PyBaMM: Mac OS Sundials bug

Descirbe the bug scikits.odes does not work (“image not found”) when following installation instructions

Explanation As I understand it the problem is that scikits.odes looks for libsundials_sunlinsolklu.3.dylib, but brew install sundials installs a more recent version, which only has

libsundials_sunlinsolklu.dylib
libsundials_sunlinsollapackband.3.5.0.dylib

so libsundials_sunlinsolklu.3.dylib cannot be found.

This is not caught by the Mac OS tests since in CI the Mac OS tests use the script install_KLU_Sundials.py

Furthermore, if installing locally, with tox -e pybamm-requires, the script is used (which installs the correct version of sundials) but only LD_LIBRARY_PATH is updated, and not DYLD_LIBRARY_PATH as should be the case for mac. This means that scikits.odes is still looking in /usr/local/opt/ for sundials, where it finds the incorrect brew installation, instead of in ~/.local/lib

** Solution **

Remove the requirement for brew install sundials from docs
Use the KLU script to install sundials on mac, and also update DYLD_LIBRARY_PATH

This could also be an opportunity to clean up the install docs, which I still find a little bit confusing

About this issue

Original URL
State: closed
Created 4 years ago
Comments: 15 (9 by maintainers)

Most upvoted comments

Hi @shday and @tinosulzer, I sense there is a bit of confusion here, which I hope I can clear.

Short answer

If you’re on MacOS, you must install the sundials library yourself. There are several ways to do that, but the most straightforward is to use Homebrew, following the instructions available here. I suggest you give it a try and tell us the result.

Longer answer:

Whenever you type pip install pybamm, pip fetches the PyBaMM package from the Python Package Index (PyPI). However, pip does not download all python files one by one, but rather an archive that contains the PyBaMM’s source code, some metadata and compiled modules, like the idaklu module. Indeed, if you look into PyBaMM’s sources, you’ll find that the idaklu module is actually written in C++, and must therefore be compiled before being available for import. As a user, you don’t have to do that yourself though because the module was compiled by us before hand, and the resulting idaklu.cpython-38-darwin.so file is included in the archive pip downloads and installs. However, the idaklu module has a runtime dependency on the sundials library, that must be available (in the form of a shared library) on your system when you import the module. For GNU/Linux systems, the compiled version of sundials is also included in the archive pip downloads, therefore a pip install pybamm is all that is required to get everything running. On Mac however, the compiled sundials is not included in that archive, and therefore users must install sundials themselves. Thanks to Homebrew, that’s just another short command.

Now, you could also choose to clone the PyBaMM repo and install pybamm from that instead of the archive available on PyPI. This would be a good choice if you wanted to e.g. modify/contribute to PyBaMM. In this case however, you don’t benefit from the pre-compiled modules and dependencies, and you’ll have to do it yourself. As you’ve noticed already, the PyBaMM repo contains a python script that automatically downloads, compile and install the sundials library (install_KLU_Sundials.py). The idaklu module is automatically compiled when you invoke pip on the PyBaMM repo. The compilation and installation of PyBaMM from the repo is described here.

I hope that’s helpful - both in practice as well as to help understand the different moving parts. Please let us know if youŕe confused by the installations instructions: we’re about to refine them to hopefully make them clearer, and any feedback is useful.

tlestang on Jan 4, 2021