Start/Stop AiiDA

Regardless of whether you have switched off AiiDA or restarted your computer. To start recording provenance with this plugin, you will need to start up your AiiDA instance. Likewise, once you have finished using AiiDA, it is best practice to shut things down gracefully. These steps also assume you have already followed the steps within Installation and have already a fully working install of the toolchain.

The first step in starting AiiDA is to activate your conda environment, for example:

conda activate aiida-2.4.0

Initialising the AiiDA database

If this is the first time you are using AiiDA, then initialise your AiiDA database:

initdb -D ~/.aiida/aiida_db

This creates a directory called ~/.aiida, where data created via AiiDA is stored.

Starting AiiDA

The next step is to start the AiiDA database:

pg_ctl -D ~/.aiida/aiida_db -l ~/.aiida/logfile start
rabbitmq-server -detached

Then start the AiiDA process daemon:

verdi daemon start 2

You can then confirm all is well by checking the status of verdi:

verdi status

Creating an AiiDA Database Profile

To start using AiiDA-gromacs to track the inputs and outputs of GROMACS commands, AiiDA first requires for a profile to be set up for each project via verdi. Verdi is the command line tool in AiiDA used to interact with the AiiDA database. All commands run via the AiiDA-GROMACS plugin are tracked and stored in the AiiDA database. Create a profile within the AiiDA database:

verdi quicksetup
    Info: enter "?" for help
    Info: enter "!" to ignore the default and set no value
    Profile name: username
    Email Address (for sharing data): your@email.com
    First name: Your
    Last name: Name
    Institution: where-you-work

That is it, you are now free to use your AiiDA toolchain.

Stopping AiiDA

It is best to stop your AiiDA instance gracefully than to simply close your VM or shutdown your computer, this protects against any issues that might corrupt your database.

Firstly stop the verdi process daemon:

verdi daemon stop

Next stop the database process:

pg_ctl -D ~/.aiida/aiida_db stop
rabbitmqctl stop

Finally you can deactivate your conda environment:

conda deactivate

That is it, you now have fully disabled the AiiDA toolchain.

Switching AiiDA Database Profile

If you are working on multiple projects, you can create a new profile as before and view all created profiles:

verdi profile list

If you want to switch to a different <PROFILE>:

verdi profile setdefault <PROFILE>

And to delete a profile no longer needed:

verdi profile delete <PROFILE>

You can now create, switch and delete profiles saved in the AiiDA database.