AiiDA CLI Cheatsheet

Here we will list some useful commands for working with AiiDA. Have a look here to explore all available AiiDA command line subcommands.

Monitoring Submitted Processes

List all submitted processes:

verdi process list -a

Delete a process node, identified by its primary key value <PK>:

verdi node delete <PK>

Delete multiple process nodes between primary key values <PK_1> and <PK_n>:

verdi node delete {<PK_1>..<PK_n>}

View all the nodes associated with a process node:

verdi node show <PK>

View attributes of a process node (such as retrieved files and find the path on disk where outputs are stored temporarily):

verdi node attributes <PK>

From the node attributes output dictionary, you can find where the input and output files are temporarily stored for a process in the “remote_workdir” value.

Debugging

Any aiida errors are logged in .aiida/daemon/log/.

If any changes to the plugin code are made, after an update for example, restart the daemon if it is already running to implement the code changes:

verdi daemon restart --reset

To view details of a submitted process, such as the inputs, state, log messages, etc., use the following command:

verdi process show <PK>

To view where in the source code an exception has occured if a calculation has failed:

verdi process report <PK>

Sharing Data

When you are ready to share data, the AiiDA database and accompanying files inputted and outputted in each process can be archived into a single file:

verdi archive create --all archive_name.aiida

where the --all flag saves all the data in the AiiDA profile.

To import an existing AiiDA archive file to a loaded profile:

verdi archive import archive_name.aiida

Visualise Data Provenance

Visualise your submitted jobs as a provenance graph outputted in a .pdf file. Select the latest <PK> to include all previous nodes in the graph:

verdi node graph generate <PK>

An example provenance graph for the first eight steps of the lysozyme tutorial, will look something like this:

../_images/53.dot.png

Plugin Specfic AiiDA Commands

The following commands are only available with the aiida-gromacs plugin.

Show Provenance on CLI

Show a list of the commands run and the connected inputs/outputs associated with any processes that have been run using:

verdi data provenance show

An example output on the command line will look like this:

Step 1.
        command: gmx pdb2gmx -f 1AKI_clean.pdb -ff oplsaa -water spce -o 1AKI_forcefield.gro -p 1AKI_topology.top -i 1AKI_restraints.itp
        executable: gmx
        input files:
                1AKI_clean.pdb
        output files:
                pdb2gmx.out
                1AKI_forcefield.gro
                1AKI_topology.top
                1AKI_restraints.itp

Step 2.
        command: gmx editconf -f 1AKI_forcefield.gro -center 0 -d 1.0 -bt cubic -o 1AKI_newbox.gro
        executable: gmx
        input files:
                1AKI_forcefield.gro <-- from Step 1.
        output files:
                editconf.out
                1AKI_newbox.gro

Step 3.
        command: gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -p 1AKI_topology.top -o 1AKI_solvated.gro
        executable: gmx
        input files:
                1AKI_newbox.gro <-- from Step 2.
                1AKI_topology.top <-- from Step 1.
        output files:
                solvate.out
                1AKI_solvated.gro
                1AKI_topology.top