Latest revision as of 09:55, 20 June 2024

Deprecation Notice

IMPORTANT NOTICE: If you're looking to set up a python environment for a particular program (eg. xcube, bwa etc) please use the miniconda virtual environments which are set up here. It is very likely in the future all python environments will be virtual environments using miniconda.

Application Details

There are two types of python provided on Viper, if you looking for the Original Python click here.

• Description: Python is a high-level interpreted programming language for general-purpose programming, supported by a large number of libraries for many tasks
• Versions:
  • Python 2.7.11 and 3.5.1
  • Anaconda v4.0 Python 2.7 and 3.5
  • Anaconda v4.1.1 Python 2.7
  • Anaconda v4.6 miniconda python 3.7 (Virtual Enviroments only)
• Module names:
  • python/2.7.11 python/3.5.1
  • python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 python/anaconda/4.6/miniconda/3.7 (VE)
• License: Free to use
  • Python Python Software Foundation License
  • Anaconda Python New BSD License

Usage Examples

Interactive

Interactive with command line:

[username@c170 ~]$ module add python/anaconda/4.0/2.7
[username@c170 ~]$ python
Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>>

Interactive with command line with IPython:

[username@c170 ~]$ ipython
Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
Type "copyright", "credits" or "license" for more information.

IPython 5.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]:

Batch Submission

#!/bin/bash
#SBATCH -J PythonTest                # Job name, you can change it to whatever you want
#SBATCH -N 1                                  # Number of nodes 
#SBATCH --ntasks-per-node 1    # Number of cores per node
#SBATCH -o %N.%j.out                # Standard output will be written here
#SBATCH -e %N.%j.err                 # Standard error will be written here
#SBATCH -p compute                  # Slurm partition, where you want the job to be queued 

 
module purge
module add python/anaconda/4.0/3.5
 
python PythonTest.py

This is then submitted as follows:

[username@login01 ~]$ sbatch Pythontest.job
Submitted batch job 289522

Python Packages

Common packages such as SciPy and NumPy are available across all Python modules. Other commonly used packages are listed below:

import matplotlib
matplotlib.use('Agg')

Further Information

• Python Programming
• Miniconda python virtual environments

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