INSTALL

MrBayes 3.2.7a

This document describes how to install the most recent release of
MrBayes using Homebrew on macOS, Linux, or on Window subsystem for
Linux (WSL).  It also describes how to build the development sources of
MrBayes from the GitHub repository sources.


========================================================================
Installing MrBayes on macOS using Homebrew
------------------------------------------------------------------------

MrBayes is available for macOS through the Homebrew package manager.
See https://brew.sh/ for general information about Homebrew and for
Homebrew installation instructions.

On a macOS system with Homebrew, MrBayes may be installed through the
following two commands in a terminal:

    brew tap brewsci/bio
    brew install mrbayes

The first command adds the "brewsci/bio" repository to your Homebrew
system. This is a Homebrew repository that contains various software
related to bioinformatics. Once the repository is available, you install
MrBayes with the second command above.

This will install MrBayes with support for the Beagle library.  If you
need additional MPI support, use

    brew install mrbayes --with-open-mpi

This will likely download the neccesary Homebrew packages for building
MrBayes with MPI support and then proceed to automatically build and
install it on your macOS system (this may take a bit of time).


========================================================================
Installing MrBayes on Linux or WSL using Homebrew ("Linuxbrew")
------------------------------------------------------------------------

The instructions for installing MrBayes on Linux systems are identical
to those for installing MrBayes on macOS.  It relies on Homebrow
being available on the Linux system where it's being installed.
Installing Homebrew on Linux is a matter of following the instructions
at https://docs.brew.sh/Homebrew-on-Linux

We have found that the pre-compiled binaries may not work on all systems
and that you may get an "Illegal instruction (core dumped)" error when
you try starting MrBayes.  In that case, install the MrBayes package
from sources instead.  This can still be done through Homebrew like
this:

    brew reinstall -s mrbayes

Likewise, you may possibly want to compile the Beagle library locally,

    brew reinstall -s beagle


========================================================================
Installing MrBayes from the GitHub sources on Unix
------------------------------------------------------------------------

Make a shallow clone of the MrBayes repository:

    git clone --depth=1 https://github.com/NBISweden/MrBayes.git

(a shallow clone requires about 27 MB of disk space, a full clone
requires about 77 MB)


Building MrBayes using the supplied "configure" script:
------------------------------------------------------------------------

To build MrBayes, you will need a C compiler (gcc or clang works well),
the "make" utility, and optionally the "pkg-config" utility.  MrBayes
may also be compiled with support for the Beagle library and for
parallelization using MPI.

The code in the MrBayes Git repository comes with a standard GNU
"configure" script.  On any Unix system, these are the steps required to
compile and optionally install MrBayes:

* Run "configure" in the top-level directory to create "Makefile" (see
  "./configure --help" for info about enabling and disabling features of
  MrBayes, or how to install in non-standard locations etc., and also
  read further down in this document):

    ./configure

* Make (i.e. compile) the project:

    make

  Note that if "pdflatex" or "bibtex" could not be found by the
  "configure" script, the PDF documentation in doc/manual will not
  be rebuilt, even if the PDF documents are outdated or missing.

* Install it on the system (optional).  This will install
  the executable "mb" in /usr/local/bin, the documentation
  in /usr/local/share/doc/mrbayes, and the example files in
  /usr/local/share/examples/mrbayes unless the default installation
  prefix ("/usr/local") is changed with the "--prefix" option when
  running "configure".

    make install

* We also support configuring and building the project away from the
  checked out source repository.  This avoids littering the source
  repository checkout with temporary files.  This is done through the
  following steps:

  1. Create and enter a build directory somewhere (its name and location
     is arbitrary)

        mkdir build
        cd build

  2. Call the "configure" script

        location-of-MrBayes-checkout/configure

  3. Build and optionally install the project

        make
        make install


Building MrBayes using the GNU autotools (Autoconf and Automake):
------------------------------------------------------------------------

MrBayes uses the GNU autotools, i.e. Automake and Autoconf, for its
configuration and build system.  If you tinker with "configure.ac"
and/or any of the "Makefile.am" files and then want to regenerate the
"configure" script and associated files, there are some prerequisites
that need to be in place:

* Make sure Automake 1.15 (http://www.gnu.org/software/automake/)
  is installed.

* Make sure Autoconf 2.69 (http://www.gnu.org/software/autoconf/)
  is installed.

The "configure.ac" script uses the "pkg-config" tool for detection
of external libraries (Beagle) and also uses m4 macros from the
autoconf-archive collection for detection of MPI, Readline, and some
architecture-dependent compiler flags.  Therefore,

* Make sure pkg-config (https://www.freedesktop.org/wiki/Software/pkg-config/)
  is installed.

* Make sure autoconf-archive 2016.03.20 (or later)
  (http://www.gnu.org/software/autoconf-archive/) is installed.

* On some systems that uses metaauto for wrapping multiple versions of
  the GNU autotools (OpenBSD for example):

    export AUTOCONF_VERSION=2.69
    export AUTOMAKE_VERSION=1.15

* On Ubuntu Linux, installing the following packages installs all of the
  above prerequisites:

    1. automake
    2. autoconf
    3. pkg-config
    4. autoconf-archive

  These may be installed through

    sudo apt install automake autoconf pkg-config autoconf-archive

When all the prerequisites are in place:

* Run "autoreconf" to generate the "configure" script:

    autoreconf -i

* Then continue as outlined earlier in this document.


Disabling the SSE, AVX and FMA code paths
------------------------------------------------------------------------

MrBayes will use SSE, AVX and FMA instructions to speed up computations
on CPUs that support these instruction sets, if the compiler supports
it.  These code paths are however optional, and if you suspect a bug in
part of this code, you may use "--disable-sse", "--disable-avx" and/or
"--disable-fma" to disable it when running the "configure" script.

Note however, that disabling SSE will also disable AVX and FMA, and
disabling AVX will also disable FMA.

Note also that disabling these accelerated code paths will not remove
the "-msse" (etc.) compiler flags.  These compiler flags affects what
instructions the compiler is allowed to generate, not what code path is
chosen for compilation.


Picking up the Beagle library:
------------------------------------------------------------------------

MrBayes uses the Beagle library
(https://github.com/beagle-dev/beagle-lib) if it is available.  It will
make use of release 3.1.2 of Beagle but should also work with release
2.1.3 of the library.

Assuming Beagle was compiled and installed in a standard location, it
will be picked up by the "configure" script automatically.  If it isn't
found, or the "configure" script is run with "--without-beagle", Beagle
will not be used.

If Beagle is installed in a non-default location, there are three ways
of telling the "configure" script how to find it:

* Use the flag "--with-beagle=PATH" where "PATH" is the prefix path
  where the Beagle headers and libraries may be found.  For example
  "$HOME/local", "/opt" etc.  The paths "/usr/local" and "/usr" are
  tested if no path is specified.

* Point the "PKG_CONFIG_PATH" environment variable to the "pkgconfig"
  directory that Beagle installed its "hmsbeagle-1.pc" file into.  This
  file is installed if Beagle was compiled from sources, and may be
  found in the installation's "lib" directory.  The detection of Beagle
  will fall back on using "pkg-config" which picks up this file.

* As a last resort, it's also possible to set the "BEAGLE_CFLAGS" and
  "BEAGLE_LIBS" environment variables prior to running "configure" (the
  example shows how to use these variables when Beagle was installed
  under the path "$HOME/local"):

    env BEAGLE_CFLAGS="-I$HOME/local/include/hmsbeagle-1" \
        BEAGLE_LIBS="-L$HOME/local/lib -Wl,-rpath=$HOME/local/lib -lhmsbeagle" \
        ./configure


Building the Beagle library for MrBayes
------------------------------------------------------------------------

Ideally, you would use a pre-built distribution of the Beagle library,
as setting up the required prerequisites for things like OpenCL etc. is
a bit cumbersome to say the least.

If you none the less want to try building and installing it, this is the
executive summary for how to do this on a Unix system, not including
installation of prerequisites (since these will differ between systems).
It's assumed that the Beagle library is being installed in the default
location, under "/usr/local". Note that the Beagle Java library is not
needed by MrBayes.

    git clone --branch=v3.1.2 --depth=1 \
	'https://github.com/beagle-dev/beagle-lib.git'
    cd beagle-lib

    ./autogen.sh
    ./configure --without-jdk LDFLAGS=-Wl,-rpath=/usr/local/lib

    make
    sudo make install

See also the "INSTALL" document supplied with the Beagle library's
source distribution.


Picking up and using MPI:
------------------------------------------------------------------------

The "configure" script will find any available MPI C compiler or
compiler wrapper and use it (for example the one provided by OpenMPI
(https://www.open-mpi.org/) or MPICH (https://www.mpich.org/)) if
the "--with-mpi" flag is used.  If this flag is not used, or if
"--without-mpi" is used, MrBayes will be compiled without support for
MPI parallelization.

You may set the "MPICC" environment variable to the name or path of a
specific MPI C compiler, if you have many to choose from:

        env MPICC="/usr/local/bin/mpicc" ./configure --with-mpi


About support for the GNU Readline library:
------------------------------------------------------------------------

MrBayes will be compiled with support for the GNU Readline Library
(https://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) (which allows
for command line history within an interactive session, and command
completion through pressing the "tab" key) if the Readline library
and its associated header files are available.  However, it seems as
if the Readline library doesn't work well together with common MPI
implementations, such as OpenMPI (https://www.open-mpi.org/) and MPICH
(https://www.mpich.org/), so if MrBayes is configured with support for
MPI parallelization, Readline support will be automatically disabled.

A possible workaround is to use a "Readline wrapper", such as "rlwrap"
(https://github.com/hanslub42/rlwrap), which gives you persistent
command line history between sessions, but no command tab-completion.
To use rlwrap with an MPI-enabled MrBayes, simply start MrBayes like
this:

        rlwrap mb


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