Thursday 4 April 2013

Why You Should Not Use WinBUGS (or OpenBUGS)

The BUGS project did a lot to bring Gibbs sampling to the masses. But by using a non-mainstream development environment, it has painted itself into a corner.

My initial objection to using BUGS was that WinBUGS only ran on Windows PCs. That meant I couldn't run it on my desktop, and I couldn't run it on the university high-end cluster. The only way I could run it on a Linux box would be to set up a Windows Virtual Machine.

Attempts to run it using Wine on my desktop would fail with odd errors - current one is "trap #101" and a traceback list, although I've also seen various memory errors once I have started it. I can't trust it to be doing anything right.

Trust was another reason I was far from keen on using WinBUGS. It was released under a closed-source license. There was no right to modify or redistribute WinBUGS. There was even a fee for a registration code that unlocked some features - although that fee is currently $0 and the unlocking key is freely available.

The last patch for WinBUGS was dated August 2007, over five years ago. The most recent update on the WinBUGS development page talks about a beta-test period ending nearly nine years ago. Because things have moved on. In 2004, OpenBUGS was born. The code was made available under the GNU GPL, a license that allows modifications and redistributions, and most of all allows - indeed insists on - access to the source code.

So let's look at the source code. The Download page on the OpenBUGS site even has a Linux Download section with a link to a 'source package'. But this turns out to be misleading - its actually a binary shared library with a short C file that links to it and calls the main routine in it. Where is the source code? It supposes to be on SourceForge, but although there appears to be code checkins, I find nothing in the SVN repo:

I'm sure this has all worked before. So what's going on now? In desperation, I emailed one of the developers. He reports they are ironing out a few wrinkles in the source code, and everything will be back to normal within a few weeks.

Even when I do have the source code, development is problematic. The code is written in Component Pascal, and can only be read with the BlackBox Component Builder from Oberon Microsystems. The files are not plain text. The Component Builder only runs on Windows. An email on the OpenBUGS mailing list in July 2012 claims that the BlackBox tools have been abandoned by their own developers, which is why there's no true 64-bit OpenBUGS.

How the Linux binary is produced is also a mystery. I can't find any clues on the OpenBUGS developer pages about how to build it. Clearly some kind of cross-compilation or embedding of Windows code is needed. But a handy guide to do it, I can not find.

Other open-source software is not as difficult as this. Most R packages install from source code with a one-line build command. Installing python packages can be as simple as 'pip install packagename'. I can configure, compile, and build a major open-source GIS in two command lines. Why has OpenBUGS got so difficult?

  • It used a very niche language and toolset. Pascal, and Component Pascal, was a minority interest back when the BUGS project started. But they got in deep pretty soon. Even though the language is perhaps richer than the C and C++ systems of its time, they've been hit by the problem outlined in "Don't be Distracted By Superior Technology" by James Hague.
  • It targeted Windows only, providing a low barrier to entry for simple users. However, by not building a cross-platform solution it alienated more technical users running Unix variants, the sort of people who form the majority of developers.
  • It failed to build a community. By not attracting developers, development was reliant on the paid staff. The current page of "Future Developments" has plenty of things that people could be getting on with, but the esoteric and restricted development environment shuts out many people.
  • It opened up too late. Now we have true open-source alternatives that can run many of the BUGS models - such as JAGS, stan, PyMC, and several specialised R packages. These packages are also easy to extend with custom distributions and models. Few people are going to put development effort into OpenBUGS now.
So what of the future? If the BlackBox Component Builder is dead, then there is a big brick wall ahead once that stops working with the current version of Windows. It is Open Source, but probably requires an elite skill set to get it working. But if that goes not only will you not be able to run your models, you won't even be able to open your model files. That's so important I'll repeat that. You will not be able to read your model files. Imagine not being able to open your old Word files. Oh wait, you probably cant.

 There's a paper in Statistics in Medicine (2009) by David Lunn et al that talks about a foundation for BUGS code, but there's no sign of this existing as of now. Plenty of other projects thrive without needing a foundation, you just have to open the code, make working with it easy, and people will come. I'm not sure if this is possible without re-implementing OpenBUGS in a mainstream language such as C++ or Python. Without doing that, OpenBUGS is a dead end.


  1. Do you think reimplementing BUGS in another language is a worthwhile endeavour?

    Is there anything BUGS can do that JAGS/Stan can't yet?

    1. Well, most of the BUGS methodology and the BUGS language for describing models is already implemented in JAGS. Do we need a 'Doodle'-like interface for constructing models? I'm not sure.

      This post was getting a bit long already without really expanding on the alternatives to BUGS section. Maybe next time...

  2. Last I checked, jags couldnt do spatial models. What's the alternative if you need car.normal and spatial.exp?

    1. Learn C++ and add it to JAGS. Or pay someone to develop it for JAGS and open-source it. Both options not available to OpenBUGS users at the moment, which was my point - its a development dead end.

      Does package:CARBayes do what you want? Or I think I've seen it done in PyMC.

    2. What I used bugs for is nesting a spatial random effect in a more complex model. CARBayes and INLA can fit log-linear models. could probably achieve the same flexibility as bugs with PyMC but it doesn't seem as easy to use...

    3. You've missed my point. Just because you can do what you did yesterday with OpenBUGS doesn't mean you'll still be able to do that tomorrow or you'll be able to do what you want to do tomorrow tomorrow if its not implemented in OpenBUGS. Development dead end.