# Python on Hydra

## System Python vs. Conda

If you type `python --version` on Hydra, it will tell you that the "system" Python is version 2.6.6. Python 2.6 was first released in 2008, and is very out-of-date, so avoid using this version of Python to run any scripts.

Whether you are writing your own Python code, or utilizing other people's Python scripts, we recommend using the Conda ecosystem to locally install your own custom Python environment.

## Locally installing miniconda and setting up a modulefile

Detailed explanation of this process

## Conda Environments

Explain why they're needed, and then show how to set up

## Python Gotchas

Talk about the single-thread Numpy version, and how some Python programs will attempt to use as many threads as possible.

## Jupyter Interface

Jupyter notebooks deliver a "literate programming" interface with Python that combines MarkDown-based documentation with code cells.

Using Jupyter on Hydra is especially helpful for:
* Keeping a record of a your analysis in notebook format, that can be accessed later
* Working with images or visualizations that cannot be viewed through the command line interface.

From the log-in node, access the interactive queue.

qrsh -pe mthread [N]

Then load the conda module, and activate a specific module with jupyter, if necessary.

module load ~/modulefiles/miniconda
source activate jupyter

Now run the following command to launch a jupyter notebook. It will run it from the directory you are in, so make sure you are "above" the directory where you want your notebooks to live. The interactive queue puts you into your `/home` directory by default.

 jupyter notebook --no-browser --ip=`hostname` --port=8888

This will launch a notebook, and produce a bunch of output looking something like this:

[I 14:38:44.628 NotebookApp] Serving notebooks from local directory: /pool/genomics/triznam
[I 14:38:44.628 NotebookApp] The Jupyter Notebook is running at:
[I 14:38:44.628 NotebookApp] http://compute-8-31.local:8888/?token=e54bd4f1469387555c114697278fe2ff10089cbf723c595b
[I 14:38:44.628 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 14:38:44.636 NotebookApp]

    To access the notebook, open this file in a browser:
        file:///home/triznam/.local/share/jupyter/runtime/nbserver-25198-open.html
    Or copy and paste one of these URLs:
        http://compute-8-31.local:8888/?token=e54bd4f1469387555c114697278fe2ff10089cbf723c595b

Now on your local computer, open up a terminal, and run the following command:

ssh -N -L 8888:compute-8-31:8888 [e-mail]

If it worked, it will prompt you for your Hydra password. Enter it.

Now open a browser and go to http://localhost:8888. It should be a Jupyter-looking window, but will ask for a token or password before you can continue. Copy and paste the long token from the end of the URL that was printed out when you launched Jupyter on Hydra above. In that case it would be: *e54bd4f1469387555c114697278fe2ff10089cbf723c595b*