[gmx-users] gromacs.org_gmx-users Digest, Vol 166, Issue 129

[Marc Hoemberger]

Hi Justin,

I did try to reproduce the behavior of the GPU-calculation crash with a
vanilla gromacs (5.1.4) version. No matter if I use vanilla gromacs or the
patched gromacs version I do see that on CPU node only the calculation runs
without problems, as soon as I try to run the simulation with GPU the
simulation crashes with the aforementioned error.

I am currently compiling gromacs 2018 and will report back if I see the
same behavior for gromacs 2018.


-Marc


> Message: 2
> Date: Wed, 28 Feb 2018 13:13:22 -0500
> From: Marc Hoemberger <hoemberg at brandeis.edu>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Gromacs on CPU runs fine, same calculation
>         crashes on GPU with nonbonded interaction larger than table limit
> Message-ID:
>         <CALj=QVqfXyT8x66rFgpWjJmDotW4Ugu0eri=0_ve_x_cMv29ww at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi everyone,
>
> I ran a targeted md simulation with gromacs 5.1.4 + plumed 2.4.0 on a
> 32-core node. The simulation worked well, however when I wanted to try to
> run the identical simulation (same starting points etc) on a CPU/GPU node
> the run crashes with two warnings of the following type:
>
> WARNING: Listed nonbonded interaction between particles X and Y at distance
> Z which is larger than the table limit W nm.
>
> I know that my system is equilibrated well, and the same setup does work
> perfect on the CPU only run.
>
> For running the GPU run I use -ntomp 4 and one gpu, with -pin on. I use
> CUDA 7.0.28 and gromacs 5.1.4 with plumed 2.4.0.
>
> If there is any additional information that could help, let me know and I
> will provide it.
>
> Best,
> Marc
>
>
> Message: 4
> Date: Wed, 28 Feb 2018 13:14:49 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Gromacs on CPU runs fine, same calculation
>         crashes on GPU with nonbonded interaction larger than table limit
> Message-ID: <4e9deb70-0d37-09e7-36ff-99bf880adb5b at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 2/28/18 1:13 PM, Marc Hoemberger wrote:
> > Hi everyone,
> >
> > I ran a targeted md simulation with gromacs 5.1.4 + plumed 2.4.0 on a
> > 32-core node. The simulation worked well, however when I wanted to try to
> > run the identical simulation (same starting points etc) on a CPU/GPU node
> > the run crashes with two warnings of the following type:
> >
> > WARNING: Listed nonbonded interaction between particles X and Y at
> distance
> > Z which is larger than the table limit W nm.
> >
> > I know that my system is equilibrated well, and the same setup does work
> > perfect on the CPU only run.
> >
> > For running the GPU run I use -ntomp 4 and one gpu, with -pin on. I use
> > CUDA 7.0.28 and gromacs 5.1.4 with plumed 2.4.0.
> >
> > If there is any additional information that could help, let me know and I
> > will provide it.
>
> Can you reproduce the problem with a vanilla GROMACS version
> (non-PLUMED), preferably something newer?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>