Compilation guide

MPBoot

Downloading source code

You can clone the source code from GitHub with:

git clone https://github.com/diepthihoang/mpboot.git

Compiling under Linux

1. Create folder build outside folder mpboot.
2. Open Terminal.
3. Change directory to build
4. Configure source code with CMake:
   cmake ../mpboot -DIQTREE_FLAGS=avx -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++

Replace avx by sse4 in above command if you decide to run MPBoot on SSE architecture

5. Run command make -j4 to compile source code with 4 processes:

Option j specifies the number of processes used to compile source code with make.

The compiler will generate an executable file named mpboot-avx

In case of running MPBoot on SSE architecture, the executable file is named mpboot.

6. To analyst file example.phy, run command:
   ./mpboot-avx -s example.phy

Compiling under Mac OS X

1. Create folder build outside folder mpboot.
2. Open a Terminal.
3. Change directory to build
4. Configure source code with CMake:
   cmake ../mpboot -DIQTREE_FLAGS=avx

Replace avx by sse4 in above command if you decide to run MPBoot on SSE architecture

5. Run command make -j4 to compile source code with 4 processes:

Option j specifies the number of processes used to compile source code with make.

The compiler will generate an executable file named mpboot-avx

In case of running MPBoot on SSE architecture, the executable file is named mpboot.

6. To analyst file example.phy, run command:
   ./mpboot-avx -s example.phy

Compiling under Windows

• Requirements:
  • cmake version >= 3.21
  • TDM-GCC

1. Create folder build outside folder mpboot.
2. Open a Terminal.
3. Change directory to build
4. Configure source code with CMake:
   cmake -G "MinGW Makefiles" -DIQTREE_FLAGS=avx ../mpboot

Replace avx by sse4 in above command if you decide to run MPBoot on SSE architecture.
Due to having conflicts with Vectorization, please not using Clang to configure source code.

5. Run command mingw32-make -j4 to compile source code with 4 processes:

Option j specifies the number of processes used to compile source code with make.

The compiler will generate two executable files named mpboot-avx and mpboot-avx-click

In case of running MPBoot on SSE architecture, the executable files are named mpboot and mpboot-click.

6. To analyst file example.phy:

• Run command ./mpboot-avx -s example.phy
• Or:
  1. Open mpboot-click by double click on it
  2. Press y to start enter command
  3. Type -s and press Enter
  4. Press e to continue entering command
  5. Type example.phy and press Enter
  6. Press y to finish command

MPBoot-MPI

Downloading source code

You can clone the source code from GitHub with:

git clone https://github.com/diepthihoang/mpboot.git
Switch to branch which contains MPBoot-MPI source code:

• git checkout mpboot-mpi-sync for synchronous version
• git checkout mpboot-mpi-async for asynchronous version

Compiling under Linux

1. Create folder build outside folder mpboot.
2. Open a Terminal.
3. Change directory to build
4. Configure source code with CMake:
   cmake ../source -DIQTREE_FLAGS=avx -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx

Replace avx by sse4 in above command if you decide to run MPBoot on SSE architecture

5. Run command make -j4 to compile source code with 4 processes:

Option j specifies the number of processes used to compile source code with make.

The compiler will generate an executable file named mpboot-avx

In case of running MPBoot on SSE architecture, the executable file is named mpboot.

6. To analyst file example.phy with 2 processes, run command:
   mpirun -np 2 ./mpboot-avx -s example.phy

Option np specifies the number of processes used to run MPBoot-MPI

Compiling under Mac OS X

1. Create folder build outside folder mpboot.
2. Open a Terminal.
3. Change directory to build
4. Configure source code with CMake:
   cmake ../mpboot -DIQTREE_FLAGS=avx -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx

Replace avx by sse4 in above command if you decide to run MPBoot on SSE architecture

5. Run command make -j4 to compile source code with 4 processes. Option j specifies the number of processes used to compile source code with make.

The compiler will generate an executable file named mpboot-avx

In case of running MPBoot on SSE architecture, the executable file is named mpboot.

6. To analyst file example.phy with 2 processes, run command:
   mpirun -np 2 ./mpboot-avx -s example.phy

Option np specifies the number of processes used to run MPBoot-MPI

Compiling under Windows

• Requirements:
  • cmake version >= 3.21
  • TDM-GCC
  • MSMPI

1. Create folder build outside folder mpboot.
2. Open a Terminal.
3. Change directory to build
4. Configure source code with CMake:
   cmake -G "MinGW Makefiles" -DIQTREE_FLAGS=mpiavx ../mpboot

Replace mpiavx by mpisse4 in above command if you decide to run MPBoot on SSE architecture.
Due to having conflicts with Vectorization, please not using Clang to configure source code.

5. Run command mingw32-make -j4 to compile source code with 4 processes:

Option j specifies the number of processes used to compile source code with make.

The compiler will generate an executable file named mpboot-avx

In case of running MPBoot on SSE architecture, the executable file is named mpboot.

6. To analyst file example.phy with 2 processes, run command:
   mpiexec -n 2 ./mpboot-avx -s example.phy

Option n specifies the number of processes used to run MPBoot-MPI