Hi all, I am wondering if anyone out there has successfully integrated novoalignMPI with a scheduler - specifically SGE who could provide me some direction in troubleshooting my setup.
My setup appears to be correct but I must have missed something somewhere because any alignment job sent through the scheduler hangs. The novoalignMPI PIDs are running on my compute nodes but no output is returned to my working directory and the job remains in run state.
I am running novoalign 2.0.13 w/ MPI, SGE 6.2, CentOS 6.2, MPICH2 1.4.1p1.
The alignment runs if I run mpiexec on our compute nodes without the scheduler and simple mpich2 jobs run through the scheduler fine as well. Only when SGE and novoalignMPI are brought together do I have this problem.
Attached is my sge job script