NOTE: These instructions are for compiling the development branch.
You can also compile with meson instead of cmake.
You will need to have C++ compiler installed on your computer. GCC 6 (or higher) and Apple Clang from XCode 11 (or higher) should work. If you don’t have a C++ compiler, you should install Xcode.
You will also need to have CMake (3.5.1 or higher) and Boost (1.74 or higher) installed
The typical way to install boost and cmake is to use the homebrew package manager.
If homebrew is not already installed, you can install it with:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
You can then use homebrew to install cmake and boost:
brew install cmake boost
First you will need to install cmake
Then you can compile boost:
curl -O -L https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.gz
tar -xzvf boost_1_74_0.tar.gz
cd boost_1_74_0
./bootstrap.sh --with-libraries=atomic,chrono,filesystem,system,regex,thread,date_time,program_options,math,serialization --prefix=../installed-boost-1.74.0
./b2 link=static install
echo -e "\n BOOST root is at $(cd ../installed-boost-1.74.0; pwd)\n"
This creates a new directory called installed-boost-1.74.0 that contains the boost installation.
This directory is called the BOOST “root”.
You will need the path to the BOOST root for the next step.
To set up an IDE such as XCode, the following directory should be added to compiler include paths:
/path/to/installed-boost-1.74.0/include
The following directory should be added to linker library paths:
/path/to/installed-boost-1.74.0/lib
Download RevBayes from our github repository. Clone the repository using git by running the following command in the terminal
git clone --branch development https://github.com/revbayes/revbayes.git revbayes
To compile with the system Boost library:
cd revbayes/projects/cmake
./build.sh
You will likely see some compiler warnings (e.g. clang: warning: optimization flag '-finline-functions' is not supported). This is normal.
To compile revbayes using a locally compiled boost, do the following. Be sure to replace the paths in the build command with those you got from boost in the previous step.
./build.sh -boost_root /path/to/installed-boost-1.74.0
For the MPI version:
./build.sh -mpi true
This produces an executable called rb-mpi.
Note that compiling the MPI version requires that an MPI library is installed.
rb: command not found
The problem is that you tried to run RevBayes but your computer doesn’t know where the executable is. The easiest way is to add the directory in which you compiled RevBayes to your system path:
export PATH=<your_revbayes_directory>/projects/cmake:$PATH
Error cmake not found!
Please double check that CMake is installed. For OS X, go to step 2 above.
Error can't find the libboost_filesystem.dylib library or Library not loaded: libboost_filesystem.dylib
You need to add the boost libraries to your path variable. You may find that you have to export this DYLD_LIBRARY_PATH every time you open a new terminal window. To get around this, you can add this to your .bash_profile or .bashrc file (which lives in your home directory). To change this, open a new terminal window and you should be in the home directory. If you do not have either of these files, use the text editor nano to create this file type:
cd ~
touch .bash_profile
nano .bash_profile
Then add the following lines, replacing /root with wherever you put the boost libraries:
export DYLD_LIBRARY_PATH=/root/boost_1_74_0/stage/lib:$DYLD_LIBRARY_PATH
Then save the file using ctrl^o and hit return, then exit using ctrl^x. Now quit the Terminal app and reopen it and the boost libraries will forever be in your path.