[gmx-users] Number of hardware threads does not match OpenMP

[Dries Van Rompaey]

Dear all,

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)?
Am I correct in thinking this won’t affect the results from my simulations?

Thanks in advance

Dries