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https://github.com/ncar/ncar-python-tutorial
Numerical & Scientific Computing with Python Tutorial
https://github.com/ncar/ncar-python-tutorial
cartopy dask jupyter matplotlib numpy python scipy tutorial xarray
Last synced: 4 months ago
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Numerical & Scientific Computing with Python Tutorial
- Host: GitHub
- URL: https://github.com/ncar/ncar-python-tutorial
- Owner: NCAR
- License: cc-by-4.0
- Archived: true
- Created: 2019-03-01T16:25:17.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2020-04-02T20:05:44.000Z (almost 5 years ago)
- Last Synced: 2024-10-01T06:03:33.793Z (4 months ago)
- Topics: cartopy, dask, jupyter, matplotlib, numpy, python, scipy, tutorial, xarray
- Language: Jupyter Notebook
- Homepage: https://ncar.github.io/ncar-python-tutorial
- Size: 49.4 MB
- Stars: 66
- Watchers: 16
- Forks: 33
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://circleci.com/gh/NCAR/ncar-python-tutorial/tree/master)
# NCAR Python Tutorial
- [NCAR Python Tutorial](#ncar-python-tutorial)
- [Setup](#setup)
- [Step 1: Clone NCAR Python Tutorial Repository](#step-1-clone-ncar-python-tutorial-repository)
- [Step 2: Install Miniconda and Create Environments](#step-2-install-miniconda-and-create-environments)
- [Step 3: Close and re-open your current shell](#step-3-close-and-re-open-your-current-shell)
- [Step 4: Run the Setup Verification Script](#step-4-run-the-setup-verification-script)
- [Launch Jupyter Lab](#launch-jupyter-lab)
- [1. Cheyenne or DAV via JupyterHub (Recommended)](#1-cheyenne-or-dav-via-jupyterhub-recommended)
- [2. Cheyenne or DAV via SSH Tunneling](#2-cheyenne-or-dav-via-ssh-tunneling)
- [3. Hobart via SSH Tunneling](#3-hobart-via-ssh-tunneling)
- [4. Personal Laptop](#4-personal-laptop)
----
## Setup
This tutorial covers the installation and setup of a Python environment on:
- Cheyenne
- Casper
- CGD's Hobart
- Personal laptop/desktop with a UNIX-variant Operating System
**NOTE:** For windows users, setup scripts provided in this repository don't work on Windows machines for the time being.
### Step 1: Clone NCAR Python Tutorial Repository
Run the following commmand to clone this repo to your system(e.g. cheyenne, casper, your laptop, etc...):
```bash
git clone https://github.com/NCAR/ncar-python-tutorial.git
```
### Step 2: Install Miniconda and Create Environments
- Change directory to the cloned repository
```bash
cd ncar-python-tutorial
```
- Run the [`configure`](./setup/configure) script:
**NOTE**: Be prepared for the script to take up to 15 minutes to complete.
```bash
./setup/configure
```
```bash
$ ./setup/configure --help
usage: configure [-h] [--clobber] [--download] [--prefix PREFIX]
Set up tutorial environment.
optional arguments:
-h, --help show this help message and exit
--clobber, -c Whether to clobber existing environment (default:
False)
--download, -d Download tutorial data without setting environment up
(default: False)
--prefix PREFIX, -p PREFIX
Miniconda3 install location)
```
Default values for ``--prefix`` argument are:
- Personal laptop / Hobart: `$HOME/miniconda3`
- Cheyenne or Casper: `/glade/work/$USER/miniconda3`
**NOTE**:
In case the default `prefix` is not appropriate for you (due to limited storage), feel free to specify a different miniconda install location. For instance, this install location may be a `project` workspace on a shared filesystem like GLADE or Hobart's filesystem.
The `configure` script does the following:
- Install `conda` package manager if it is unable to find an existing installation. Otherwise, it will update the `base` environment
- Create or Update `python-tutorial` conda environment.
- Download data if not on Cheyenne or Casper or Hobart. If on Cheyenne or Casper or Hobart, create soft-links to an existing/local data repository.
### Step 3: Close and re-open your current shell
For changes to take effect, close and re-open your current shell.
### Step 4: Run the Setup Verification Script
- Check that *conda info* runs successfully:
```bash
conda info
```
- From the `ncar-python-tutorial` directory, activate `python-tutorial` conda environment:
```bash
conda activate python-tutorial
```
- Run the setup verification script to confirm that everything is working as expected:
```bash
cd ncar-python-tutorial
./setup/check_setup
```
This step should print **"Everything looks good!"**.
----
## Launch Jupyter Lab
### 1. Cheyenne or DAV via JupyterHub (Recommended)
- JupyterHub link: https://jupyterhub.ucar.edu/
To use the Cheyenne or DAV compute nodes,we recommend using JupyterLab via NCAR's JupyterHub deployment.
Open your preferred browser (Chrome, Firefox, Safari, etc...) on your ``local machine``, and head over to https://jupyterhub.ucar.edu/.
**You will need to authenticate with either your _yubikey_ or your _DUO_ mobile app**
### 2. Cheyenne or DAV via SSH Tunneling
In case you are having issues with jupyterhub.ucar.edu, we've provided utility scripts for launching JupyterLab on both Cheyenne and Casper via SSH Tunneling:
```bash
conda activate base
./setup/jlab/jlab-ch # on Cheyenne
./setup/jlab/jlab-dav # on Casper
```
### 3. Hobart via SSH Tunneling
For those interested in running JupyterLab on CGD's Hobart, you will need to use SSH tunneling script provided in [``setup/jlab/jlab-hobart``](./setup/jlab/jlab-hobart)
```bash
conda activate base
./setup/jlab/jlab-hobart
```
```bash
$ ./setup/jlab/jlab-hobart --help
Usage: launch dask
Possible options are:
-w,--walltime: walltime [default: 08:00:00]
-q,--queue: queue [default: medium]
-d,--directory: notebook directory
-p,--port: [default: 8888]
```
### 4. Personal Laptop
For those interested in running JupyterLab on their local machine, you can simply run the following command, and follow the printed instructions on the console:
```bash
conda activate base
jupyter lab
```