Troubleshoot

Here is an overview of some common/known problems and how to solve them.

I don’t want to read this whole thing — I just have a question!

Please do not file an issue to ask a question. You can use the discussion tab on GitHub if you have a question. You are also free to get in touch with us using some other channel.

Installation of the virtual environment

On certain Linux systems (e.g. specific versions of Debian and Ubuntu), the creation of the virtualenv will fail with the output:

Error: Command [...] returned non-zero exit status 1

This due to a problem with a specifc version of pyenv. To fix the problem do the following:

rm -r venv
python3 -m venv --without-pip venv
source venv/bin/activate
curl https://bootstrap.pypa.io/get-pip.py | python
deactivate
source venv/bin/activate
pip install -r requirements.txt
deactivate

and everything should be setup correctly. Now, continue following the Installation instructions.

Unable to open HDF5 file

HDF5 files are known to sometimes cause problems on NFS-mounted filesystems. This can cause errors of the form:

OSError: Unable to open file (unable to lock file, errno = 37, error message = 'No locks available')

To fix this, just run the following in the shell:

export HDF5_USE_FILE_LOCKING=‘FALSE’

and try again. If the problem persists, just add the line to your ~/.bashrc (or equivalent). However, it might have unknown side-effects!