Install Popular Data Science Tools on Atmosphere or Jetstream Instances¶
- EZ Installation of Popular Data Scientist Tools
- Installation of RStudio on an Atmosphere Instance
- Advanced Installation of Docker
Downloads, access, and services¶
In order to complete this tutorial you will need access to the following services/software
We will use the following CyVerse platform(s):
|Platform||Interface||Link||Platform Documentation||Quick Start|
|Atmosphere||Command line (ssh) and/or Desktop (VNC, Guacamole WebDesktop)||Atmosphere||Atmosphere Manual||Guide|
|Jetstream||Command line (ssh) and/or Desktop (VNC, Guacamole WebDesktop)||Jetstream||Jetstream Manual||XSEDE Portal|
``ez`` is deployed on all featured instances in Atmosphere and Jetstream
ssh using a terminal.
Connect via the instance’s web shell via the Atmosphere Instance’s web page.
EZ Install Anaconda (Jupyter, Jupyter Lab, Jupyter Hub)¶
- From your terminal session, you can install Anaconda Jupyter using the following
- Jupyter notebooks with Python 3 (default)
- Jupyter notebooks with Python 2
- Jupyter notebooks with R Kernel
- Jupyter Hub
After the ezj installation, you will be provided a URL (e.g. http ://220.127.116.11:8888/?token=2d6c40a7c8ee4b4933eaae5898101846bbfcd1e5d6bae37b) in your terminal session. Copy paste this into your new browser tab.
A Jupyter Notebook is running as an active process in the foreground on your Atmosphere instance. If you disconnect from your Atmosphere terminal session, the Jupyter Notebook will terminate.
One trick to keep the session running is to use a
tmuxand disconnect the session before you close your browser tab.
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.
Restart a new Jupyter session on a VM with EZ already installed
At the terminal command prompt retype
ezj, this will restart the conda virtual environment and a new Jupyter notebook. Connect to the notebook using the URL as in the instructions above. Don’t forget to use tmux!
Jupyter Lab (new)¶
Jupyter Lab (Beta) is now included in the base Anaconda installation
To start a new Jupyter Lab session type:
Install Jupyter Hub (new)¶
From terminal type
The installation may take up to 10 minutes to complete.
Once the install is complete, and a session is running, you’ll get a URL address to the VM.
Copy paste the URL into your new browser tab.
You will be re-directed back to a CyVerse CAS service, log into your account.
The Jupyter Hub should now be loaded in the browser tab.
EZ Install Singularity¶
From your terminal, type the following command:
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.
singularity run shub://vsoch/hello-world
EZ Install Docker¶
From your connected session, you can install Docker using the following command:
sudo docker run hello-world
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
sudowith Docker commands in the Advanced Docker Setup section.
Some common next steps include: