A Parallel Implementation for Cellular Potts Model with Software Transactional Memory
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Cellular Potts Model is a mathematical model used to simulate biological systems in a wide scale range, from cells to organs. The model uses a Monte-Carlo approach to determinate for each cell, new state and actions like mitosis, movements or emission of pseudopods. Literature shows multiple implementations of CPM model, even incorporating parallel processing. These works use a data division approach that requires to take locks on data structures, or to spread information between tasks, slowing down simulations. This work proposes a fast implementation for CPM using software transactional memory to synchronize parallel tasks and to apply it to breast cancer in situ (DCIS). Execution times and speedups are calculated. Results show appreciable speedups.
KeywordsCellular automaton Cellular Potts Model (Breast cancer in situ) DCIS Gland Locks Multicore Parallel programming Shared memory Software transactional memory speedup
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