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Data Science Virtual Machines on Atmosphere or Jetstream

Description: Provision VM for analyzing NEON AOP data

CyVerse operates a cloud service called Atmosphere. Users can request up to 2,000 allocation units [units are hours (hr)] per month. E.g. a 1-core instance uses 1 AU/hr, a 4-core instance uses 4 AU/hr, and a 16-core instance uses 16 AU/hr. Allocations are automatically reset to 128 AU on the 1st of each month.

Users can request more AU by clicking the Request More Resources button in the Atmosphere UI. You can also get help by asking questions in the Intercom (blue button in the lower right of the CyVerse website pages).



Requests are typically approved in <1 hour during business hours, and <24 hours on nights and weekends.

XSEDE Jetstream uses the same UI interface as Atmosphere. Startup allocations typically range from 25,000 - 250,000 AU per year. Research allocations between 250,000 to several million AU are also available through XSEDE.


Log into CyVerse Atmosphere

Atmosphere Manual

Alternately, log into XSEDE Jetstream

Fill in your username and password and click “LOGIN”

Create a Project

This is something you only need to do once.

  • Click on the “Projects” tab on the top and then click “CREATE NEW PROJECT”
  • Enter a name, e.g. “NEON2018” into the Project Name field.
  • the Description can be something complex and long (like an extended abstract, or tutorial), or something short like “Data Institute 2018”.
  • Select the newly created project

Start a new Instance

From your Project folder, you can select “New” and “Instance”

  1. Suggest you select a featured image with a Graphic User Interface (GUI).

Suggested Atmosphere Image(s):

Atmosphere Image(s):

Here are the tested Ubuntu images.

Warning: The latest version of Ubuntu (18.04) may not have current packages for some software.

Image Name Version Description Link
Ubuntu 16.04 GUI 2.1 Ubuntu 16.04 GUI XFCE Base Image
Ubuntu 16.04 non-GUI 1.6 Ubuntu 16.04 non-GUI Base Image
Ubuntu 18.04 GUI 1.0 Ubuntu 18.04 GUI XFCE Base Image
Ubuntu 18.04 non-GUI 1.0 Ubuntu 18.04 non-GUI Base Image

Suggested Jetstream Image(s):

Image Name Version Description Link
Ubuntu 16.04 GUI 1.13 Ubuntu 16.04 LTS Development + GUI support + Docker Image
Ubuntu 14.04 GUI 1.17 Base Ubuntu 14.04.3 + Xfce + Xfce-goodies, firefox, icon sets and themes Image
  • Find the “Ubuntu 16.04” image, click on it
  • Give it a short name that is distinct “my_first_vm”
  • Select ‘tiny1 (CPU: 1, Mem: 4GB, Disk: 30GB)’. Because this is your first attempt at provisioning a virtual machine it doesn’t need to be a workhorse (yet).
  • Leave rest of the fields as default.
  • Wait for it to become active
  • Be Patient (but not too patient - if it takes >10 minutes the system may be at capacity, if you’re trying to launch a large or extra large VM, try something smaller).
  • You can click on your new instance to get more information.

Accessing the Shell

Once the instance is active, you can access it via ssh or by using the Web Shell provided by Atmosphere.

  • Click “Open Web Shell”, or, if you know how to use ssh,

you can ssh in with your CyVerse username on the IP address of the machine


You should see something like this

Welcome to Ubuntu 16.04.2 LTS (GNU/Linux 4.4.0-81-generic x86_64)

  Get cloud support with Ubuntu Advantage Cloud Guest:

155 packages can be updated.
0 updates are security updates.

*** System restart required ***
Welcome to
    _   _                             _
   / \ | |_ _ __ ___   ___  ___ _ __ | |__   ___ _ __ ___
  / _ \| __| '_ ` _ \ / _ \/ __| '_ \| '_ \ / _ \ '__/ _ \
 / ___ \ |_| | | | | | (_) \__ \ |_) | | | |  __/ | |  __/
/_/   \_\__|_| |_| |_|\___/|___/ .__/|_| |_|\___|_|  \___|


Note, this instance is running an older version of Ubuntu 16.

A good practice before installing any new software is to run:

sudo apt-get update && sudo apt-get upgrade

After the new updates are installed you can reboot the machine from terminal or from the Atmosphere UI

sudo reboot

If you’re using the Web Shell, the instance will exit. Wait a few minutes for the instance to reboot and refresh the screen.


To access the Clipboard in an Apache Guacamole Web Shell:

  • Open Clipboard and virtual keyboard - On a standard keyboard: ctrl + alt + shift key - On a MAC OS X keyboard: control + command ⌘ + shift key
  • Select your text or paste text into the clipboard window.
  • Close the Clipboard window by selecting control + command ⌘ + shift keys again
  • Right click with your mouse or double tap fingers on touchpad to paste in the web shell or Desktop

Suspending an instance

  • When you’re done using an instance it is wise to ‘Suspend’ the instance in the Actions.
  • This will kill any process that is still running.
  • Your data and all of your programs will be fine. It is however wise to move your data back onto your DataStore or back it up somewhere else so it will be available.
  • Suspending the instance will leave it ready for reuse when you want to “resume” working on it.
  • You will not be charged any AU while the instance is suspended.

Deleting your instance

  • To completely remove your instance, you can select the “delete” buttom from the instance details page.
  • This will open up a dialogue window. Select the “Yes, delete this instance” button.
  • It may take Atmosphere a few minutes to process your request. The instance should disappear from the project when it has been successfully deleted.

Imaging an instance

The use of Docker and Singularity take a lot of the problems out of building unique software stacks on cloud - but sometimes these cannot be avoided.

  • Have you created a unique software stack that you need to launch on a larger number of future instances?
  • Does it take a long time to compile your software stack each time you launch a new instance?
  • Only create images from the smallest possible versions of your instance. A larger imaged instance cannot be run on a smaller instance.

To request that your instance be imaged click the “Image” button from Actions.


It is advisable to delete the machine if you are not planning to use it in future to save valuable resources. However if you want to use it in future, you can suspend it.

If you want to keep the instance for a future project, you can also “shelve” the instance. It will take a longer period of time to resume a shelved instance.

EZ Installation of Project Jupyter

We install Project Jupyter (Notebooks and Lab) using the Anaconda distribution. Within the Anaconda distribution is the conda package manager which can be used to both build and install software.

Anaconda is different than a basic Python installation. It serves as both a package manager and an environment. While this has many benefits, it also adds some complexity to running your Python environments. Still confused? Read about the myths and misconceptions of Anaconda.

For more details about installing software on Atmosphere visit the CyVerse Data Science Quickstart Tutorial or the Jetstream EZ Tutorial. There are instructions for ez installation of Docker, Singularity, and Anaconda.

If you’re on an instance which already has Anaconda installed, you’ll still need to re-run ez to restart the Anaconda virtual environment.

  1. Install Anaconda with Python3 (ez comes preloaded on featured instances on Atmosphere and Jetstream) by typing:

  2. Once the installation completes, you’re done! A Jupyter Notebook should now be running on the VM.


  1. Click the link showing the notebook URL (notice this is not the localhost:8888).


To install your own packages you’ll need to change ownership of the Anaconda installation:

sudo chown $(id -u):$(id -g) /opt/anaconda3 -R

Down version Python 3.6 to 3.5

To use GDAL you may need to reverse version Python to an earlier version

Kernel installation instructions

python -m pip install ipykernel
conda create -n ipykernel_py35 python=3.5 ipykernel
source activate ipykernel_py35    # On Windows, remove the word 'source'
python -m ipykernel install --user

List of Jupyter Kernels


conda install -c r irkernel


sudo apt-get install nodejs-legacy npm ipython ipython-notebook
sudo npm install -g ijavascript


Add Jupyter PPA

sudo add-apt-repository ppa:chronitis/jupyter -y
sudo apt-get update
sudo apt-get install -y iruby

Python2 Kernel

conda create -n ipykernel_py2 python=2 ipykernel
source activate ipykernel_py2
python -m ipykernel install --user
source deactivate ipykernel_py2
conda activate base # switch back to base Python3 environment

Julia Kernel

First, install Julia, here we are installing v0.6.

Once Julia as been installed, run julia from the prompt.

tar xvzf julia-0.6.3-linux-x86_64.tar.gz
sudo mv julia-d55cadc350/ /opt/julia
rm -rf julia-0.6.3-linux-x86_64.tar.gz
sudo ln -s /opt/julia/bin/julia /usr/local/bin/julia

Now, from Julia prompt install the iJulia Kernel.

ENV["JUPYTER"] = "/opt/anaconda3/bin/jupyter"

Bash Kernel

pip install bash_kernel
python -m bash_kernel.install

Geospatial dependencies

conda install -c conda-forge gdal
sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
sudo apt update
sudo apt install gdal-bin python-gdal python3-gdal libgdal1-dev

Script of Scripts

Official documentation

pip install sos
pip install sos-notebook
python -m sos_notebook.install

Installing RStudio-Server

RStudio can be installed in several ways.

First, you can follow the RStudio-Server instructions for Linux

Second, you can use Docker (following the same ez documentation as for Anaconda). We suggest using containers from Docker Hub Rocker on the instance.

sudo usermod -aG docker $USER
docker pull rocker/geospatial
docker run -d -p 8787:8787 rocker/geospatial

Third, you can use Anaconda

Here we are going to use ezj to install both Anaconda (Jupyter) and R

ezj -R

This will trigger the Ansible playbook to install r-base, r-essentials, and a few other commonly used R Data Science packages.

After ezj -R has finished, you can install RStudio-Server

Install these misc. dependencies

export PATH="/opt/anaconda3/bin":$PATH
sudo chown $(id -u):$(id -g) /opt/anaconda3/ -R
conda update conda
conda install gxx_linux-64
conda install gcc_linux-64

Set Path and install gdebi

sudo apt-get install gdebi-core

Install RStudio-Server with gdebi:

echo "export RSTUDIO_WHICH_R='/opt/anaconda3/bin/R'" >> ~/.bash_profile
sudo gdebi --non-interactive rstudio-server-1.1.447-amd64.deb

The installation of RStudio-Server is going to fail because we haven’t told it which R to use. Because we are using Anaconda’s installation of R, and not the basic installation of R, we have to reassign RStudio to look for Anaconda

sudo sh -c 'echo "rsession-which-r=/opt/anaconda3/bin/R" >> /etc/rstudio/rserver.conf'
# export RSTUDIO_WHICH_R='/opt/anaconda/lib/R/bin/R'
# sudo sh -c 'echo "launchctl setenv RSTUDIO_WHICH_R $RSTUDIO_WHICH_R" >> ~/.bash_profile'

Restart the server

sudo rstudio-server start
  1. You can launch Jupyter Lab by exiting the notebook and typing jupyter lab - but this will allow Lab to only be available on the localhost, with no way to connect from a remote terminal. Exit the notebook by pressing ctrl + c twice, and then start a Jupyter Lab.


To ensure your session doesn’t die when you close your terminal use tmux or screen to start your remote sessions and to detach the screen before exiting.

  • detach screen: ctrl + b then d
  • list tmux sessions: tmux ls
  • re-attach screen: tmux attach -t <session id #>

Establishing a Secure Connection

  1. On the VM start the Lab in terminal (don’t forget to use tmux)

    jupyter lab --no-browser --ip=* --port=8888

Option 1: SSH tunnel

You must have the ability to use ssh on your localhost to use this method.

  1. Start Jupyter

    jupyter lab --no-browser --ip= --port=8888
  2. Open a new terminal on your localhost.

    ssh -nNT -L 8888:localhost:8888 CyVerseUserName@<IPADDRESS>

    Enter your password when prompted.

    The terminal should stop responding after this.

  3. In your browser, open a new tab and go to http://localhost:8888

Option 2: Caddy

You can use this method with tmux in the Web Shell

  1. Follow the same step #1 above

  2. In the terminal start a new tmux session. Then copy/paste the following:

    echo "$(hostname)
    proxy / {
    " > Caddyfile
    curl | bash -s personal http.nobots

    The Caddyserver will output a secure URL https:// for the Atmosphere VM which you can then connect in a new browser tab.

  3. Copy / Paste the URL into a new browser tab.

Description of output and results

Congratulations - you’ve got a Virtual Machine ready to do some serious data science!

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