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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

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