GROMACS version: 5.1.5
GROMACS modification: No
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Hello,
I compiled GROMACS 5.1.5 in a cluster with the SLURM queue system as:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=~/bin/GROMACS_5.1.5 -DGMX_CUDA_TARGET_COMPUTE=60
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.
Best,
Yasser