On a clean Ubuntu 16.04 install the pip install command
pip install -e aiida_coremay fail due to a problem with dependencies on the
numpypackage. 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
numpyindividually through pip in your virtual env, i.e.:
pip install numpy
followed by executing the original install command once more:
pip install -e .
This should fix the dependency error.
pip installcommand gives you an error that resembles the one shown below, you might need to downgrade to an older version of pip:
Cannot fetch index base URL https://pypi.python.org/simple/
To downgrade pip, use the following command:
sudo easy_install pip==1.2.1
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
notebookoption 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=<aiida.kernel.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 -> <aiida.kernel.name>
When installing the
ssh_kerberosoptional requirement through Anaconda you may encounter the following error on Ubuntu machines:
version 'GFORTRAN_1.4' not found (required by /usr/lib/libblas.so.3)
This is related to an open issue in anaconda ContinuumIO/anaconda-issues#686. A potential solution is to run the following command:
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.
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
~/.bashrcfile similar to the following:
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):
Similarly, if the package installs but then errors occur during the first of AiiDA (with
Symbol not founderrors 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
~/.bashrcand then open a new shell:
(you should of course adapt the path to the PostgreSQL libraries).
For some reasons, on some machines (notably often on Mac OS X) there is no default locale defined, and when you run
verdi setupfor 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
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
pygtkis 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:
python-gtk2package. Under Ubuntu, do:
sudo apt-get install python-gtk2
lib/python2.7/dist-packagesfolder within your virtual environment:
mkdir <AIIDA_VENV_FOLDER>/lib/python2.7/dist-packages chmod 755 <AIIDA_VENV_FOLDER>/lib/python2.7/dist-packages
<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
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/pygtk.py pygtk.py ln -s /usr/lib/python2.7/dist-packages/cairo cairo
verdi data structure show --format=ase <PK>should work.
[Only for developers] The developer tests of the SSH transport plugin are performed connecting to
localhost. The tests will fail if a passwordless ssh connection is not set up. Therefore, if you want to run the tests:
make sure to have a ssh server. On Ubuntu, for instance, you can install it using:
sudo apt-get install openssh-server
Configure a ssh key for your user on your machine, and then add your public key to the authorized keys of localhsot. The easiest way to achieve this is to run:
(it will ask your password, because it is connecting via ssh to
localhostto install your public key inside ~/.ssh/authorized_keys).