Abhisek, Generally, if you built openmpi with PBS support, it will automatically using the appropriate nodes with ‘mpirun <application>’ If not, you can use the environment variables provided to your session:
mpirun --hostfile $PBS_NODEFILE -np $(cat $PBS_NODEFILE|wc -l) <application> Brian Andrus ITACS/Research Computing Naval Postgraduate School Monterey, California voice: 831-656-6238 From: users [mailto:users-boun...@open-mpi.org] On Behalf Of abhisek Mondal Sent: Monday, August 03, 2015 10:00 AM To: Open MPI Users Subject: [OMPI users] pbs vs openmpi node allocation Hi, I'm using openmpi-1.6.4 to distribute a jobs in 2 different nodes using this command: "mpirun --hostfile myhostfile -np 10 nwchem my_code.nw" Here, "myhostfile" contains: cx0937 slots=5 cx0934 slots=5 But as I have to submit the jobs using .pbs script, I'm wondering in this case, how "mpirun" going to choose the node (free node allocation is done by pbs) from "myhostfile". I mean, does it happen that until the specific-nodes (as mentioned in myhostfile) become free "mpirun" is going to wait and then start ? How can I forward the allocated node name(by pbs) to mpirun command ? A little light on this matter would be really great. Thank you. -- Abhisek Mondal Research Fellow Structural Biology and Bioinformatics Indian Institute of Chemical Biology Kolkata 700032 INDIA
