Hi,
That user's input can't use OpenMP, like the message says. So try the other
options. (And again, don't run mpirun on a thread-MPI mdrun!)
Mark
On Mon, Oct 10, 2016 at 1:02 PM Mahmood Naderan
wrote:
> Sorry for the previous incomplete email.
>
> Program mdrun, VERSION 5.1
> Source code file
Sorry for the previous incomplete email.
Program mdrun, VERSION 5.1
Source code file:
/share/apps/chemistry/gromacs-5.1/src/programs/mdrun/resource-division.cpp,
line: 746
Fatal error:
OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme V
>mpirun -np 1 mdrun_mpi -v -ntomp 2
Agree with that.
>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 cop
Hi,
Yeah, but that run is very likely
a) useless because you're just running two copies of the same simulation
because you're not running MPI-enabled mdrun
b) and even if not, less efficient than the thread-MPI version
mdrun -v -nt 2
c) and even if not, likely slightly less efficient than the r
OK. I understood the documents.
Thing that I want is to see two processes (for example) each consumes 100%
cpu. The command for that is
mpirun -np 2 mdrun -v -nt 1
Thanks Mark.
Regards,
Mahmood
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Hi,
On Sun, Oct 9, 2016 at 2:06 PM Mahmood Naderan 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 chan
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