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Why does Python hang when running mpirun within a subprocess?

I have a very simple MPI script using mpi4py

# mpitest.py
from mpi4py import MPI
import time

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

time.sleep(100)

If I run this normally with mpirun everything works fine

$ mpirun --np 4 python mpitest.py  # just fine

However if I run this from within Python using the subprocess module then things run, but my interpreter becomes very sluggish

>>> import subprocess
>>> proc = subprocess.Popen(['mpirun', '--np', '2', 'python', 'mpitest.py'])

I've already tried keyword arguments like shell=True.

Environment

I've installed Python, mpi4py, and mpich using latest Miniconda for Linux

mrocklin@carbon:~/workspace/play$ conda list | grep mpi
mpi4py                    2.0.0                    py36_2  
mpich2                    1.4.1p1                       0  

https://conda.io/miniconda.html

Reproducible Steps

mrocklin@carbon:~/workspace/play$ conda create -n test-mpi python=3.6 mpi4py
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /home/mrocklin/Software/anaconda/envs/test-mpi:

The following NEW packages will be INSTALLED:

    mpi4py:     2.0.0-py36_2 
    mpich2:     1.4.1p1-0    
    openssl:    1.0.2l-0     
    pip:        9.0.1-py36_1 
    python:     3.6.2-0      
    readline:   6.2-2        
    setuptools: 27.2.0-py36_0
    sqlite:     3.13.0-0     
    tk:         8.5.18-0     
    wheel:      0.29.0-py36_0
    xz:         5.2.3-0      
    zlib:       1.2.11-0     

xz-5.2.3-0.tar 100% |################################| Time: 0:00:00   3.79 MB/s
zlib-1.2.11-0. 100% |################################| Time: 0:00:00   5.68 MB/s
#
# To activate this environment, use:
# > source activate test-mpi
#
# To deactivate an active environment, use:
# > source deactivate
#

mrocklin@carbon:~/workspace/play$ source activate test-mpi
(test-mpi) mrocklin@carbon:~/workspace/play$ python
Python 3.6.2 |Continuum Analytics, Inc.| (default, Jul 20 2017, 13:51:32) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import subprocess
>>> proc = subprocess.Popen(['mpirun', '--np', '2', 'python', 'mpitest.py'])
like image 563
MRocklin Avatar asked Aug 30 '17 17:08

MRocklin


1 Answers

This can be solved by adding the stdin=subprocess.DEVNULL keyword to the subprocess.Popen call as follows:

>>> proc = subprocess.Popen(['mpirun', '--np', '2', 'python', 'mpitest.py'], 
                            stdin=subprocess.DEVNULL)

It turns out that mpirun hijacks the stdin pipe a bit, which then makes it so that many of the keystrokes destined for the python process don't arrive.

like image 53
MRocklin Avatar answered Sep 20 '22 18:09

MRocklin