OpenMP¶

HJCFIT will by default be compiled with openmp support. The parallelisation is by default over either the number of bursts or over the individual open close transitions within the burst. Typically experiments either have many short bursts or a few long bursts so it really only makes sense to parallelise over one of these axes. The code takes care of detecting which axis to parallelise over automatically. The number of threads can be controlled by the usual environmental variable OMP_NUM_THREADS. Running on a PC this will probably be set to the number of cores in the computer which is probably the optimal solution in most cases.

CMake takes care of identifying the correct compiler flags and enables OpenMP automatically on all supported platforms. Currently (2016) Clang on OSX does not support OpenMP (but the code can be compiled on OSX using gcc from homebrew or similar)

OpenMP can be disabled explicitly by setting the CMake variable openmp to off.

MPI¶

Write something about MPI