[gmx-developers] reproducability of md sims

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 2 11:34:06 CET 2014

On 2014-12-02 10:27, Bogdan Costescu wrote:
> On Sun, Nov 30, 2014 at 9:05 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> Hi,
>> I'm trying to test reproducibility of simulations of liquids. The simulation
>> systems are flexible (no constraints) and run with the -reprod flag,
>> starting from the same tpr, on a single core. However after a few hundred fs
>> the energy starts to diverge.
>> Are there factors impacting the reproducibility that are not controlled by
>> the -reprod flag?
> About 3 years ago, I have run extensive tests of binary
> reproducibility with GROMACS 4.5.3, also with no constraints, for up
> to 1ns. However I was interested in parallel runs, not single core
> ones, for performance reasons. With '-reprod -dlb no' I was able to
> achieve what I wanted, after I was told that with DLB enabled this is
> not possible:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2011-July/005323.html
> Apart from these flags, reproducibility also requires keeping the same
> number of ranks, architecture of nodes, libs, etc. to avoid the
> rounding and order-of-operations problems mentioned earlier. I have
> not redone these tests with 4.6.x or newer.

It is reproducible still with 4.6.7, it was due to user (me) error.

> Cheers,
> Bogdan

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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