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.

中文翻译：

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用于神经元反应和扩散的多线程随机 PDES

当分子数量很少时，细胞表现出随机行为。因此，能够大规模工作的随机反应扩散模拟器可以提供更准确的细胞内分子动力学视图。本文介绍了一种并行离散事件模拟器，神经元时间扭曲多线程 (NTW-MT)，用于模拟神经元的反应扩散模型。据我们所知，这是第一个面向神经元化学反应随机模拟的并行离散事件模拟器。该模拟器是作为 NEURON 项目的一部分开发的。NTW-MT 是乐观和基于线程的，它试图利用高性能机器中使用的多核架构。它使用多级队列来处理未决事件集，并使用单个回滚消息代替单个反消息来分散争用并减少处理回滚的开销。全局虚拟时间在进程内部和进程之间异步计算，以消除同步线程的开销。管理内存使用是为了在分配和释放内存时避免锁定和解锁，并最大限度地提高缓存局部性。我们在钙缓冲模型上验证了我们的模拟器。我们检查了它在钙波模型上的性能，将其与基于进程的乐观模拟器和为每个线程使用单个优先级队列的线程模拟器的性能进行了比较。我们的多线程模拟器显示出比这些模拟器更出色的性能。最后，