Tag Archives: evolution

MrBayes and multicore processors

Turns out setting up and using MrBayes on an Ubuntu system is much easier than I had thought. If all you want is the normal (serial) version of MrBayes, you can just download it from the repositories. However, if you want a serious speed up in the time it takes to get a good result, you can also run it in parallel on a multicore system (that is, pretty much any computer made in the last 4 years). To get it set up and running on Linux, I used some information I found in a forum post. To recap from there:

  1. Install the parallel libraries you need from the repositories. The package names I used were: mpich2, libmpich2-dev, and libmpich2-1.2, and libreadline6-dev.
  2. Download the source code file for MrBayes and unarchive it (on Ubuntu you can just right-click and select ‘Extract Here’
  3. Find the ‘Makefile’ in the source code and change the line that says ‘MPI ?= no’ so that it says ‘MPI = yes’
  4. Open a terminal, and navigate to the MrBayes folder (e.g. type in ‘cd /path/to/folder/mrbayes-3.1.2/’) and then make the package (type ‘Make’ at the prompt).  It might also be a good idea to change the file called ‘mb’ that is created to something like ‘mbpar’ so that you know it’s the parallel version. Also, I needed to make the file executable, so I typed ‘chmod +x mbpar’  to do that.
  5. Now, you’ll need to create a file in your home folder called ‘.mpd.conf’ with the line MPD_SECRETWORD=<secretword> in it. Change the <secretword> to something else though; it can be pretty much any word you like.
  6. ‘mpd &’ will launch the MPICH daemon, which needs to be running in order to handle communicating between the different cores.
  7. After all this, I was able to type ‘mpirun -np 2 /path/to/mrbayes/mbpar’ to run the parallel version of MrBayes in parallel on both cores of my dual core system. If you have more cores, you can always change the -np argument (e.g. to run it using 4 cores, type ‘mpirun -np 4 /path/to/mrbayes/mbpar’)

With the few tests I’ve done so far, I’ve seen about a 80% speed up by just using 2 cores instead of 1. It’s nice not to have to wait nearly so long to get my results. We’ll see what kind of time savings this could bring if I did it on an 8-core computer.

Evolution Essentials

A great summary on Ars Technica about 5 essential things that most people don’t understand about evolution. It’s a good read even if you do think you know a lot about evolution, as it emphasizes some points that I think are often muddled in a lot of scientific discussions (subobtimal solutions being better than no solution, for example).

Patented Phylogenetics

Ars Technica has a story about how Microsoft tried to patent clustering phylogenetic methods. If the patent would have gone through, it could have meant that anyone who wanted to use a phylogenetics clustering program (PAUP, Mesquite, etc) would have suddenly found themselves unable to do so, at least not without paying Microsoft first the associated fees for licensing their patent (or else by pirating the software, which seems to be a common theme in cash strapped labs). Luckily, there is plenty of prior art (meaning, Microsoft was obviously not the first person to do it), so they won’t be granted the patent in the end. Something like this makes an (arguably) good case for scientists to release any code and programs they produce under an Open Source license, which in effect would preserve their work in the public domain for future scientists to use.

Creationism 2.0

If you happen to take William Dembski’s course on ‘Intellient Design’ at Southwestern Baptist Theological Seminary, you will be pleased to know that you can get an easy 20% of your mark from simply posting replies defending creationism ‘Intelligent Design’  on ‘hostile’ websites (presumably, that means ANY scientific website). Richard Dawkins (who is very intelligent while simultaneously arrogant,  or at least so he seemed from the talk I saw) mentions this as well as plucking out some other gems from the course, such as a question from the Christian Faith and Science module which reads:

Trace the connections between Darwinian evolution, eugenics, abortion, infanticide, and euthanasia. Why are materialists so ready to embrace these as a package deal? What view of humanity and reality is required to resist them?

Remember kids: don’t evolve.