Hi, On Sun, Oct 9, 2016 at 2:06 PM Mahmood Naderan <mahmood...@gmail.com> wrote:
> 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? > http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html > > 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. > This is not a problem to solve by running applications differently. You will have users running jobs with single ranks/processes that use threading of various kinds to fill the cores. That's a feature, not a bug. Either configure PBS to cope with decades-old technology, or don't worry about it. :-) As I read the documentation, I think the replacement of "mdrun -v" should be > > > > mpirun -np N mdrun -v > > > > Am I correct? > No, because that mdrun isn't configured with MPI support (else it would be called mdrun_mpi). If it was, then mpirun -np N mdrun_mpi is plausible, but less efficient than the alternatives. Your mdrun is using the built in thread-MPI that you can read about at that link. Mark > > > > Regards, > > Mahmood > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.