Introduction

On this page we'll see how to use Python on the maya cluster. Before proceeding, make sure you've read the How To Run tutorial first. Python is a popular full-featured scripting language. It can be used interactively or through scripting.

Change version

There are several versions of Python installed on maya. To use the default version, just enter python

[jongraf1@maya-usr2 Python]$ python
Python 2.7.2 (default, Jul 10 2014, 19:21:09) 
[GCC 4.6.4 20120303 (prerelease)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

To list all the scl packages available, use the following command:

[jongraf1@maya-usr2 Python]$ scl -l
python27
python33
ruby200

To invoke scl packages (in a sub-shell), such as phthon27, use:

[hu6@maya-usr1 ~]$ scl enable python27 bash

Then when you enter python, you can see the version has been changed:

[hu6@maya-usr1 ~]$ python
Python 2.7.5 (default, Dec  3 2013, 08:35:16)

To directly run a command that requires a specific version of python:

[hu6@maya-usr1 ~]$ scl enable python27 'command'

Example batch script

We'll write a simple Python script that says "hello", and performs a few calculations.

#!/bin/env python

import math
x = math.factorial(10)
print "Hello world! 10! = %d" % (x)

Download: ../code/python_hello/hello.py

Notice that the first line is not the usual "#!/usr/bin/python", which points to an older version of Python on maya. Instead, "#!/bin/env python" ensures that the module-loaded version of Python is used when invoking the script without the interpreter. Make sure that the permission for the file include the ability to execute.

[araim1@maya-usr1 python_hello]$ ./hello.py 
Hello world! 10! = 3628800
[araim1@maya-usr1 python_hello]$

We can launch it with a standard SLURM script.

#!/bin/bash -l
#SBATCH --job-name=hello_python
#SBATCH --output=slurm.out
#SBATCH --error=slurm.err
#SBATCH --partition=develop

module load python/2.7.2
./hello.py

Download: ../code/python_hello/run.slurm

Now we launch the job

[araim1@maya-usr1 python_hello]$ sbatch run.slurm
sbatch: Submitted batch job 2618
[araim1@maya-usr1 python_hello]$ ls
hello.py  run.slurm  slurm.err  slurm.out
[araim1@maya-usr1 python_hello]$ cat slurm.out
Hello world! 10! = 3628800
[araim1@maya-usr1 python_hello]$

Also note that hello.py can be run directly on the user node (which is okay here because it's a small job) using the "python" command

[araim1@maya-usr1 python_hello]$ python hello.py
Hello world! 10! = 3628800
[araim1@maya-usr1 python_hello]$

Running Python interactively

Python can also be used interatively on the user node, as in the following example

[araim1@maya-usr1 ~]$ python
Python 2.7.2 (default, Sep  8 2011, 21:04:00) 
[GCC 4.1.2 20080704 (Red Hat 4.1.2-50)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import math
>>> x = math.factorial(10)
>>> print "Hello world! %d" % (x)
Hello world! 3628800
>>> quit()
[araim1@maya-usr1 ~]$

As always, this should only be used for smaller computations. Intensive programs should be submitted to the compute nodes.