When importing Numpy from Flask in Virtualenv Numpy gives multiarray import error

Imports under mod_wsgi can be tricky, particularly with Python C extension libraries.

The issue here turned out to be setting the WSGIDaemonProcess python-path= option to a venv with the compiled module. From those docs:

If using a Python virtual environment, rather than use this option to refer to the site-packages directory of the Python virtual environment, you should use the python-home option to specify the root of the Python virtual environment instead.

In all cases, if the directory contains Python packages which have C extension components, those packages must have been installed using the same base Python version as was used to compile the mod_wsgi module. You should not mix packages from different Python versions or installations.

So, the python-home= option must be used for the venv dir given, and either Python 2.7 should be used for the venv, or the Python 3 build of mod_wsgi must be installed (libapache2-mod-wsgi-py3 on Ubuntu).

For some applications, the WSGIApplicationGroup needs to be configured as follows too:

WSGIApplicationGroup %{GLOBAL}

In the case that any of the C extensions use the simplified threading api.

From similar questions, α, β, this seems to be a common issue.