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Install Popular Data Science Tools on Atmosphere or Jetstream Instances

Goal

The ez command line program allows users to install popular data science packages such as Anaconda (Jupyter notebooks, Python 2/3, R), Docker, and Singularity with simple commands on any running Atmosphere or Jetstream instance.

.. toctree::
        :maxdepth: 2

        EZ Installation of Popular Data Scientist Tools <self>
        Installation of RStudio on an Atmosphere Instance <rstudio.rst>
        Advanced Installation of Docker <docker.rst>

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise Register
Atmosphere access You must have access to Atmosphere Request Access

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Quick Start
Atmosphere Command line (ssh) and/or Desktop (VNC) Atmosphere Atmosphere Manual Guide

Atmosphere Images

In order to complete this quickstart you will need to have the following:

A running Atmosphere image Notes
A running Atmosphere or Jetstream Image EZ can be used on any running instance created from any image

Get Started

EZ Install (Jupyter, R, Python 2, Python 3)

Tip

EZ allows "easy" installation of tools using anaconda. This quickstart will cover specific commands for installing:

  1. Navigate to an Atmosphere or Jetstream project with a running instance
  2. Connect to Atmosphere via ssh.
  3. From your connected session, you can install Jupyter using the following commands:
  • Jupyter notebooks with Python 3 (default)
    ezj
  • Jupyter notebooks with Python 2
    ezj -2
  • Jupyter notebooks with R Kernel
    ezj -R or ezj -r
Connect to a Atmosphere instance running a Jupyter Notebook
  1. After the installation, you will be provided with a URL (e.g. 'http ://128.196.65.162:8888/?token=2d6c40a7c8ee4b4933eaae5898101846bbfcd1e5d6bae37b' ) copy and paste the URL provided into your local computer's browser.

Note

The Jupyter notebook is running as an active process on your atmosphere session. If you disconnect from your Atmosphere session, the Jupyter Notebook will terminate.

  1. To terminate your Jupyter Notebook, close the browser page with the Jupyter notebook interface. In your Atmosphere ssh session, press: control + C to terminate the Jupyter notebook.
Start a new Jupyter session on a VM with EZ already installed
  1. Connect (ssh) into your Atmosphere instance and type ezj, this will start a new Jupyter notebook. Connect to the notebook using the URL as in step 1 of the Connection instructions above.

EZ Install Singularity

  1. Connect to Atmosphere via ssh.
  2. From your connected session, you can install Singularity using the following command: ezs

You should see

Updating ez singularity and installing singularity (this may take a few minutes, coffee break!)
[sudo] password for YourCyVerseUserName:

Wait for the installation to complete.

  1. Test Singularity
singularity run shub://vsoch/hello-world

EZ Install Docker

  1. Connect to Atmosphere via ssh.

  2. From your connected session, you can install Docker using the following command:

    ezd

  3. Test Docker

    sudo docker run hello-world

Note

You need to use sudo permissions with Docker. After using the sudo command, Atmosphere will ask you for your CyVerse password for security purposes. You can remove the need to use sudo with Docker commands in the Advanced Docker Setup section.

Next Steps:

Some common next steps include:

  1. Installation of RStudio on an Atmosphere Instance
  2. Advanced Docker Setup

Additional Information

Search for an answer: CyVerse Learning Center or CyVerse Wiki

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