Okay, I see what's going on here. The problem stems from a combination of two
things:
1. your setup of the hostfile guarantees we will think there is only one slot
on each host, even though Slurm will have assigned more. Is there some reason
you are doing that? OMPI knows how to read the Slurm
1. Intell mpi is located here: /opt/intel/impi/4.1.0/intel64/lib. I have added
OMPI path at the start and got the same output.
2. here is my cmd line:
export OMP_NUM_THREADS=8; export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/mnt/data/users/dm2/vol3/semenov/_scratch/openmpi-1.9.0_mxm-3.0/lib;
sbatch -
Hmmm...couple of things here:
1. Intel packages Intel MPI in their compiler, and so there is in fact an
mpiexec and MPI libraries in your path before us. I would advise always putting
the OMPI path at the start of your path envars to avoid potential conflict
2. I'm having trouble understanding
There is only one path to mpi lib.
echo $LD_LIBRARY_PATH
/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64:/opt/intel/composer_xe_2013.2.146/compiler/lib/intel64:/home/users/semenov/BFD/lib:/home/users/semenov/local/lib:/usr/lib64/:/mnt/data/users/dm2/vol3/semenov/_scratch/openmpi-1.9.0_mxm-3.0/l
