Source: http://mrbayes.sourceforge.net/download.php http://mrbayes.sourceforge.net/wiki/index.php/Advanced_Topics_3.2

Usage

Any one the following module files:

 module load bioinformatics/mrbayes/3.2.1-openmpi-cuda-gnu
OR
 module load bioinformatics/mrbayes/3.2.1-openmpi-gnu
OR
 module load bioinformatics/mrbayes/3.2.1-serial-gnu
OR
 module load bioinformatics/mrbayes/3.2.1-serial-intel

Installation

mkdir -p /sw/mrbayes/3.2.1/install

mkdir -p /sw/mrbayes/3.2.1/mpi-intel
mkdir -p /sw/mrbayes/3.2.1/mpi-intel-cuda
mkdir -p /sw/mrbayes/3.2.1/openmpi
mkdir -p /sw/mrbayes/3.2.1/serial
mkdir -p /sw/mrbayes/3.2.1/serial-intel
mkdir -p /sw/mrbayes/3.2.1/serial-cuda


cd /sw/mrbayes/3.2.1/install

tar -zxvf mrbayes-3.2.1.tar.gz
cd /sw/mrbayes/3.2.1/install/mrbayes_3.2.1

beagle-lib

MrBayes 3.2 uses the BEAGLE library by default. You should either install the
BEAGLE library from http://code.google.com/p/beagle-lib/ or disable use of the
library by invoking the configure script with option "--with-beagle=no". i.e.

Ref: http://code.google.com/p/beagle-lib/wiki/LinuxInstallInstructions

mkdir -p /sw/library/beagle
svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib

>>>>>>>>>>>>>>>>>>>>
A    beagle-lib/m4
A    beagle-lib/m4/acx_pthread.m4
....
 U   beagle-lib
Checked out revision 1082.
>>>>>>>>>>>>>>>>>>>>

cd /sw/library/beagle/beagle-lib
./autogen.sh  2>&1 |tee autogen_beagle-nocuda.txt

>>>>>>>>>>>>>>>>>>
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `.config'.
libtoolize: copying file `.config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: copying file `m4/libtool.m4'
libtoolize: copying file `m4/ltoptions.m4'
libtoolize: copying file `m4/ltsugar.m4'
libtoolize: copying file `m4/ltversion.m4'
libtoolize: copying file `m4/lt~obsolete.m4'
configure.ac:64: installing `.config/config.guess'
configure.ac:64: installing `.config/config.sub'
configure.ac:56: installing `.config/install-sh'
configure.ac:56: installing `.config/missing'
examples/complextest/Makefile.am: installing `.config/depcomp'
Makefile.am: installing `./INSTALL'

>>>>>>>>>>>>>>>>

beagle-lib without cuda

cd /sw/library/beagle/beagle-lib
module purge
make clean all

./configure --prefix=/sw/library/beagle/beagle-nocuda  2>&1 |tee configure_beagle-nocuda.txt
 
make install 2>&1 |tee make_beagle-nocuda.txt

beagle-lib with cuda

ssh n021
cd /sw/library/beagle/beagle-lib
module purge
module load cuda/4.0
./configure --prefix=/sw/library/beagle/beagle-cuda  --with-cuda=/usr/local/cuda  2>&1 |tee configure_Cuda.txt
make install 2>&1 |tee make_beagle-cuda.txt

MrBayes - Serial build

Serial compiled with icc (Intel Compiler)

ssh n021
cd /sw/mrbayes/3.2.1/serial-intel
module purge
module load library/beagle/beagle-lib-nocuda
cd /sw/mrbayes/3.2.1/install/mrbayes_3.2.1/src
module load intel-cc-11/11.1.072
export CC=icc
#DID not work#export CFLAGS="$CFLAGS -fast -w0 -I/sw/library/beagle/beagle-nocuda/lib/include"
#DID not work#export LDFLAGS="$LDFLAGS -L/sw/library/beagle/beagle-nocuda/lib"
make clean all
autoconf
./configure  --prefix=/sw/mrbayes/3.2.1/serial-intel  --with-beagle=/sw/library/beagle/beagle-nocuda 2>&1 |tee configure_serial_intel_noCuda.txt
make 2>&1 |tee make_serial_intel_noCuda.txt

The compilation will produce an executable in the source directory with the name
"mb". To start the program, simply type

cd ../
cp -rp src/ /sw/mrbayes/3.2.1/serial-intel 
cd /sw/mrbayes/3.2.1/serial-intel
./mb

Serial compiled with gcc (gnu compiler)

cd /sw/mrbayes/3.2.1/serial-gnu
module purge
module load library/beagle/beagle-lib-nocuda
cd /sw/mrbayes/3.2.1/install/mrbayes_3.2.1/src

make clean all
autoconf
./configure  --prefix=/sw/mrbayes/3.2.1/serial-gnu  --with-beagle=/sw/library/beagle/beagle-nocuda 2>&1 |tee configure_serial_gnu_noCuda.txt
make 2>&1 |tee make_serial_gnu_noCuda.txt
The compilation will produce an executable in the source directory with the name
"mb". To start the program, simply type
cp mb /sw/mrbayes/3.2.1/serial-gnu

./mb

MrBayes - mpi build

MrBayes-mpi compiled with intelmpi

ssh n021

MrBayes-mpi compiled with openmpi and gnu compilers

ssh n021

module purge
module load mpi/openMPI/1.4.3-gnu
module load library/beagle/beagle-lib-nocuda
cd /sw/mrbayes/3.2.1/install/mrbayes_3.2.1/src
export CC=mpicc
make clean all
rm -f *.o *~ mb
autoconf
./configure  --prefix=/sw/mrbayes/3.2.1/openmpi-gnu  --with-beagle=/sw/library/beagle/beagle-nocuda  --enable-mpi=yes 2>&1 |tee configure_openmpi_gnu_noCuda.txt
make 2>&1 |tee make_openmpi_gnu_noCuda.txt
The compilation will produce an executable in the source directory with the name
"mb". To start the program, simply type
cp mb /sw/mrbayes/3.2.1/openmpi-gnu
cd ../
cp -rp src /sw/mrbayes/3.2.1/openmpi-gnu
cd /sw/mrbayes/3.2.1/openmpi-gnu
./mb

MrBayes-mpi compiled with openmpi and cuda support

ssh n021
module purge
 module load cuda/4.0
 module load mpi/openMPI/1.4.3-gnu
module load library/beagle/beagle-lib-cuda
cd /sw/mrbayes/3.2.1/install/mrbayes_3.2.1/src
export CC=mpicc
make clean all
rm -f *.o *~ mb
autoconf
./configure  --prefix=/sw/mrbayes/3.2.1/openmpi-gnu-cuda  --with-beagle=/sw/library/beagle/beagle-cuda  --enable-mpi=yes 2>&1 |tee configure_openmpi_gnu_Cuda.txt
make 2>&1 |tee make_openmpil_gnu_Cuda.txt
The compilation will produce an executable in the source directory with the name
"mb". To start the program, simply type
cp mb /sw/mrbayes/3.2.1/openmpi-gnu-cuda
cd ../
cp -rp src /sw/mrbayes/3.2.1/openmpi-gnu-cuda
cd /sw/mrbayes/3.2.1/openmpi-gnu
./mb