[OMPI users] Lots of errors when running OpenMPI-2.0.1

[Juan A. Cordero Varelaq]

Hi,

I am seriously struggling with running OpenMPI on my SGE HPC under
Ubuntu 12.04:

* Every time I run a command from OpenMPI, let's say ompi_info, I get
the following as the first line of the output:
o Warning: Conflicting CPU frequencies detected, using: 2001.000000.
* I get the attached error and output when I run the following script
with qsub (making use of queues):
o #!/bin/bash
#$-cwd
#$ -S /bin/bash
#$ -V
#$ -q normal
#$ -pe mpi 40
#$ -P Lab219
#$ -o output
#$ -e error
module load PhyML/3.3
mpirun --mca pml yalla --mca orte_base_help_aggregate 0 -np 40
phyml-mpi -i proteic -b 10 -d aa

It seems /dev/knem is set somehow so that it only allows "RDMA" user
group to execute it, but I did change the 10-knem.rules files such that
it is on mode "0666" and every user can use it.

I can't understand why the "Warning: Conflicting CPU frequencies
detected, using: 2001.000000.", the "MXM: Got signal 11 (Segmentation
fault)" and the "PML yalla cannot be selected" errors are happening,
and can't figure out at all how to tackle them.


I would appreciate a lot any minimal hint about this issues.


Thanks a lot in advance