[gmx-users] Effect of hardware threads mismatch on simulation

[Dries Van Rompaey]

Dear gmx-users,

When running a simulation of a protein in solution on my university’s
cluster I get the two following notifications:

Number of hardware threads detected (20) does not match the number
reported by OpenMP (1).
Consider setting the launch configuration manually!

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity.

My PBS file is:
#!/bin/bash
#PBS -l nodes=2:ppn=20,pmem=2gb
#PBS -l walltime=55:00:00
#PBS -N GromacsmTSLP
module load hopper/2015a
module load GROMACS/5.0.4-intel-2015a-hybrid

cd $PBS_O_WORKDIR
mpirun gmx_mpi mdrun -s md_calcua.tpr -o $VSC_DATA/MD.trr -cpo
$VSC_DATA/MD.cpt -c $VSC_DATA/MD.gro -e $VSC_DATA/MD.edr -g
$VSC_DATA/MD.log

The performance of the system seems to be allright (120 ns/day on 2
Xeon E5-2680 v2 @ 2.80GHz), 20 000 atoms).
The number of processes launched seems to be correct as well (40).
I tried looking through the mailing list, and from what I can gather
these notifications should only have an effect on the system
performance (which seems to be okay in my case)?

Could anyone tell me if this has an effect on the reliability of my
simulations or not?


Thanks in advance

Dries