Hi, Where is -np option in mpirun ?
--Masrul On Sun, Oct 16, 2016 at 12:45 PM, Mahmood Naderan <mahmood...@gmail.com> wrote: > Hi, > A PBS script for a gromacs job has been submitted with the following > content: > > #!/bin/bash > #PBS -V > #PBS -q default > #PBS -j oe > #PBS -l nodes=2:ppn=10 > #PBS -N LPN > #PBS -o /home/dayer/LPN/mdout.out > cd $PBS_O_WORKDIR > mpirun gromacs-5.1/bin/mdrun_mpi -v > > > As I ssh'ed to the nodes and saw mdrun_mpi process, I noticed that the cpu > utilization is not good enough! > > > [root@compute-0-1 ~]# ps aux | grep mdrun_mpi > dayer 7552 64.1 0.0 199224 21300 ? RNl Oct15 1213:39 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7553 56.8 0.0 201524 23044 ? RNl Oct15 1074:47 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7554 64.1 0.0 201112 22364 ? RNl Oct15 1213:25 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7555 56.5 0.0 198336 20408 ? RNl Oct15 1070:17 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7556 64.3 0.0 225796 48436 ? RNl Oct15 1217:35 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7557 56.1 0.0 198444 20404 ? RNl Oct15 1062:26 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7558 63.4 0.0 198996 20848 ? RNl Oct15 1199:05 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7562 56.2 0.0 197912 19736 ? RNl Oct15 1062:57 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7565 63.1 0.0 197008 19208 ? RNl Oct15 1194:51 > gromacs-5.1/bin/mdrun_mpi -v > dayer 7569 56.7 0.0 227904 50584 ? RNl Oct15 1072:33 > gromacs-5.1/bin/mdrun_mpi -v > > > > [root@compute-0-3 ~]# ps aux | grep mdrun_mpi > dayer 1735 0.0 0.0 299192 4692 ? Sl Oct15 0:03 mpirun > gromacs-5.1/bin/mdrun_mpi -v > dayer 1740 9.5 0.0 209692 29224 ? RNl Oct15 180:09 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1741 9.6 0.0 200948 22784 ? RNl Oct15 183:21 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1742 9.3 0.0 200256 21980 ? RNl Oct15 177:28 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1743 9.5 0.0 197672 19100 ? RNl Oct15 180:01 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1744 9.6 0.0 228208 50920 ? RNl Oct15 183:07 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1746 9.3 0.0 199144 20588 ? RNl Oct15 176:24 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1749 9.5 0.0 201496 23156 ? RNl Oct15 180:25 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1751 9.1 0.0 200916 22884 ? RNl Oct15 173:13 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1755 9.3 0.0 198744 20616 ? RNl Oct15 176:49 > gromacs-5.1/bin/mdrun_mpi -v > dayer 1758 9.2 0.0 226792 49460 ? RNl Oct15 174:12 > gromacs-5.1/bin/mdrun_mpi -v > > > > Please note that the third column is the cpu utilization. > Gromacs is a compute intensive application, so there is little IO or > something else for that. > > > Please also note that in compute-0-3 the first process is "mpirun > gromacs-5.1...." while the others are only "gromacs-5.1...." > > > Any idea is welcomed. > > 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.