1. Getting set up¶
If you are using the Quantum Mobile virtual machine locally inside VirtualBox, you can skip this section.
1.1. Connect to your virtual machine¶
You should each have received from the instructors:
an IP address
a private SSH key
a public SSH key
The steps below explain how to use these in order to connect to your personal virtual machine (VM) on Amazon Elastic Cloud 2 using the Secure Shell protocol. The software on this VM is based on Quantum Mobile and already includes a pre-configured AiiDA installation as well as some test data for the tutorial.
If you decide to work in pairs, one of you should forward their credentials to the other, and you should both use the same IP address and ssh key. Since you will be sharing the VM and user account, be careful not to delete the work of your colleague.
1.1.1. Linux and MacOS¶
It’s recommended for you to place the ssh key you received in a folder dedicated to your ssh configuration, to do so:
If not already present, create a
.sshdirectory in your home (
mkdir ~/.ssh), and set its permissions:
chmod 700 ~/.ssh
Copy the two keys
Set the correct permissions on the private key:
chmod 600 ~/.ssh/aiida_tutorial_NUM. You can check check with
ls -lthat the permissions of this file are now
After the ssh key files are in place, add the following block to your
Host aiidatutorial Hostname IP_ADDRESS User max IdentityFile ~/.ssh/aiida_tutorial_NUM ForwardX11 yes ForwardX11Trusted yes LocalForward 8888 localhost:8888 LocalForward 5000 localhost:5000 ServerAliveInterval 120
replacing the IP address field (
IP_ADDRESS) and the
NUM with what you received earlier.
Afterwards you can connect to the server using this simple command:
Here’s a copy-paste ready command for you to use directly with zero configuration:
ssh \ -i ~/.ssh/aiida-tutorial-max.pem \ -L 8888:localhost:8888 \ -L 5000:localhost:5000 \ -o ServerAliveInterval=120 \ -X -C \ max@IP_ADDRESS
On MacOS you need to install XQuartz in order to use X-forwarding.
If you’re running Windows 10, you may want to consider installing the Windows Subsystem for Linux (and then follow the instructions above). Alternatively:
Install the PuTTY SSH client.
aiida_tutorial_NNprivate key (button “Load”). You may need to choose to show “All files (.)”, and select the file without any extension (Type: File).
In the same window, click on “Save private Key”, and save the key with the name
aiida_tutorial_NN.ppk(don’t specify a password).
It will add a new icon near the clock, in the bottom right of your screen.
Right click on this Pageant icon, and click on “View Keys”.
Click on “Add key” and select the
aiida_tutorial_NN.ppkyou saved a few steps above.
Put the given IP address as hostname, type
aiidatutorialin “Saved Sessions” and click “Save”.
Go to Connection > Data and put
maxas autologin username.
Go to Connection > SSH > Tunnels, type
8888in the “Source Port” box, type
localhost:8888in “Destination” and click “Add”.
Repeat the previous step for port
Go back to the “Session” screen, select “aiidatutorial” and click “Save”.
Finally, click “Open” (and click “Yes” on the putty security alert to add the VM to your known hosts). You should be redirected to a bash terminal on the virtual machine.
Next time you open PuTTY, select
aiidatutorial and click “Load” before clicking “Open”.
In order to enable X-forwarding:
1.2. Start jupyter¶
Once connected to your virtual machine, type in the remote terminal
This will enable the virtual environment in which AiiDA is installed, allowing you to use AiiDA. Now type in the same shell:
jupyter notebook --no-browser
This will run a server with a web application called
jupyter, which is used to create interactive python notebooks.
In order to connect to the jupyter notebook server:
Copy the URL that has been printed to the terminal (similar to
Open a web browser on your laptop and paste the URL.
You will see a list of folders on your personal VM.
While keeping the first
ssh connection running, open a second
ssh connection in a separate terminal and execute
workon aiida there as well.
We will use the second terminal to directly interact with the virtual machine on the command line, while we use the first one to only serve the jupyter notebook.
You can safely ignore all warnings related to port forwarding when opening a second ssh connection. Those are caused by the fact that the ports are now already in use which in this context is perfectly fine.
1.3. Downloading files¶
Throughout this tutorial, you will encounter links to download python scripts, jupyter notebooks and more.
These files should be downloaded to the environment/working directory you use to run the tutorial.
In particular, when running the tutorial on a Linux VM, copy the link address and download the files to the machine using
wget in the terminal:
where you replace
<URL> with the actual HTTPS URL copied from the tutorial text in your browser.
This will download the file to the current directory.
If you encounter errors such as
ImportError: No module named aiidaor
No command ’verdi’ found, double check that you have loaded the virtual environment with
workon aiidabefore launching
jupyternotebook server. Your command line prompt should start with
If your browser cannot connect to the jupyter notebook server, check that you have correctly configured SSH tunneling/forwarding as described above. Keep in mind that you need to start the jupyter server from the terminal connected to the VM, while the web browser should be opened locally on your laptop.
See the jupyter notebook documentation for compatibility of jupyter with various web browsers.