[gmx-developers] Segmentation fault switching from group to verlet cutoff shceme

[Bu Wang]

Hi Berk,

It might be rare in biological simulations, but for simulations of
inorganic materials, it is very common. I think it is a shame that the
scope of GROMACS is limited to biomaterials. Lots of researches in my field
could benefit from the GROMACS' efficiency and functionality. And some
small improvements would enable that.

Anyway, I guess we will have to invest some effort to figure this out
ourselves. To help us get started, do we need cuda programing experiences
to modify this part of the code?

Thanks,
Bu


On Sat, Mar 16, 2013 at 12:09 PM, Berk Hess <hess at kth.se> wrote:

> Hi,
>
> Buckingham is not a high priority, as it is rarely used.
> But you can easily edit the cuda kernel and put in the Buckingham formula.
> The main issue would be to pass the parameters, as LJ uses two paramater,
> but Buckingham three.
>
> Cheers,
>
> Berk
>
> On 03/16/2013 04:21 PM, Bu Wang wrote:
> Berk,
>
> Thank you for clarifying the issue. Do hope that the support for
> Buckingham potentials could be added soon so we can utilize our GPU cards.
>
> Regards,
> Bu
>
> On Sat, Mar 16, 2013 at 5:07 AM, Berk Hess <hess at kth.se<mailto:hess at kth.se>>
> wrote:
> Hi,
>
> Yes, that is probably the issue.
> I forgot to add a check for Buckingham. I will add this to grompp and
> mdrun.
>
> Cheers,
>
> Berk
>
> On 03/16/2013 03:52 AM, Bu Wang wrote:
> Hi Mark,
>
> Thanks for your attention.
>
> Taking the group scheme .tpr and -testverlet fails in the same way. I've
> opened an issue as per your instruction.
>
> I just noticed that the manual says the Verlet scheme only works with
> plain LJ. We are using Buckingham potentials for non-bonded interactions.
> Could this be the issue? Grompp didn't complain though.
>
> Thanks,
> Bu
>
> On Fri, Mar 15, 2013 at 5:48 PM, Mark Abraham <mark.j.abraham at gmail.com
> <mailto:mark.j.abraham at gmail.com><mailto:mark.j.abraham at gmail.com<mailto:
> mark.j.abraham at gmail.com>>> wrote:
>
>
> On Fri, Mar 15, 2013 at 8:58 PM, Bu Wang <bw2 at alfred.edu<mailto:
> bw2 at alfred.edu><mailto:bw2 at alfred.edu<mailto:bw2 at alfred.edu>><mailto:
> bw2 at alfred.edu<mailto:bw2 at alfred.edu><mailto:bw2 at alfred.edu<mailto:
> bw2 at alfred.edu>>>> wrote:
> Hello,
>
> We encountered a problem with the verlet cutoff scheme in GROMACS 4.6.1. A
> simulation that works fine with the group scheme will crash with
> "Segmentation fault: 11" error using the verlet method. GDB shows that it
> happens in pme.c: 415 idxptr[ZZ] = pme->nnz[tiz], but we are not sure how
> to proceed from here.
>
> Sounds suspicious. Please open an issue at redmine.gromacs.org<
> http://redmine.gromacs.org><http://redmine.gromacs.org><
> http://redmine.gromacs.org> with a description of your simulation, and
> preferably .mdp and .tpr files.
>
> It is possible that our simulation is blowing up, as we can see the
> non-bonded energy becomes absurd in the very first step after switching to
> verlet scheme. However, we don't see how it is possible that the same
> simulation would work with the group scheme. The group scheme gives correct
> energies, and can run to the end without any problem.
>
> That does make it sound like it might be a bug. Can you take your group
> scheme .tpr and use mdrun -testverlet successfully?
>
> To further diagnose the problem, we are wondering how we can let GROMACS
> output the neighbor list. We would also greatly appreciate any suggestion
> to resolve the problem.
>
> The construction of the neighbour lists is different between group and
> Verlet kernels, so there is not much to gain from inspecting them. Knowing
> the combination of algorithms in use is of more interest (so .mdp and any
> mdrun command line options).
>
> Mark
>
>
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