How to download and compile the most recent version of MrBayes 3.2 (Mac and Unix) from the MrBayes svn repository on SourceForge
1. If a Mac, open Terminal (located in Applications/Utilities). Then check that you have gcc installed by typing
$ which gcc
This should result in the directory location of your current copy of gcc, if you have one installed. If not, install one from the Developer Tools CD that came with your computer. Most Unix systems will already have gcc installed.
2. Type (on one line):
svn co mrbayes./svnroot/mrbayes/trunk/src mrbayes
You should now get a number of files downloaded to your directory, in a folder named ”mrbayes”.
3. Change to the mrbayes directory by typing:
$ cd mrbayes
4. Create the Makefile, which contains the instructions for the compiler (the ”make” command), by typing:
$ ./configure
5. Now compile the program by typing:
$ make
It will take a few minutes for the compiler to asmble the binary version of the program.
6. Run the program by typing:
$ ./mb
You may want to put the executable in your path. Consult a Unix savvy person on how to do this.
Compiling and running the MPI version of MrBayes
1. Download the source code and shift to the ”mrbayes” directory as described above.
2. In step 4, u the following command to create the Makefile instead:
$ ./configure --enable-mpi=yes
3. Now compile the program by typing
$ make
It will take a few minutes for the compiler to asmble the binary version of the program. If the first entry on each line printed during the compilation step is ”mpicc”, you are compiling the parallel version. If it is ”gcc”, something went wrong during the configure step and you are compiling the rial version instead.
If you have already compiled the rial version of the program in the same directory, you first need to remove the compiled objects by running
$ make clean
Then you run the ”make” command as above. Note that the compiled program is going to be called ”mb” both for the rial and the parallel version, so the compilation of the parallel version will overwrite the rial version unless you rename or move the latter executable first.
4. Run the parallel version of the program using the command
$ mpirun -np 2 ./mb
where 2 is the number of available processors or processor cores. The MrBayes header should say that you are running the parallel version and it should also give the number of processors (cores) available.
5. In practical u, it is often convenient to run the MPI version of MrBayes in batch mode. For instance, you can prepare a Nexus batch file ””, which contains a MrBayes block. To u such a file and have the screen output written to the log file
””, u the command:
$ mpirun -np 2 ./ > &
You can now look into the end of the log file every now and then to e what the run is doing currently using
$
If you wish to continuously follow what is being printed to the log file, you can u
$ tail -
There are many other ways of running the MPI version of MrBayes. Clusters often come with special instructions on how to run mpi programs; they typically involve launching the MrBayes MPI runs through an appropriate script. Consult your supercomputer support for instructions.
