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

[Marc Hoemberger]

I was not aware that the way I set it up temperature and pressure from NVT
and NPT equilibrations were not taken over. After supplying the checkpoint
file to grompp via grompp -t the simulation now runs smoothly.

Thanks for your help.
-Marc



On Thu, Mar 1, 2018 at 4:26 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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-- 
Marc Hoemberger
Ph.D. Candidate, Biochemistry and Biophysics,
Laboratory of Dorothee Kern
MS-009, 415 South St.
Brandeis University
Waltham, MA, 02453