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Python
Table of Contents
- Homepage: http://www.python.org/
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Versions available:
- 2.7.3-gmpolf-1.4.8
- 2.7.3-goolf-1.5.14
- 2.7.3-goolf-1.5.14-QIIME
- 2.7.3-ictce-5.4.0
- 2.7.6-goolf-1.5.14
- 2.7.8-goolf-1.5.14
- 2.7.8-ictce-5.4.0
- 3.4.1-goolf-1.5.14
Python is a programming language that lets you work more quickly and integrate your systems more effectively. - Homepage: http://python.org/
Activation of Python versions is done by using the module command, e.g.,
module load Python/2.7.8-goolf-1.5.14
This command will only work on one of the build nodes, or on the compute nodes if you use it in your SLURM script.
To deactivate the activated Python environment:
module unload Python/2.7.8-goolf-1.5.14
To see which Python packages are available:
pip freeze
or for Python 3,
pip3 freeze
For Python 2:
module load Python/2.7.8-goolf-1.5.14
virtualenv --system-site-packages ~/mypython
The output reads:
New python executable in /home/mfel395/mypython/bin/python Installing setuptools, pip...done.
For Python 3:
module load Python/3.4.1-goolf-1.5.14
pyvenv --system-site-packages ~/mypython
Unfortunately, pip is NOT installed into the virtual environment. Add it now
source ~/mypython/bin/activate
curl https://raw.githubusercontent.com/pypa/pip/master/contrib/get-pip.py | python
Not that under Python3 virtualenv is called pyvenv.
module load Python/2.7.8-goolf-1.5.14 )
source ~/mypython/bin/activate
Note how the system prompt changed to indicate that you are using your new environment You can now install additional packages into this environment as follows:
pip install cogent
To deactivate this environment:
deactivate
Job description (download)
#!/bin/bash
#SBATCH -J PythonTest
#SBATCH -A uoa99999 # Project Account
#SBATCH --time=00:01:00 # Walltime
#SBATCH --mem-per-cpu=1G # memory/cpu
#SBATCH --output=stdout.txt
#SBATCH --error=stderr.txt
# Load the Python module.
module load Python/2.7.8-goolf-1.5.14
# In addition, enable your virtual environment, if needed.
# Just delete or comment out the following line if you don't need your virtual environment.
source ~/mypython/bin/activate
# Do something with Python.
python -V 2>&1