Mahmood Naderan
2016-10-16 18:34:32 UTC
Hi,
I am running two softwares that use OMPI-2.0.1. Problem is that the CPU
utilization is low on the nodes.
For example, see the process information below
[***@compute-0-1 ~]# ps aux | grep siesta
mahmood 14635 0.0 0.0 108156 1300 ? S 21:58 0:00 /bin/bash
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta.p1 A.fdf
mahmood 14636 0.0 0.0 108156 1300 ? S 21:58 0:00 /bin/bash
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta.p1 A.fdf
mahmood 14637 61.6 0.2 372076 158220 ? Rl 21:58 0:38
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta
mahmood 14639 59.6 0.2 365992 154228 ? Rl 21:58 0:37
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta
Note that the cpu utilization is the third column. The "siesta.pl" script is
#!/bin/bash
BENCH=$1
export OMP_NUM_THREADS=1
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta < $BENCH
I also saw a similar behavior from Gromacs which has been discussed at
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-October/108939.html
It seems that there is a tricky thing with OMPI. Any idea is welcomed.
Regards,
Mahmood
I am running two softwares that use OMPI-2.0.1. Problem is that the CPU
utilization is low on the nodes.
For example, see the process information below
[***@compute-0-1 ~]# ps aux | grep siesta
mahmood 14635 0.0 0.0 108156 1300 ? S 21:58 0:00 /bin/bash
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta.p1 A.fdf
mahmood 14636 0.0 0.0 108156 1300 ? S 21:58 0:00 /bin/bash
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta.p1 A.fdf
mahmood 14637 61.6 0.2 372076 158220 ? Rl 21:58 0:38
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta
mahmood 14639 59.6 0.2 365992 154228 ? Rl 21:58 0:37
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta
Note that the cpu utilization is the third column. The "siesta.pl" script is
#!/bin/bash
BENCH=$1
export OMP_NUM_THREADS=1
/share/apps/chemistry/siesta-4.0-mpi201/spar/siesta < $BENCH
I also saw a similar behavior from Gromacs which has been discussed at
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-October/108939.html
It seems that there is a tricky thing with OMPI. Any idea is welcomed.
Regards,
Mahmood