Installing MrBayes for MPI and 64-bit

Let the home page describe what it is about (in the worst possible English): "MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees."

Sourcefiles for MrBayes can be downloaded with a familiar process of extracting (tar xvf mrbayes-3.1.2.tar.gz) into an appropriate location (e.g., /usr/local/src/MRBAYES/mrbayes/3.1.2. Installing MrBayes should be just the matter of typing make but for MPI there is a number of modifications required top the Makefile and the sourcecode.

Firstly, edit the Makefile, set MPI=yes

Secondly, patch the sourcecode (patch -p 1 filename.patch) in the order listed. Download the patch files in an appropriate directory.

  1. Fix problem with SumP hanging in MPI on error: mrbayes-3.1.2-fix-sump-mpi.diff
  2. Change mcmcdiagn default to NO: mrbayes-3.1.2-fix-mcmcdiagn-disable.diff
  3. For 64-bit architecture, apply mb_64bit_safe.patch and compile with parameter _64BIT=yes. When applying this patch, use -R (the patch is in reverse format).

So, step by step:

Copy the patches into an appropriate directory

mkdir /usr/local/src/MRBAYES/patches
cd /usr/local/src/MRBAYES/patches

Add the patches

cd /usr/local/src/MRBAYES/mrbayes-3.1.2
patch -p 1 patch -R -p 1

Find the right acml library and add it the path

export LD_LIBRARY_PATH=/usr/local/acml/4.3.0/pgi64_int64/lib/:$LD_LIBRARY_PATH

Run the make

module load openmpi-gcc
OBJECT_MODE=64 make _64BIT=yes

Thanks to Vladimir Mencl (University of Canterbury) and Sam Morrison (Victorian Partnership for Advanced Computing) in the development of this document.