[gmx-users] Multithread run issues

[Mahmood Naderan]

Hi,
Users issue the command "mdrun -v" and that will automatically read input
files in the working directory. There are two issue with that which I am
not aware of the solution.

1- How the number of cores can be changed?
2- Viewing the output of "top" command, it is saying that mdrun uses 400%
cpu. That mean 4 cores are occupied. Problem is that we prefer to see four
processes each consumes 100% cpu. Why? Because in the first situation, PBS
wrongly sees that one cores is used (while 4 cores are used), but in the
later, it will correctly sees 4 cores.

As I read the documentation, I think the replacement of "mdrun -v" should be

mpirun -np N mdrun -v

Am I correct?

Regards,
Mahmood