[gmx-users] Launch hybrid MPI/openMP run on multiple nodes

[Chunlei ZHANG]

Dear GMX developers and users,

I have a cluster of 24 nodes, each having two 10-core intel CPUs.
Gromacs 5.1 is compiled by using intel mpi (version 5.1.1) and mkl.

I can successfully run a simulation by using pure MPI (480 MPI processes).
But the performance is not good and the log file of mdrun suggests using
fewer MPI processes.
I try to launch 240 MPI processes, each using 2 openMP threads, by the
command:
mpirun -ppn 20 -np 240 gmx_mpi mdrun -ntomp 2

But only a fraction of the nodes are running mdrun and the log file says:

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

Does anyone know how to solve this problem?
Thanks in advance.

Best,
Chunlei