If you experience any problems, first check that all services are up and running:

$ verdi status

✓ version:     AiiDA v2.0.0
✓ config:      /path/to/.aiida
✓ profile:     default
✓ storage:     Storage for 'default' @ postgresql://username:***@localhost:5432/db_name / file:///path/to/repository
✓ rabbitmq:    Connected as amqp://
✓ 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. If all services are up and running and you are still experiencing problems or if you have trouble with the installation of aiida-core and related services, consider the commonly encountered problems below.

Installation issues#

RabbitMQ incompatibility#

AiiDA is currently not compatible with RabbitMQ v3.8.15 and up with default configuration. When AiiDA is run with an incompatible version of RabbitMQ, the following warning will be displayed:

RabbitMQ v3.8.15 is not supported and will cause unexpected problems!
It can cause long-running workflows to crash and jobs to be submitted multiple times.
See for details.

There are two possible solutions:

  1. Configure the RabbitMQ server to set a long time for the consumer_timeout parameter.

  2. Downgrade the RabbitMQ server to v3.8.14 or earlier

Newer versions of RabbitMQ can be made compatible with AiiDA, but the server will have to be configured. Note that for this administrator access will most likely be required. The name and location of the configuration file depends on the operating system (see the RabbitMQ documentation for details). It is possible that the configuration file does not yet exist, in which case it should be created.

Add the consumer_timeout parameter to the config file and give it a sufficiently large number:

consumer_timeout = 36000000000 # 10,000 hours in milliseconds

For AiiDA to operately safely, this value should be larger than the longest expected run time of any AiiDA workflow or calculation. The suggested number of 10,000 hours should typically be sufficient. See the RabbitMQ documentation on timeouts for more details and how with advanced configuration the consumer timeout can even be completely disabled.

Note that when you have properly configured RabbitMQ, AiiDA will continue to emit the warning because it can only check the version. To suppress the warning set the warnings.rabbitmq_version to False:

verdi config set warnings.rabbitmq_version False

Downgrading the RabbitMQ server will be dependent on the operating system and/or on how the server was installed. Please refer to the RabbitMQ installation documentation for instructions.

Further details are maintained on this wiki page of the repository.

numpy dependency#

On a clean Ubuntu 16.04 install the pip install command pip install -e aiida-core may fail due to a problem with dependencies on the numpy package. In this case you may be presented with a message like the following:

from numpy.distutils.misc_util import get_numpy_include_dirs
ImportError: No module named numpy.distutils.misc_util

To fix this, simply install numpy individually through pip in your virtual env, i.e.:

$ pip install numpy

followed by executing the original install command once more:

$ pip install -e aiida-core

This should fix the dependency error.

Database installation and location#

If the installation fails while installing the packages related to the database, you may have not installed or set up the database libraries.

In particular, on Mac OS X, if you installed the binary package of PostgreSQL, it is possible that the PATH environment variable is not set correctly, and you get a “Error: pg_config executable not found.” error. In this case, discover where the binary is located, then add a line to your ~/.bashrc file similar to the following:

export PATH=/the/path/to/the/pg_config/file:${PATH}

and then open a new bash shell. Some possible paths can be found at this Stackoverflow link and a non-exhaustive list of possible paths is the following (version number may change):

  • /Applications/

  • /Applications/

  • /Library/PostgreSQL/9.3/bin/pg_config

Similarly, if the package installs but then errors occur during the first of AiiDA (with Symbol not found errors or similar), you may need to point to the path where the dynamical libraries are. A way to do it is to add a line similar to the following to the ~/.bashrc and then open a new shell:


(you should of course adapt the path to the PostgreSQL libraries).

Autodetection of the PostgreSQL setup#

Sometimes AiiDA fails to autodetect the local configuration of PostgreSQL when running verdi quicksetup. In that case try to:

  1. Create the database manually in PostgreSQL (see here).

  2. Then run the full verdi setup command (see here).

RabbitMQ Installation (Unix)#

If in verdi status RabbitMQ is not connected, first check that RabbitMQ is actually running:

$ sudo rabbitmqctl status
Status of node rabbit@ph-tsm15-025 ...

By default, AiiDA profiles are configured to connect to RabbitMQ via amqp://guest:guest@, hence this port should be open for connections. In Linux / Mac OSX you can also check which ports a PID has open using:

$ sudo lsof -Pan -p 86960 -i
beam.smp 98979 user1   75u  IPv4 0x9d838dc03d5a2485      0t0  TCP *:25672 (LISTEN)
beam.smp 98979 user1   76u  IPv4 0x9d838dc047588625      0t0  TCP> (ESTABLISHED)
beam.smp 98979 user1   86u  IPv6 0x9d838dc034033ea5      0t0  TCP *:5672 (LISTEN)
beam.smp 98979 user1   87u  IPv4 0x9d838dc018071a15      0t0  TCP *:15672 (LISTEN)

If a connection cannot be found, try starting rabbitmq-server in non-detached mode. If you encounter an output similar to that below, it may be that your versions of RabbitMQ and erlang (the programming language which RabbitMQ is written in) are incompatible.

$ rabbitmq-server


Error description:


Stack trace:


Error description:


{"init terminating in do_boot",noproc}

init terminating in do_boot (noproc)

Crash dump is being written to: erl_crash.dump...done

You can check your version of erlang using:

$ erl -eval '{ok, Version} = file:read_file(filename:join([code:root_dir(), "releases", erlang:system_info(otp_release), "OTP_VERSION"])), io:fwrite(Version), halt().' -noshell

and your version of rabbitmq-server with:

$ rabbitmqctl --version

Then see RabbitMQ Erlang Version Requirements, to check if these are compatible, and reinstall as appropriate.

See also the RabbitMQ Troubleshooting for further information.

Ensuring a UTF-8 locale#

For some reasons, on some machines (notably often on Mac OS X) there is no default locale defined, and when you run verdi setup for the first time it fails (see also this issue of django). Run in your terminal (or maybe even better, add to your .bashrc, but then remember to open a new shell window!):

export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"

and then run verdi setup again.

Possible Ubuntu dependencies#

Several users reported the need to install also libpq-dev (header files for libpq5 - PostgreSQL library):

$ apt-get install libpq-dev

But under Ubuntu 12.04 this is not needed.

verdi not in PATH#

Installing the aiida-core python package should add the verdi CLI to your PATH automatically.

If the verdi executable is not available in your terminal, the folder where pip places binaries may not be added to your PATH

For Linux systems, this folder is usually something like ~/.local/bin:

export PATH=~/.local/bin:${PATH}

For Mac OS X systems, the path to add is usually ~/Library/Python/2.7/bin:

export PATH=~/Library/Python/2.7/bin:${PATH}

After updating your PATH, the verdi command should be available.


A preprequisite for verdi to work is that the aiida python package is importable. Test this by opening a python or ipython shell and typing:

import aiida

If you get an ImportError (and you are in the environment where AiiDA was installed), you can add it to the PYTHONPATH manually:

export PYTHONPATH="${PYTHONPATH}:<AiiDA_folder>"

Configuring remote SSH computers#

ssh_kerberos installation#

When installing the ssh_kerberos optional requirement through Anaconda you may encounter the following error on Ubuntu machines:

version 'GFORTRAN_1.4' not found (required by /usr/lib/

This is related to an open issue in anaconda ContinuumIO/anaconda-issues#686. A potential solution is to run the following command:

$ export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/

Output from .bashrc and/or .bash_profile on remote computers#


This also applies to computers configured via local transport.

When connecting to remote computers, AiiDA (like other codes as sftp) can get confused if you have code in your .bashrc or .bash_profile that produces output or e.g. runs commands like clean that require a terminal.

For instance, if you add a echo "a" in your .bashrc and then try to SFTP a file from it, you will get an error like Received message too long 1091174400.

If you still want to have code that needs an interactive shell (echo, clean, …), but you want to disable it for non-interactive shells, put at the top of your file a guard like this:

if [[ $- != *i* ]] ; then
# Shell is non-interactive.  Be done now!

Everything below this will not be executed in a non-interactive shell.


Still, you might want to have some code on top, like e.g. setting the PATH or similar, if this needs to be run also in the case of non-interactive shells.

To test if a the computer does not produce spurious output, run (after configuring):

$ verdi computer test <COMPUTERNAME>

which checks and, in case of problems, suggests how to solve the problem.


If the methods explained above do not work, you can configure AiiDA to not use a login shell when connecting to your computer, which may prevent the spurious output from being printed: During verdi computer configure, set -no-use-login-shell or when asked to use a login shell, set it to False. Note, however, that this may result in a slightly different environment, since certain startup files are only sourced for login shells.

Improvements for dependencies#

Activating the ASE visualizer#

Within a virtual environment, attempt to visualize a structure with ase (either from the shell, or using the command verdi data structure show --format=ase <PK>), might end up with the following error message:

ImportError: No module named pygtk

The issue is that pygtk is currently not pip-installable. One has to install it separately and create the appropriate bindings manually in the virtual environment. You can follow the following procedure to get around this issue:

Install the python-gtk2 package. Under Ubuntu, do:

$ sudo apt-get install python-gtk2

Create the lib/python2.7/dist-packages folder within your virtual environment:

$ mkdir <AIIDA_VENV_FOLDER>/lib/python2.7/dist-packages
$ chmod 755 <AIIDA_VENV_FOLDER>/lib/python2.7/dist-packages

where <AIIDA_VENV_FOLDER> is the virtual environment folder you have created during the installation process.

Create several symbolic links from this folder, pointing to a number of files in /usr/lib/python2.7/dist-packages/:

$ cd <AIIDA_VENV_FOLDER>/lib/python2.7/dist-packages
$ ln -s /usr/lib/python2.7/dist-packages/glib glib
$ ln -s /usr/lib/python2.7/dist-packages/gobject gobject
$ ln -s /usr/lib/python2.7/dist-packages/gtk-2.0 gtk-2.0
$ ln -s /usr/lib/python2.7/dist-packages/pygtk.pth pygtk.pth
$ ln -s /usr/lib/python2.7/dist-packages/
$ ln -s /usr/lib/python2.7/dist-packages/cairo cairo

After that, verdi data structure show --format=ase <PK> should work.

Use in ipython/jupyter#

In order to use the AiiDA objects and functions in Jupyter, this latter has to be instructed to use the iPython kernel installed in the AiiDA virtual environment. This happens by default if you install AiiDA with pip including the notebook option, and run Jupyter from the AiiDA virtual environment.

If for any reason, you do not want to install Jupyter in the virtual environment, you might consider to install it out of the virtual environment, if not already done:

$ pip install jupyter

Then, activate the AiiDA virtual environment:

$ source ~/<aiida.virtualenv>/bin/activate

and setup the AiiDA iPython kernel:

$ pip install ipykernel
$ python -m ipykernel install --user --name=<>

where you have chosen a meaningful name for the new kernel.

Finally, start a Jupyter server:

$ jupyter notebook

and from the newly opened browser tab select New -> <>

Increasing the logging verbosity#

By default, the logging level of AiiDA is minimal to avoid too much noise in the logfiles. Only warnings and errors are logged to the daemon log files, while info and debug messages are discarded.

If you are experiencing a problem, you can increase the default minimum logging level of AiiDA messages, with:

$ verdi config logging.aiida_loglevel DEBUG

You might also be interested in reviewing the circus log messages (the circus library is the daemonizer that manages the daemon runners),

$ verdi config logging.circus_loglevel DEBUG

however those messages are usually only relevant to debug AiiDA internals.

For each profile that runs a daemon, there are two unique logfiles, one for AiiDA log messages (named aiida-<profile_name>.log) and one for the circus logs (named circus-<profile_name>.log). Those files can be found in the ~/.aiida/daemon/log folder.

After restarting the daemon (verdi daemon restart), the number of messages logged will increase significantly and may help in determining the source of the problem.


Besides DEBUG, you can also use the levels defined in the standard Python logging module. In addition to those, AiiDA defines the custom REPORT level, which, with a value of 23, is more verbose than the WARNING level, but less verbose than INFO. The REPORT level is AiiDA’s default logging level.

When the problem is solved, we suggest to reset the default logging level, with:

$ verdi config logging.circus_loglevel --unset
$ verdi config logging.aiida_loglevel --unset

to avoid too much noise in the logfiles.

The config options set for the current profile can be viewed using

$ verdi profile show

in the options row.