期刊
ACM TRANSACTIONS ON MODELING AND COMPUTER SIMULATION
卷 27, 期 2, 页码 -出版社
ASSOC COMPUTING MACHINERY
DOI: 10.1145/2987373
关键词
Stochastic neuronal simulation; PDES; multiple thread
资金
- China Scholarship Council, National Natural Science Foundation of China [61170048]
- Research Project of State Key Laboratory of High Performance Computing of National University of Defense Technology [201303-05]
- Research Fund for the Doctoral Program of High Education of China [20124307110017]
- National Institutes of Health [R01MH086638, T15LM007056]
Cells exhibit stochastic behavior when the number of molecules is small. Hence a stochastic reaction-diffusion simulator capable of working at scale can provide a more accurate view of molecular dynamics within the cell. This article describes a parallel discrete event simulator, Neuron Time Warp-Multi Thread (NTW-MT), developed for the simulation of reaction diffusion models of neurons. To the best of our knowledge, this is the first parallel discrete event simulator oriented toward stochastic simulation of chemical reactions in a neuron. The simulator was developed as part of the NEURON project. NTW-MT is optimistic and thread based, which attempts to capitalize on multicore architectures used in high performance machines. It makes use of a multilevel queue for the pending event set and a single rollback message in place of individual antimessages to disperse contention and decrease the overhead of processing rollbacks. Global Virtual Time is computed asynchronously both within and among processes to get rid of the overhead for synchronizing threads. Memory usage is managed in order to avoid locking and unlocking when allocating and deallocating memory and to maximize cache locality. We verified our simulator on a calcium buffer model. We examined its performance on a calcium wave model, comparing it to the performance of a process based optimistic simulator and a threaded simulator which uses a single priority queue for each thread. Our multithreaded simulator is shown to achieve superior performance to these simulators. Finally, we demonstrated the scalability of our simulator on a larger Calcium-Induced Calcium Release (CICR) model and a more detailed CICR model.
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