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

[Mark Abraham]

Hi,

Very likely that simulation is too small to make good use of that many
cores (though if there's hyper-threading going on, then there may only be 8
real cores, and you may do better with hyper-threading off...). Gromacs use
of OpenMP does not do very well with lots of threads and few atoms. If you
share a link to a log file on a file-sharing service, there might be
relevant observations people could make. If running multiple replicates of
your simulation is a sensible thing to do, you will likely get much better
value from your hardware by running several such simulations per node (e.g.
with mdrun_mpi -multi)

Mark

On Mon, Oct 13, 2014 at 10:55 AM, Олег Титов <titovoi at qsar.chem.msu.ru>
wrote:

> 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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