With all prerequisites in place, we can now install AiiDA and its python dependencies.
Virtual python environment¶
AiiDA depends on a number of third party python packages, and usually on specific versions of those packages. In order not to interfere with third party packages needed by other software on your system, we strongly recommend isolating AiiDA in a virtual python environment. In the following, we describe how to create a virtual python environment using the virtualenv tool, but feel free to use your preferred environment manager (e.g. conda).
Creating the virtual environment¶
To create and activate a new virtual environment, run the following commands:
pip install --user --upgrade virtualenv # install virtualenv tool virtualenv ~/.virtualenvs/aiida # create "aiida" environment source ~/.virtualenvs/aiida/bin/activate # activate "aiida" environment
AiiDA requires a python 3 virtual environment.
If your system runs python 2 by default but has a
python3 executable, you can still set up a python 3 virtual environment using:
virtualenv --python python3 ~/.virtualenvs/aiida
This will create a directory in your home directory named
.virtualenvs, and a directory
aiida inside of it where all the packages will be installed.
After activation, your prompt should have
(aiida) in front of it, indicating that you are working inside the virtual environment.
The activation script ensures that the python executable of the virtualenv is the first in
PATH, and that python programs have access only to packages installed inside the virtualenv.
To leave or deactivate the environment, simply run:
(aiida) $ deactivate
You may need to install
setuptools in your virtual environment in case the system or user version of these tools is old:
(aiida) $ pip install -U setuptools pip
Aiida python package¶
aiida-core python package from PyPI using:
(aiida) $ pip install aiida-core
If you are installing AiiDA in your system environment,
consider adding the
--user flag to avoid the need for
Alternatively, you can create a directory where to clone the AiiDA source code and install AiiDA from source:
$ mkdir <your_directory> $ cd <your_directory> $ git clone https://github.com/aiidateam/aiida-core (aiida) $ pip install -e aiida-core
There are additional optional packages that you may want to install, which are grouped in the following categories:
atomic_tools: packages that allow importing and manipulating crystal structure from various formats
ssh_kerberos: adds support for ssh transport authentication through Kerberos
REST: allows a REST server to be ran locally to serve AiiDA data
docs: tools to build the documentation
notebook: jupyter notebook - to allow it to import AiiDA modules
testing: python modules required to run the automatic unit tests
In order to install any of these package groups, simply append them as a comma separated list in the
pip install command:
(aiida) $ pip install -e aiida-core[atomic_tools,docs]
If you are installing the optional
ssh_kerberos and you are on Ubuntu you might encounter an error related to the
To fix this you need to install the
sudo apt-get install libffi-dev libkrb5-dev
AiiDA uses the reentry package to keep a fast cache of entry points for a snappy
After installing AiiDA packages, always remember to update the reentry cache using:
AiiDA profile setup¶
After successful installation, you need to create an AiiDA profile via AiiDA’s command line interface
Most users should use the interactive quicksetup:
verdi quicksetup <profile_name>
which leads through the installation process and takes care of creating the corresponding AiiDA database.
For maximum control and customizability, one can use
and set up the database manually as explained below.
AiiDA uses a database to store the nodes, node attributes and other information, allowing the end user to perform fast queries of the results. Currently, the highly performant PostgreSQL database is supported as a database backend.
To manually create the database for AiiDA, you need to run the program
psql to interact with postgres.
On most operating systems, you need to do so as the
postgres user that was created upon installing the software.
To assume the role of
postgres run as root:
su - postgres
(or, equivalently, type
sudo su - postgres, depending on your distribution) and launch the postgres program:
Create a new database user account for AiiDA by running:
CREATE USER aiida WITH PASSWORD '<password>';
<password> with a password of your choice.
You will need to provide the password again when you configure AiiDA to use this database through
If you want to change the password you just created use the command:
ALTER USER aiida PASSWORD '<password>';
Next, we create the database itself. We enforce the UTF-8 encoding and specific locales:
CREATE DATABASE aiidadb OWNER aiida ENCODING 'UTF8' LC_COLLATE='en_US.UTF-8' LC_CTYPE='en_US.UTF-8' TEMPLATE=template0;
and grant all privileges on this DB to the previously-created
GRANT ALL PRIVILEGES ON DATABASE aiidadb to aiida;
You have now created a database for AiiDA and you can close the postgres shell by typing
To test if the database was created successfully, you can run the following command as a regular user in a bash terminal:
psql -h localhost -d aiidadb -U aiida -W
and type the password you inserted before, when prompted.
If everything worked well, you should get no error and see the prompt of the
If you use the same names as in the example commands above, then during the
verdi setup phase the following parameters will apply to the newly created database:
Database engine: postgresql_psycopg2 Database host: localhost Database port: 5432 AiiDA Database name: aiidadb AiiDA Database user: aiida AiiDA Database password: <password>
Do not forget to backup your database (instructions here).
If you want to move the physical location of the data files on your hard drive AFTER it has been created and filled, look at the instructions here.
Database setup using ‘peer’ authentication¶
On Ubuntu Linux, the default PostgreSQL setup is configured to use
peer authentication, which allows password-less login via local Unix sockets.
In this mode, PostgreSQL compares the Unix user connecting to the socket with its own database of users and allows a connection if a matching user exists.
This is an alternative route to set up your database - the standard approach will work on Ubuntu just as well.
Below we are going to take advantage of the command-line utilities shipped on Ubuntu to simplify creating users and databases compared to issuing the SQL commands directly.
Assume the role of
sudo su postgres
Create a database user with the same name as the UNIX user who will be running AiiDA (usually your login name):
<username> with your username.
Next, create the database itself with your user as the owner:
createdb -O <username> aiidadb
Exit the shell to go back to your login user. To test if the database was created successfully, try:
verdi setup phase, use
! to leave host empty and specify your Unix user name as the AiiDA Database user.:
Database engine: postgresql_psycopg2 Database host: ! Database port: 5432 AiiDA Database name: aiidadb AiiDA Database user: <username> AiiDA Database password: ""
After the database has been created, do
verdi setup <profile_name>
where <profile_name> is a profile name of your choosing.
verdi setup command will guide you through the setup process through a series of prompts.
The first information asked is your email, which will be used to associate the calculations to you. In AiiDA, the email is your username, and acts as a unique identifier when importing/exporting data from AiiDA.
The password, in the current version of AiiDA, is not used (it will be used only in the REST API and in the web interface). If you leave the field empty, no password will be set and no access will be granted to the user via the REST API and the web interface.
Then, the following prompts will help you configure the database. Typical settings are:
Default user email: [email protected] Database engine: postgresql_psycopg2 PostgreSQL host: localhost PostgreSQL port: 5432 AiiDA Database name: aiida_dev AiiDA Database user: aiida AiiDA Database password: <password> AiiDA repository directory: /home/wagner/.aiida/repository/ [...] Configuring a new user with email '[email protected]' First name: Richard Last name: Wagner Institution: BRUHL, LEIPZIG The user has no password, do you want to set one? [y/N] y Insert the new password: Insert the new password (again):
Remember that in order to work with AiiDA through for example the
command, you need to be in your virtual environment.
If you open a new terminal for example, be sure to activate it first with:
Start the daemon¶
The AiiDA daemon process runs in the background and takes care of processing your submitted calculations and workflows, checking their status, retrieving their results once they are finished and storing them in the AiiDA database.
The AiiDA daemon is controlled using three simple commands:
verdi daemon start: start the daemon
verdi daemon status: check the status of the daemon
verdi daemon stop: stop the daemon
While operational, the daemon logs its activity to a file in
~/.aiida/daemon/log/ (or, more generally,
Get the latest log messages via
verdi daemon logshow.
verdi status command to check that all services are up and running:
verdi status ✓ profile: On profile quicksetup ✓ repository: /repo/aiida_dev/quicksetup ✓ postgres: Connected to [email protected]:5432 ✓ rabbitmq: Connected to amqp://127.0.0.1?heartbeat=600 ✓ daemon: Daemon is running as PID 2809 since 2019-03-15 16:27:52
In the example output, all service have a green check mark and so should be running as expected.
At this point, you’re ready to get started.
For configuration of tab completion , using AiiDA in jupyter & more, see the configuration instructions before moving on.