GROMACS 5.1.5 parallelization

GROMACS version: 5.1.5
GROMACS modification: No
Here post your question
I compiled GROMACS 5.1.5 in a cluster with the SLURM queue system as:


The SLURM options in my script are:
#SBATCH --job-name=test_gromacs
#SBATCH --partition=compute24
#SBATCH --nodes=1
#SBATCH --tasks-per-node=16
#SBATCH --time=23:59:59

… and the command to run GROMACS is:
mpirun -np 16 gmx_mpi mdrun -deffnm equilibration

When the script starts, it gets stuck, non-parallelized, and the output says:
Number of logical cores detected (48) does not match the number reported by OpenMP (16). Consider setting the launch configuration manually!
Fatal error: Setting the number of thread-MPI ranks is only supported with thread-MPI and GROMACS was compiled without thread-MPI

However, in the INSTALL file of the GROMACS source it says:
“GROMACS can run in parallel on multiple cores of a single workstation
using its built-in thread-MPI. No user action is required in order to
enable this.”

Am I missing something?

Thanks in advance.


You installed non-mpi version, yet asking for MPI parallellization. See, if following works,

gmx_mpi  mdrun -v -deffnm equilibration -ntomp 16 

I did compiled MPI-gromacs (gmx_mpi). I just copied the wrong cmake line in the post, sorry. Anyways, I will recompile and try again that option.