This web-page is intended to help you running MPI Python applications on the Odyssey cluster using mpi4py.
To use mpi4py you need to load an appropriate Python software module. We have the Anaconda Python distribution from Continuum Analytics. In addition to mpi4py, it includes hundreds of the most popular packages for large-scale data processing and scientific computing.
You can load python in your user environment by running in your terminal:
source new-modules.sh module load python/2.7.6-fasrc01
Below is a simple example code using mpi4py.
#!/usr/bin/env python #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ # Program: mpi4py_test.py #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ from mpi4py import MPI nproc = MPI.COMM_WORLD.Get_size() # Size of communicator iproc = MPI.COMM_WORLD.Get_rank() # Ranks in communicator inode = MPI.Get_processor_name() # Node where this MPI process runs if iproc == 0: print "This code is a test for mpi4py." for i in range(0,nproc): MPI.COMM_WORLD.Barrier() if iproc == i: print 'Rank %d out of %d' % (iproc,nproc) MPI.Finalize()
Running the program
You could use the following SLURM batch-job submission script to submit the job to the queue:
#!/bin/bash #SBATCH -J mpi4py_test #SBATCH -o mpi4py_test.out #SBATCH -e mpi4py_test.err #SBATCH -p general #SBATCH -n 16 #SBATCH -t 30 #SBATCH --mem-per-cpu=4000 source new-modules.sh module load python/2.7.6-fasrc01 srun -n $SLURM_NTASKS --mpi=pmi2 python mpi4py_test.py
If you name the above script
run.sbatch, for instance, the job is submitted to the queue with
Upon job completion, job output will be located in the file
mpi4py_test.out with the contents:
This code is a test for mpi4py. Rank 0 out of 16 Rank 1 out of 16 Rank 2 out of 16 Rank 3 out of 16 Rank 4 out of 16 Rank 5 out of 16 Rank 6 out of 16 Rank 7 out of 16 Rank 8 out of 16 Rank 9 out of 16 Rank 10 out of 16 Rank 11 out of 16 Rank 12 out of 16 Rank 13 out of 16 Rank 14 out of 16 Rank 15 out of 16
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