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

[Олег Титов]

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".

I believe that this is caused by "plain C kernels" as GROMACS warns me. Is
there any possibility to overcome this issue?

I have access only to old gcc 4.1.2 (without SSE4.1) and buggy icc 11.1 on
this machine.

Thanks for your help.

Oleg Titov