[OMPI users] Low CPU utilization

[Mahmood Naderan]

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

[Reuti]

Hi,

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
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.

Sounds like the two jobs are using the same cores by automatic core binding as one instance doesn't know anything about the other. For a first test you can start both with "mpiexec --bind-to none ..." and check whether you see a different behavior.

`man mpiexec` mentions some hints about threads in applications.

-- Reuti

Regards,
Mahmood
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