Applications/Anaconda
From HPC
Contents
Application Details
- 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 Python v4.0 Python 2.7 and 3.5
- Anaconda Python v4.1.1 Python 2.7
- 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
- License: Free to use
- Python Python Software Foundation License
- Anaconda Python New BSD License
Usage Examples
Python Libraries
Common libraries such as SciPy and NumPy are available across all Python modules. Other commonly used libraries/packages are listed below:
| Python module | Import Command | Description | Available in |
|---|---|---|---|
| Biopython | import Bio | Collection of Python tools for computational biology and bioinformatics, containing classes to represent biological sequences and sequence annotations, and it is able to read and write to a variety of file formats. Also allows for a programmatic means of accessing online databases of biological information, such as those at NCBI. Separate modules extend Biopython's capabilities to sequence alignment, protein structure, population genetics, phylogenetics, sequence motifs, and machine learning. | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 |
| IPython | import IPython | Enhanced interactive shell for Python, including tools for parallel computing | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 |
| Matplotlib | import matplotlib | Plotting library for Python and its numerical mathematics extension NumPy | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 |
| MPI4Py | import mpi4py | Provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. | python/anaconda/4.0/3.5 |
| OBITools | import obitools | Set of programs developed to simplify the manipulation of sequence files, mainly designed to help analyzing Next Generation Sequencer outputs in the context of DNA Metabarcoding | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 |
| Theano | import theano | Numerical computation library, primarily designed for machine learning | python/anaconda/4.0/2.7 python/anaconda/4.1.1/2.7 |
| YT | import yt | Package for analyzing and visualizing volumetric data | python/anaconda/4.0/2.7 python/anaconda/4.0/3.5 python/anaconda/4.1.1/2.7 |
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 (for Matlab should be always one) #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/4.0/2.7 python PythonTest.py
This is then submitted as follows:
[username@login01 ~]$ sbatch Pythontest.job Submitted batch job 289522