Dear all,
I'm trying to employ replica-exchange with solute tempering 2 (REST2) in a system, but I have performance issues in the calculations. I'm using openmpi-3.0.0 and gromacs 2019.4 patched with plumed 2.5.5.
To run the simulation, I am using the following configuration,
#PBS -l select=10: ncpus=6
export=OMP_NUM_THREADS=10
mpirun -np 10 gmx_mpi mdrun -s production.tpr -plumed plumed.dat -v -deffnm production -multidir 0 1 2 3 4 5 6 7 8 9 -replex 400 -hrex -dlb no
and I get the following message:
WARNING: On rank 0: oversubscribing the available 48 logical CPU cores per node with 60 threads. This will cause considerable performance loss.
Could anyone help me please?
Hi, I would suggest you to do few things:
1. Check how the software was compiled and installed on your cluster.
2. Check the computer architecture which you are running simulations on, i.e. how many cores per node.
3. Then check the tutorial on plumed-page and try to run using it according to what you found out in steps 1-2 so that you won't oversubscribe the number of cores/nodes.
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