Installation Guide for HyPhy

Note: HyPhy is not currently available for Windows.

MP and MPI Versions

HyPhy can be built in two main flavors:

1. Multi-threaded (MP): Requires a compiler that supports OpenMP.
2. MPI-enabled (MPI): Designed for execution on clusters and requires an MPI-supported build and execution environment (e.g., OpenMPI).

Both multi-threading and MPI environments can significantly improve the performance of HyPhy analyses, especially for common analyses like FEL, MEME, FUBAR, and GARD.

Building from Source

To install HyPhy after downloading or cloning the repository, follow these steps:

Dependencies

Ensure you have the following dependencies before building from source:

• CMake (>= 3.12)
• GCC (>= 4.9)
• Libraries:
  • libcurl
  • libpthread
  • openmp (Install on macOS using: brew install libomp)

Step 1: Navigate to HyPhy Directory

cd hyphy

Step 2: Configure HyPhy Using CMake

Run the following command:

cmake .

• By default, HyPhy will be installed in /usr/local/. To specify a custom installation path, use:

  cmake -DCMAKE_INSTALL_PREFIX=/location/of/choice .

• To use a different build system (supported by CMake), such as XCode, configure HyPhy using the generator (-G) option:

  cmake -G Xcode .

• If you need to specify a particular C/C++ compiler (must support C++14), use:

  cmake -DCMAKE_CXX_COMPILER=/path/to/C++-compiler -DCMAKE_C_COMPILER=/path/to/C-compiler .

Step 3: Build HyPhy

You can build HyPhy with one of the following commands:

• To create the HYPHYMP executable:

  make hyphy

  For faster builds, utilize multiple processors:

  make -j hyphy

• To create the HYPHYMPI executable:

  make MPI

Note on building:

• hyphy: Builds a HyPhy executable (hyphy) that supports symmetric multiprocessing via OpenMP. If OpenMP is not supported, the executable will be single-threaded. You can check if OpenMP is enabled in the output from CMake.

• MPI: Builds a HyPhy executable (HYPHYMPI) for parallel execution using the Message Passing Interface (MPI). Ensure that an MPI library (e.g., OpenMPI) is installed and available in your path.

Step 4: Install HyPhy

Run the following command to install HyPhy:

make install

HyPhy will be installed either in its default path (/usr/local/) or the custom path specified during the CMake configuration.

• HYPHYMP(I) will be installed at /location/of/choice/bin.
• libhyphy_mp will be installed at /location/of/choice/lib.
• HyPhy's standard library of scripts/batch files will be installed at /location/of/choice/lib/hyphy.

Environment Options

To specify the path HyPhy searches for its library sources, you can do one of the following:

1. Set LIBPATH Argument:

   hyphy LIBPATH=/usr/local/lib/hyphy

2. Set Environment Variable:

   export HYPHY_LIB_PATH=/usr/local/lib/hyphy/
   hyphy

Additional Notes

The CMake script will build HyPhy with all available features on the host system (e.g., AVX and AVX-2 instructions). If you plan to execute HyPhy in a heterogeneous cluster environment where not all nodes support these instructions, use the following command to avoid AVX-related issues:

cmake -DNOAVX=ON ./

Benchmarks

For benchmarks of common HyPhy methods using mpirun with an escalating number of processors, refer to the link here.