BEAGLE
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.[1][2]
NB This BEAGLE does not seem to be the same as this Beagle by B. Browning.
Installed Versions
The version built from source code checked out on 2018-03-19 is installed on Proteus. It should run on both AMDs and Intels. (NB this is only a library, and you must use software that links to this library in order to actually run any applications with BEAGLE.)
Use this modulefile:
beagle-lib/gcc/20180319
Compiling
Getting the Source Code
The GitHub repository for the code is authoritative: https://github.com/beagle-dev/beagle-lib
However, the "released" versions are out of date. Clone the current version:
git clonehttps://github.com/beagle-dev/beagle-lib
This creates a directory named "beagle-lib" containing all the source code.
Build Platform
In order that the resulting executable(s) and libraries will work on all
systems in Proteus, this package should be built on proteusa01 (the
AMD node). Otherwise, the configuration script will pick up the Intel
CPU which has later hardware code features than the AMDs, resulting in
executables which will not run on the AMD nodes.
Pre-configure
Requires newer versions of autoconf and automake in order to run the
autogen.sh script. Load the following modules
autoconf
automake
Modify the autogen.sh script
Replace the contents of the autogen.sh script with the following, i.e.
add the "libtoolize" line:
#!/bin/sh
mkdir -p config
libtoolize
autoreconf --force --install -I config -I m4
Then, run the script:
./autogen.sh
Configure
Define the prefix to be your preferred location for installation. See the article on Installing Software for Your Research Group
./configure --prefix=/mnt/HA/wherever --enable-openmp --enable-sse --enable-avx > Configure.out 2>&1 &
Build and Install
Do:
make
make install
The installation will create two directories containing beagle-lib:
${PREFIX}/include
${PREFIX}/lib
You will have to modify the CPPFLAGS and LDFLAGS for any dependent software to point it to the include and lib directories above. The best way to this is by writing your own modulefile.[3] You can also set them in ~/.bash_profile or set them ad hoc at the command line.
References
[1] beagle-lib repository on GitHub
[2] Daniel L. Ayres, et al. BEAGLE: An Application Programming Interface
and High-Performance Computing Library for Statistical Phylogenetics,
Systematic Biology, Volume 61, Issue 1, 1 January 2012, Pages 170–173
[3] Environment Modules Quick Start Guide#Creating_Your_Own_Module_Files