[gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

[Mark Abraham]

Hi,

Your temperature before step 0 is effectively zero, so it looks like you
ran grompp from a coordinate file with no velocities, and didn't have a
checkpoint file available when you started the mdrun, so mdrun guessed that
you were OK with no checkpoint file. Thus your equlibration didn't have any
effect, and Parrinello-Rahman coupling is not suited for use with
unequilibrated systems. I suggest you give the checkpoint file from the
equilibration either to grompp -t or mdrun -cpi.

Mark

On Thu, Mar 1, 2018 at 10:18 PM Marc Hoemberger <hoemberg at brandeis.edu>
wrote:

> Hi Justing,
>
> I followed your advice and  compiled GROMACS 2016.4 version and used this
> vanilla version (no Plumed patch applied).
>
> I see a very similar behavior as described beofre, in that when starting
> the simulation on a CPU only node, the system behaves well (simulation is
> now running for 2ns+ without any problems),  however, when I start it on
> the GPU/CPU the system seems to be exploding with many LINCS warnings:
>
> Step 231, time 0.462 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 172.973862, max 7198.149414 (between atoms 2104 and 2105)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
> 2098   2101   55.5    0.1528   0.0888      0.1530
> 2101   2102  132.5    0.1304 796.0084      0.1111
>
> And many more of this kind. The system has been equilibrated well
> (NVT+NPT+unconstrained 10ns run - all on CPU only). I tried different
> combinations of GPU/Threads, but the system just seems to not behave well,
> as soon as I try to run it on the GPU node. I am using CUDA version 7.5 and
> NVIDIA GeForce GTX 780 TI cards.
>
> I uploaded both log file and error file on pastebin, in case this might
> help:
> LOGFILE: https://pastebin.com/q24WZ6vF
> ERRORLOG: https://pastebin.com/R8aMHmnD
>
> -Marc
>
>
> > 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
> >
> >
> --
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