Installation¶
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
Note
We recommend setting up 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
Note
You may need to install pip and 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 can be installed either from the python package index PyPI (good for general use) or directly from the aiida-core github repository (good for developers).
Install the aiida-core python package from PyPI using:
(aiida) $ pip install aiida-core
Note
If you are installing AiiDA in your system environment,
consider adding the --user flag to avoid the need for
administrator privileges.
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
advanced_plotting: tools for advanced plotting
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,advanced_plotting]
Note
If you are installing the optional ssh_kerberos and you are on Ubuntu you might encounter an error related to the gss package.
To fix this you need to install the libffi-dev and libkrb5-dev packages:
sudo apt-get install libffi-dev libkrb5-dev
AiiDA uses the reentry package to keep a fast cache of entry points for a snappy verdi cli.
After installing AiiDA packages, always remember to update the reentry cache using:
reentry scan
AiiDA profile setup¶
After successful installation, you need to create an AiiDA profile via AiiDA’s command line interface verdi.
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 verdi setup
and set up the database manually as explained below.
Database setup¶
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, only PostgreSQL is allowed 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:
psql
Create a new database user account for AiiDA by running:
CREATE USER aiida WITH PASSWORD '<password>';
replacing <password> with a password of your choice.
Make sure to remember it, as you will need it again when you configure AiiDA to use this database through verdi setup.
If you want to change the password you just created use the command:
ALTER USER aiida PASSWORD '<password>';
Next we create the database itself. Keep in mind that 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 aiida user:
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 \q.
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 psql shell.
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
PostgreSQL host: localhost
PostgreSQL port: 5432
AiiDA Database name: aiidadb
AiiDA Database user: aiida
AiiDA Database password: <password>
Note
Do not forget to backup your database (instructions here).
Note
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 Unix sockets¶
Instead of using passwords to protect access to the database (which could be used by other users on the same machine), PostgreSQL allows password-less logins via Unix sockets.
In this scenario PostgreSQL compares the user connecting to the socket with its own database of users and will allow a connection if a matching user exists.
Assume the role of postgres by running the following as root:
su - postgres
Create a database user with the same name as the user you are using to run AiiDA (usually your login name):
createuser <username>
replacing <username> with your username.
Next, create the database itself making sure that your user is the owner:
createdb -O <username> aiidadb
To test if the database was created successfully, you can run the following command as your user in a bash terminal:
psql aiidadb
Make sure to leave the host, port and password empty when specifying the parameters during the verdi setup phase
and specify your username as the AiiDA Database user:
Database engine: postgresql_psycopg2
PostgreSQL host:
PostgreSQL port:
AiiDA Database name: aiidadb
AiiDA Database user: <username>
AiiDA Database password:
Setup instructions¶
After the database has been created, do
verdi setup <profile_name>
where <profile_name> is a profile name of your choosing.
The 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.
Note
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: richard.wagner@leipzig.de
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 'richard.wagner@leipzig.de'
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 verdi
command, you need to be in your virtual environment.
If you open a new terminal for example, be sure to activate it first with:
source ~/.virtualenvs/aiida/bin/activate
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
Note
While operational, the daemon logs its activity to a file in ~/.aiida/daemon/log/ (or, more generally, $AIIDA_PATH/.aiida/daemon/log).
Get the latest log messages via verdi daemon logshow.
Final checks¶
Use the 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 aiida@localhost: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.