Python
From HPC
(Difference between revisions)
(→Python) |
(→Running Task array jobs) |
||
Line 18: | Line 18: | ||
#$ -N ARRAY_TEST_JOB | #$ -N ARRAY_TEST_JOB | ||
#$ -cwd -V | #$ -cwd -V | ||
+ | #$ -q short.q | ||
#$ -t 1-10 | #$ -t 1-10 | ||
Line 27: | Line 28: | ||
import os | import os | ||
os.environ.keys() | os.environ.keys() | ||
- | taskid = os.environ['JOB_ID'] | + | taskid = os.environ['JOB_ID'] |
==Managing packages with virtual environments== | ==Managing packages with virtual environments== |
Revision as of 12:07, 8 November 2016
Python
Version 2.7 and 3.5 are available on the HPC
Use the following executable binaries to start the correct version
python2 pip2
python3.5 pip3.5
Running Task array jobs
Example SGE job script (One job with 10 tasks)
#!/bin/bash #$ -N ARRAY_TEST_JOB #$ -cwd -V #$ -q short.q #$ -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