[gmx-users] Performance degradation for Verlet cutoff-scheme compared to group

[Олег Титов]

Thanks for you reply.

On a different machine I've recompiled GROMACS with icc version 13.1.0 (gcc
version 4.4.6 compatibility).
cmake command:
I_MPI_CC=nvcc CC=icc CXX=icpc cmake ../gromacs-src
-DCMAKE_INSTALL_PREFIX=~/gromacs-5.0.2/ -DGMX_FFT_LIBRARY=MKL -DGMX_MPI=OFF
-DGMX_GPU=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX=_intel -DGMX_LIBS_SUFFIX=_intel

This simulation took 10 hours on 16 CPU cores (15.5 ns/day). Is this normal
performance for a system with 1641 atoms?

2014-10-11 1:21 GMT+04:00 Mark Abraham <mark.j.abraham at gmail.com>:

> On Fri, Oct 10, 2014 at 8:16 PM, Олег Титов <titovoi at qsar.chem.msu.ru>
> wrote:
>
> > Good day.
> >
> > I've got sigmificant performance degradation when trying to use Verlet
> > cutoff-scheme for free energy calculation. My system contains 1
> > bromobenzene molecule and 543 TIP3P waters. 16 hours of calculation on
> > 8-core CPU resulted in 2.5 ns trajectory. With group scheme i've got 6.5
> ns
> > trajectory in 7h 40 min.
> >
> > Interesting that with group scheme gromacs tells me that it was using 8
> MPI
> > threads while with Verlet - 1 MPI and with 8 OpenMP threads. Both times
> > I've launched the calculation with "mdrun -deffnm test".
> >
>
> One scheme supports OpenMP, one doesn't...
>
>
> > I believe that this is caused by "plain C kernels" as GROMACS warns me.
> Is
> > there any possibility to overcome this issue?
> >
>
> Yes...
>
>
> > I have access only to old gcc 4.1.2 (without SSE4.1) and buggy icc 11.1
> on
> > this machine.
> >
>
> Gromacs requires a real compiler to get performance, like the install guide
> says. You need to get one.
>
> Mark
>
>
> > Thanks for your help.
> >
> > Oleg Titov
> > --
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