<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><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><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 href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
</div><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">
<div bgcolor="#FFFFFF" text="#000000"><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 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">
<div bgcolor="#FFFFFF" text="#000000">
<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 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>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
</div>
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