[gmx-users] Multithread run issues

[Mark Abraham]

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 <mahmood.nt at gmail.com>
wrote:

> 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 Verlet
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> I read that document from that web site but didn't understand what is the
> issue!
> Thanks
>
> Regards,
> Mahmood
>
>
>
> On Mon, Oct 10, 2016 at 2:29 PM, Mahmood Naderan <mahmood.nt at gmail.com>
> wrote:
>
> > >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 cope with decades-old technology, or don't worry about
> > it.
> >
> > I found this document
> > ​(
> > https://wiki.anl.gov/cnm/HPC/Submitting_and_Managing_Jobs/
> > Advanced_node_selection#Multithreading_using_OpenMP)
> > ​That is what I want to be sure that number of threads and cores used for
> > gromacs fits to the PBS stats.
> >
> > Instead of the variable, I wrote
> >
> >
> >
> > #PBS -l nodes=1:ppn=2​
> > export OMP_NUM_THREADS=2
> > mpirun  mdrun -v
> >
> > So that will use two cores with 4 threads totally and PBS should report 4
> > processors are occupied.
> > However, gromacs failed with the following error
> >
> >
> >
> >
> > Regards,
> > Mahmood
> >
> >
> >
> > On Mon, Oct 10, 2016 at 1:41 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> 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 real-MPI
> >> version
> >>
> >> mpirun -np 1 mdrun_mpi -v -ntomp 2
> >>
> >> top isn't necessarily reporting anything relevant. A CPU can be
> nominally
> >> idle while waiting for communication, but what does top think about
> that?
> >>
> >> Mark
> >>
> >> On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan <mahmood.nt at gmail.com>
> >> wrote:
> >>
> >> > 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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