Berk Hess wrote:
If you run in parallel, the dynamic load balancing can affective
reprodibility.
You can turn it off with -dlb no
I have a situation now that, without fail, has crashed with the same issues I've
described before while using "-dlb auto." Using "-dlb no" the run does not
fail. The .tpr file has now produced that strange error three times, and I have
run mdrun with the "-debug 1" flag. Would providing these .log files and .xvg
files provide any useful information?
I can also provide the .tpr file in a bugzilla, if that would be useful.
Please let me know and I will upload whatever files you might need.
-Justin
Another source of non-reproducibility is FFTW (with PME).
By default FFTW times which of different codes is the fastest and uses that.
Configuring FFTW with SSE makes all codes faster and the differences
smaller,
so you can configure Gromacs with --disable-fftw-measure to remove
the run time optimization without performance loss.
For debugging purposes the new -reprod switch of mdrun will try to turn
off all optimizations which might affect reproducibilty.
Berk
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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