scipion logo

Out of the box profiling

Pycharm professional (free for educational email accounts) integrates in its GUI a profiling option that is third way to execute any code apart Run or Debug. Please go here for more details.

Profiling a script

The simplest profiling you can do is to have a specific python script that does something you want to profile.

The following code will use Scipion Manager to list the available projects

from scipion.__main__ import main

# Initialize scipion environment

from pyworkflow.project import Manager, Project

# Create a new project
manager = Manager()

for i, p in enumerate(manager.listProjects()):


Note that main(justinit=True) is needed to initialize Scipion using the config file and have full API functionality.

Run configuration

Now you are going to need to have a specific pycharm run configuration. Fill:

  1. Script path: point to your performance script .py file

  2. Environment variables: You need to add SCIPION_HOME, and LD_LIBRARY_PATH

Once done you should br able to run, debug or profile your script


See skipping scipion launcher for a more detailed explanation.