How to make mpi4py run?

Question

I'm new to the concept of parallel programming. I'm supposed to use mpi4run for a project, but I don't know how to actually run it. For example, if I want to run this code :

from mpi4py import MPI
import numpy as np

comm = MPI.COMM_WORLD
rank = comm.Get_rank()

if rank == 0:
    numData = 5  
    data = np.linspace(0.0,3.14,numData)  
else:
    numData = None
numData = comm.bcast(numData, root=0)
if rank != 0:    
    data = np.empty(numData, dtype='d')  
comm.Bcast(data, root=0) 
print('Rank: ',rank, ', data received: ',data)

If i run from directly from my IDLE i get:

Rank: 0 , data received: [0. 0.785 1.57 2.355 3.14 ]

But, if I understand correctly, that's not the way we should run it to do the parallel computing, right? On the internet, I find that one runs it with writing

mpirun -n 4 python script.py.

My question is, where do I type that? I have tried on the cmd and the python shell but I get errors, syntaxerrors and so on. I feel there is something I don't understand here. Any tips?

BioGeek · Accepted Answer · 2018-10-08 10:01:32Z

1

Python programs that use MPI commands must be run using an MPI interpreter, called mpirun.

The easiest is to create a clean conda environment and install mpi4py there.

If you are on Linux and have Anaconda Python installed, that would look something like this:

$ conda create -n mpi_env
$ source activate mpi_env
(mpi_env) $ conda install mpi4py
(mpi_env) $ which mpirun # test if the MPI interpreter is correctly installed
/anaconda/envs/mpi_env/bin/mpirun
(mpi_env) $ mpirun -n 4 python script.py # run your python script, using 4 processes.

For more info, see this tutorial.

For Windows, you need to install mpiexec. See here for installation instructions.

edited Oct 8, 2018 at 10:01

answered Oct 8, 2018 at 9:50

BioGeek

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