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Multithreaded refinement
Medium-grained parallelism may be possible in the refinement stages. The idea would be to do the refinement in an interlaced pattern. Locking would only be needed near the end of a group of rows or columns.
Why don't you use OpenMP? It is supported by gcc as well. Moreover, should the decoder allocate all available processors in a machine or should it be configurable? Some people, specially when they are running the decoder on a notebook, might not like to allocate all their processors to a process.