[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

[Ramon Guixà]

Hi Justin,

I do not have access to GPUs with ECC, but I have actually run the same tpr
in different machines with different GPUs, including GTX 980, 1060 and
1080. In all cases, I get the same problem. Although they are all  non-ECC
cards, it is quite unlikely that a bit flip is behind this, isn't it?
In fact, I had simulated before CHARMM-GUI systems using GTX cards and
never had a problem. Since this has only benn happening recently to me, so
I am wondering if I should blame the new force field (CHARMM36m) or whether
CHARMM-GUI changed something in the way they generate gromacs topologies?

Ramon

On Wed, Oct 31, 2018 at 1:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/31/18 8:36 AM, Ramon Guixà wrote:
> > Hi again,
> >
> > Just confirmed that when I run the same tpr file for 500 ns using only
> > CPUs, no problems arise, please check it out here:
> > https://drive.google.com/open?id=1aI2wr2GvNjCfj4c4J0pmgCzV0ak5FRE6
> >
> > <https://drive.google.com/open?id=1aI2wr2GvNjCfj4c4J0pmgCzV0ak5FRE6>
> > I mean, is this a bug? Most of my computer resources are GPU-based, is
> > there anything I can change in the set-up or compilation so I can
> simulate
> > using gromacs, CHARMM36, and GPUs?
>
> Do you have access to a GPU with ECC? I wonder if this is a software bug
> or something going wrong with the GPU, like a bit flip. I've experienced
> this very rarely with consumer-grade cards like GTX 980, certainly not
> with the regularity you're seeing, though. There's clearly something
> wrong in your system to trigger such a sudden change. I pulled all the
> energy terms from your .edr file but it's hard to determine cause/effect
> in any of them.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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