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HemeLB Users' Guide

A simple guide to compile and run HemeLB

Dependencies

The main HemeLB application requires:

  • Unix (-ish) OS: modern Linux or MacOS
  • C++17 compiler
  • CMake version >= 3.13
  • MPI implementation supporting version 3.0 of the standard or later
  • Boost* header-only libraries version >= 1.54
  • CTemplate*
  • Catch2* (if building tests)
  • ParMETIS* graph partitioning library
  • TinyXML* XML parsing library
  • zlib* compression library (likely included in your OS)
  • MPWide* (if building for multiscale)

If using resolved blood cells, you also require: - HDF5 - VTK version 9 (for RBC mode)

The dependencies marked with * can be built automatically by the build system.

Download

Clone the repository: 

git clone https://github.com/hemelb-codes/hemelb.git

Compile

TL;DR: 

mkdir build
cmake -S path/to/source -B build -DCMAKE_INSTALL_PREFIX=/where/to/install -DCMAKE_BUILD_TYPE=Release
cmake --build build
cmake --install build

HemeLB is configured with CMake. For a basic guide see: https://cmake.org/runningcmake/

You can choose to use the top level "superbuild" which will automatically download and install any missing dependencies (of those marked with an asterisk above). If you have any of these installed on your machine (e.g. via a module system) then they can be used here also.

The system has three options for each package: - System: never build and use the system one instead - Build: always build and use that - Auto: look for the system package and use is available, otherwise build. The default is Auto. This is controlled through variables named DEPS_${PACKAGE_NAME}, e.g. DEPS_TINYXML.

Alternatively, you can use the code-only build, where you must ensure that all the dependencies are available. To use this, simply pass the path to the Code subdirectory to CMake as the source.

For development, we suggest that you first install any missing dependencies using the CMakeLists.txt in the dependencies directory (supply that path to cmake) and then do a code-only build.

In all cases, the options you can pass to CMake are given in .

We are adding machine-specific instructions to the folder .