Using Python on Gautschi cluster

Introduction of Python

Notice

Python 2.7 has reached end-of-life on Jan 1, 2020 (announcement). Please update your codes and your job scripts to use Python 3.

Python is a high-level, general-purpose, interpreted, dynamic programming language. We suggest using Anaconda which is a Python distribution made for large-scale data processing, predictive analytics, and scientific computing. For example, to use the default Anaconda distribution:

$ module load conda

For a full list of available Anaconda and Python modules enter:

$ module spider conda

Example Python Jobs

This section illustrates how to submit a small Python job to a SLURM queue.

Example 1: Hello world

Prepare a Python input file with an appropriate filename, here named hello.py:

# FILENAME:  hello.py

import string, sys
print("Hello, world!")

Prepare a job submission file with an appropriate filename, here named myjob.sub:

#!/bin/bash
# FILENAME:  myjob.sub

module load conda

python hello.py

Example 2: Matrix multiply

Save the following script as matrix.py:

# Matrix multiplication program

x = [[3,1,4],[1,5,9],[2,6,5]]
y = [[3,5,8,9],[7,9,3,2],[3,8,4,6]]

result = [[sum(a*b for a,b in zip(x_row,y_col)) for y_col in zip(*y)] for x_row in x]

for r in result:
        print(r)

Change the last line in the job submission file above to read:

python matrix.py

The standard output file from this job will result in the following matrix:

[28, 56, 43, 53]
[65, 122, 59, 73]
[63, 104, 54, 60]

Example 3: Sine wave plot using numpy and matplotlib packages

Save the following script as sine.py:

# sine.py
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

x = np.linspace(-np.pi, np.pi, 201)
plt.plot(x, np.sin(x))
plt.xlabel('Angle [rad]')
plt.ylabel('sin(x)')
plt.axis('tight')
plt.savefig('sine.png')

Change your job submission file to submit this script and the job will output a png file and blank standard output and error files.