FAQs and Known Issues

Q: My program does not terminate (i.e. it does not crash but runs forever) when I use pypet in multiprocessing mode in combination with matplotlib and savefig!?

A: Matplotlib uses numpy for linear algebra operations, these operations are often necessary when plotting. So, to solve the issues take a look at the next question.

Q: My program does not terminate (i.e. it does not crash but runs forever) when I use pypet in multiprocessing mode in combination with numpy and linalg.inv or some similar function!?

A: Numpy uses openBLAS (http://www.openblas.net/) to solve linear algebra operations. Yet, there are many issues with openBLAS and multiprocessing. To resolve this set the environment variable OPENBLAS_NUM_THREADS=1.

Q: GitPython does not work. If I specify my repository git_repository='./myrepo', pypet crashes with an AttributeError: ‘Repo’ object has no attribute ‘index’. What should I do?

A: You probably have an older version of GitPython (likely 0.1.7), install a newer one. If pip install GitPython still downloads the old version, try pip install --pre GitPython or if you simply want to upgrade use pip install --upgrade --pre GitPython.

Q: I am still using the old tree structure how can I update my hdf5files to the new one?

A: See Migrating from Old Tree-Structure to the New One

Q: If I create and environment in an IPython console everything becomes gibberish!?

A: Pypet will redirect STDOUT and STDERROR to files. Unfortunately, this messes with the IPython console. To avoid this simply disable logging of these two streams setting the log_stdout to False: env = Environment( ..., log_stdout=False, ...).