Скачать или смотреть Resolving python3: command not found Error on High-Performance Computing Systems

Learn how to troubleshoot the `python3: command not found` error while running Python scripts on high-performance computers such as Tinaroo at the University of Queensland.
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Resolving python3: command not found Error on High-Performance Computing Systems

When working with high-performance computers, users may encounter errors that seem unclear or difficult to resolve, which can impede productivity. One common issue is receiving a "command not found" error when attempting to run Python scripts via job scheduling systems such as PBS (Portable Batch System).

In this guide, we'll explore a specific case of this issue: a user trying to run a simple Python script on Tinaroo, a high-performance computer at the University of Queensland. Let’s break down the problem, the solution, and how to implement it.

The Problem

The user created a basic Python script (demo1.py) designed to log execution time by generating an output file. Although it runs successfully in their environment, the job fails when sent to the PBS job scheduler.

The error message in the output log file (out.log) reads:

[[See Video to Reveal this Text or Code Snippet]]

This means that the job script cannot locate the python3 executable while it's executing on the server.

Understanding the Error

This error typically occurs due to one of the following reasons:

Python is Not Installed: Python might not be installed on the server.

Path Configuration: The system PATH variable may not include the directory where Python is installed.

Incorrect Command Usage: The script may be using an incorrect command or alias for Python.

Solutions

Here are a couple of effective solutions to resolve the python3: command not found error:

Solution 1: Change the Python Command

In some setups, the command python could be linked to Python 3. If your cluster supports this, you can modify your PBS script:

[[See Video to Reveal this Text or Code Snippet]]

Solution 2: Create a Soft Link

If the previous solution doesn't resolve the problem, you can create a soft link that directs python3 to the correct Python executable. Here’s how:

Log into the user shell.

Navigate to the bin directory that contains Python:

[[See Video to Reveal this Text or Code Snippet]]

Create a soft link:

[[See Video to Reveal this Text or Code Snippet]]

Ensure the path is included in your system's environment variable:

[[See Video to Reveal this Text or Code Snippet]]

Solution 3: Update the PBS Script

If the system requires specific modules to be loaded, ensure that your script properly loads these modules before attempting to execute Python. In your PBS job script (simpledemo.pbs):

[[See Video to Reveal this Text or Code Snippet]]

Conclusion

Handling error messages effectively is crucial when working on high-performance computing systems. The python3: command not found error can be resolved by modifying the command to python, creating a soft link to the Python 3 executable, or ensuring the correct Python modules are loaded in your PBS submission script.

Following these guidelines can enhance your experience while working with high-performance computers and provide smoother scripting processes. If you encounter any further issues, consider reaching out to your system's support team for assistance. Happy coding!