[gmx-users] gmx sans crashes or return nan's
evanwlowry at gmail.com
Thu Sep 22 14:59:04 CEST 2016
How big is the system? This happened to me when my system required too much
memory to finish the computation. You could try running it on a subset for
your whole system to see if it works or just run it on a subgroup (not on
the group "System") to confirm if this is the problem.
Another thing to try is setting the - endq flag to a smaller value than the
default, thereby reducing the size of the computation.
On Sep 22, 2016 2:47 AM, "Jakub Krajniak" <jakub.krajniak at cs.kuleuven.be>
> I've tried to run gmx sans tool on our trajectory but unfortunately it
> crashes or returns -nan.
> The crash is when it is compiled in Release mode. I have used the latest
> 2016 release.
> GROMACS: gmx sans, version 2016
> gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10
> Select a group: 0
> Selected 0: 'System'
> Reading frame 0 time 0.000 Segmentation fault (core dumped)
> With CMAKE_BUILD_TYPE=Debug, the run does not cause the segmentation fault
> error but the sq.xvg and pr.xvg contain -nan ; This
> is independent of selected groups.
> Maybe someone know what could be the reason of such behavior? Here are the
> .tpr and .xtc files:
> Best regards,
> Jakub Krajniak
> KU Leuven, Dept. Computer Science lokaal: 01.41
> +32 477 68 84 04 / +32 16 37 39 92
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