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

[Dr. Vitaly Chaban]

What about trying a larger system, ~10,000 interaction centers?

The performance which you report is much below natural expectations for GROMACS.



Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


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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