Compiling IQ-tree

Author:Brant C. Faircloth Copyright:This documentation is available under a Creative Commons (CC-BY) license.

Steps

1. Download the source archive for IQ-Tree:

   cd /project/brant/shared/src
   wget https://github.com/Cibiv/IQ-TREE/archive/v1.6.10.tar.gz -O iq-tree-v1.6.10.tar.gz
   unzip iq-tree-v1.6.10.tar.gz
   # this makes IQ-TREE-1.6.10 in src
   

1. Before compiling IQ-Tree, you also need to download and compile/install Eigen3 . That’s not particularly complex, except that I’ve found you really do need to use cmake to “install” Eigen3 to an include directory. What follows are the steps to do that:

   # put Eigen3 source into a tmp dir
   mkdir /project/brant/shared/tmp && cd /project/brant/shared/tmp
   
   # download Eigen3 source & unzip
   http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz -O eigen-v3.3.7.tar.gz
   tar -xzvf eigen-v3.3.7.tar.gz
   
   # build
   cd eigen-eigen-323c052e1731/
   mkdir build && cd build
   cmake .. -DCMAKE_INSTALL_PREFIX=/project/brant/shared/
   make install
   
   # this will install Eigen3 to /project/brant/shared/include/eigen3/
   

Difference Levels of Parallelism

IQ-Tree, like RAxML, can use different levels of parallelism. To achieve all the options, we need to compile each version. There are essentially 3 choices: MPI, OMP, MPI-OMP Hybrid

OMP (only) Version

1. Ensure that the correct modules are loaded for compilation of the source:

   module load gcc/6.4.0
   module load cmake
   

2. Set the correct CC and CXX variables so that they catch the correct Intel Compiler versions after loading the modules. Here, we’re using GCC because there is currently an error using ICC on @supermike (probably because C++ library for ICC is old).

   export CC=`which gcc`
   export CXX=`which g++`
   

3. Now, use cmake to create the makefiles and compile with make:

   cd /project/brant/shared/src/IQ-TREE-1.6.10
   mkdir build2 && cd build2
   cmake -DEIGEN3_INCLUDE_DIR=/project/brant/shared/include/eigen3 -DIQTREE_FLAGS=omp ..
   make
   

MPI (only) Version

1. Ensure that the correct modules are loaded for compilation of the source:

   module load intel
   module load impi/2018.0.128
   module load cmake
   

2. Set the correct CC and CXX variables so that they catch the correct IMPI versions after loading the modules:

   export CC=`which mpicc`
   export CXX=`which mpicxx`
   

3. Now, use cmake to create the makefiles and compile with make:

   cd /project/brant/shared/src/IQ-TREE-1.6.10
   mkdir build && cd build
   cmake -DEIGEN3_INCLUDE_DIR=/project/brant/shared/include/eigen3 -DIQTREE_FLAGS=mpi ..
   make
   

MPI & OMP Hybrid Version

1. Ensure that the correct modules are loaded for compilation of the source:

   module load intel
   module load impi/2018.0.128
   module load cmake
   

2. Set the correct CC and CXX variables so that they catch the correct IMPI versions after loading the modules:

   export CC=`which mpicc`
   export CXX=`which mpicxx`
   

3. Now, use cmake to create the makefiles and compile with make:

   cd /project/brant/shared/src/IQ-TREE-1.6.10
   mkdir build3 && cd build3
   cmake -DEIGEN3_INCLUDE_DIR=/project/brant/shared/include/eigen3 -DIQTREE_FLAGS=omp-mpi ..
   make