Getting started with pupyMPI

pupyMPI is a pure python MPI implementation of MPI 1.3 with some added features. This document is not a manual of general MPI concepts but rather a reference manual for pupyMPI.

In the following we assume that you are familiar with the basic concepts of MPI. If you are not, there are lots of excellent introductions out there: http://www.google.com/search?q=introduction+to+mpi

We also assume that you have not previously used pupyMPI so we will start from scratch. If you know you have the required stuff installed and your pupyMPI installation is working you can skip to the section Your first pupyMPI program.

With that out of our way - let’s get this party started.

Requirements for pupyMPI

pupyMPI requires

• Python (version 2.6 or 2.7)
• SSH
• Linux or Mac OSX

pupyMPI uses SSH to start processes on remote hosts so you will need to have SSH installed. For your own sanity you should have passwordless access or you will be very busy typing passwords for each MPI process you start up.

When you are just developing or testing you can of course run everything on localhost. But eventually you will want network access to one or more hosts where you can spawn and run your MPI processes. The way you tell pupyMPI where to spawn remote processes is via the hostfile. You can read more about it here Using the hostfile to distribute processes but just ignore it for now since pupyMPI defaults to localhost if it does not find a proper hostfile.

You can check that SSH is installed and works (locally) with:

ssh localhost

This should give you a shell on your own machine which you can of course just exit from again. Note that if you are asked for a password in the terminal you have yet to setup proper passwordless access (see http://linuxproblem.org/art_9.html).

When you want to run pupyMPI on other hosts (remote machines) you should ensure that you have the same access, ie. try:

ssh SOME_REMOTE_HOST

Some installations do not have Python 2.6 as the global default Python installation. This is perfectly fine as long as there is a Python 2.6 available via the command python2.6

So if you test with:

python2.6 -V

And you get the output Python 2.6.x your Python installation should be fine.

pupyMPI assumes that your local filesystem is mirrored on the host you ssh into. This is the case when using localhost and on most cluster front-ends.

In the case where the python interpreter is somewhere else - eg. you run pupyMPI from a host where Python 2.6 is at /usr/bin/python but on the remote nodes Python 2.6 is at /usr/local/bin/python2.6 - you will have to tell pupyMPI the path to the remote python to use. This is done by adding the parameter --remote-python=PATH_TO_PYTHON eg.:

mpirun.py -c 4 --remote-python=/usr/local/bin/python2.6 hello_world.py

Differing conventions

You might already be familiar with MPI for C or FORTRAN. However, pupyMPI differs from a C/FORTRAN implementation in several different regards. The most important are:

• No data types - anything goes (there is a size limit to individual messages, however)
• Buffering / memory storage / garbage collection. No bsend etc.
• Object model. You call request.wait() instead for something like MPI_Wait(request).
• 1 or 0 replaced with True and False
• NULL handles replaced with None
• Local function changes: check the documentation and make no assumptions!

Your first pupyMPI program

The minimal pupyMPI program only needs three obligatory lines of code:

from mpi import MPI # import the pupyMPI library
mpi = MPI() # initialize pupyMPI

# If you want your program to do something, do it here.

mpi.finalize() # shut down pupyMPI nicely

But programs that do nothing are not much fun, so instead create a file called pupympi_test1.py and add the following code to it:

from mpi import MPI
mpi = MPI()

world = mpi.MPI_COMM_WORLD

rank = world.rank()

message = "Hello world, from rank:%i" % rank

if rank == 0:
    res = world.recv(1)
    print res
elif rank == 1:
    world.send(message,0)

mpi.finalize()

From the command line, run mpirun.py -c 2 pupympi_test1.py.You should receive the message: “Hello world, from rank:1”.

If you did not you have one or more problems - see Troubleshooting pupyMPI. You may also have to kill stuck Python processes with eg. killall python2.6

The test example introduces a few central concepts:

• the default communicator MPI_COMM_WORLD which always has all the started processes.
• ranking
• sending and receiving

You can read more about it all.

Troubleshooting pupyMPI

If your first pupyMPI program does not work you may have one or more symptoms:

• pupyMPI complains about a Python version problem You probably need to be explicit about your remote Python, as mentioned in Requirements for pupyMPI above.
• SSH password prompt Ensure password-less access as mentioned in Requirements for pupyMPI above.
• No message appears and your script hangs abort with Ctrl+c, kill any remaining Python processes with killall python2.6 and try againg with the debug -d parameter added. You will get a metric ton of output.