.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite">
<div><br>
</div>
<div>
<div>cpp = /usr/bin/cpp
-traditional</div>
<div>integrator = sd</div>
<div>tinit = 0</div>
<div>dt = 0.002</div>
<div>nsteps = 1000000</div>
<div><br>
</div>
<div>nstcomm = 1</div>
<div>nstcalcenergy = 1</div>
<div>nstxout = 5</div>
<div>nstvout = 100</div>
<div>nstlog = 100</div>
<div>nstenergy = 100</div>
<div><br>
</div>
<div>nstlist = 5</div>
<div>ns_type = grid</div>
<div><br>
</div>
<div>pbc = xyz</div>
<div>rlist = 0.9</div>
<div><br>
</div>
<div>optimize_fft = yes</div>
<div>coulombtype = pme</div>
<div>rcoulomb = 0.9</div>
<div>epsilon-r = 1</div>
<div>rvdw = 0.9</div>
</div>
<div><br>
</div>
<div>
<div>constraints = all-bonds</div>
<div>constraint-algorithm = Lincs</div>
<div><br>
</div>
<div>unconstrained-start = yes</div>
<div>lincs-warnangle = 30</div>
</div>
<div>
<div><br>
</div>
<div>tc_grps = System</div>
<div>tau_t = 0.1</div>
<div>ref_t = 300.0</div>
<div><br>
</div>
<div>Pcoupl =
parrinello-rahman</div>
<div>tau_p = 2</div>
<div>compressibility = 4.5e-05</div>
<div>ref_p = 1.0</div>
<div><br>
</div>
<div>gen_vel = yes</div>
<div>gen_temp = 300.0</div>
<div>gen_seed = 173529</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div>Many thanks for your help,</div>
<div> Igor</div>
<br>
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