Profiling Python code

As part of improving the system, there is need to identify and fix/improve the performance bottlenecks in the code. This document details examples of how one would run various profilers, for both GeneNetwork2 and GeneNetwork3

GeneNetwork3

cProfile

Syntax:

• env [various-env-vars] python3 -m cProfile the-script.py

where

• `[various-env-vars]` is a number of environment variables that might be needed for the running of the script, e.g. `SQL_URI` which is used to define how to connect to the database.
• `the-script.py` is the name of the python script to be run under the profiler

The output can be redirected, e.g.

• env [various-env-vars] python3 -m cProfile the-script.py 2>error.log 1>performance.log

which should help will separating errors from the performance data, for easier analysis

Tags

• type: documentation
• keywords: profiling, python