Python
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python2 | python2 | ||
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+ | pip2 install --user package_name | ||
python3.5 | python3.5 | ||
pip3.5 | pip3.5 | ||
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+ | For example | ||
+ | pip3.5 install --user package_name | ||
==Running Task array jobs== | ==Running Task array jobs== |
Revision as of 12:37, 17 March 2017
Python
Version 2.7 and 3.5 are available on the HPC
Use the following executable binaries to start the correct version
python2 pip2 For example pip2 install --user package_name
python3.5 pip3.5 For example pip3.5 install --user package_name
Running Task array jobs
Example SGE job script (One job with 10 tasks)
#!/bin/bash #$ -N ARRAY_TEST_JOB #$ -cwd -V #$ -q short.q #$ -l mem_free=1G,h_vmem=1.2G #$ -t 1-10 python2 mycode.py
To use the current SGE job task number your python code you need to access the variable and assign it.
#!/bin/python2 import os os.environ.keys() taskid = os.environ['JOB_ID']
Managing packages with virtual environments
It is recommend to use Python Virtual Environments to create isolated Python environments where you can install any package combinations you need without worrying about dependencies and versions, and indirectly permissions.
Please read | Creating Virtual Environments for more information
The basic usage is like so:
Using virtualenv: (Python 2.6)
virtualenv <DIR> source <DIR>/bin/activate
Using venv: (Pyhton 3.5)
python3.5 -m venv <DIR> source <DIR>/bin/activate