[gmx-users] Low cpu utilization

[Mahmood Naderan]

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 at 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 at 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