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...@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.abra...@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...@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 >> > -- >> > 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. >> > > -- 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.