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Molecular dynamics with ape

机译:猿的分子动力学

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摘要

In this paper we discuss the portability of Molecular Dynamics codes for the simulation of diffusive systems (liquids) on the today available parallel computers of the APE family. Structural limitations of the APE architecture have been partially overcome: the intrinsic single precision arithmetic does not seem to affect in an approeciable way the numerical accuracy, while the absence of independent local integer addressing does affect the computing speed, but it is more than compensated by the parallel nature of the machine. As a test case, we report the results of the simulation of 512 molecules of liquid butane (C_4H_(10)) at room temperature. After 180 ps of equilibration, the system was followed for a total of 1.15 ns. The effective CPU time used for the whole simulation on the Torre (512 nodes approx= 25 Gigaflops) was approx = 48 hours.
机译:在本文中,我们讨论了分子动力学代码的可移植性,用于在当今可用的APE系列并行计算机上模拟扩散系统(液体)。 APE体系结构的结构性局限性已得到部分克服:固有的单精度算术似乎不会以适当的方式影响数值精度,而缺少独立的局部整数寻址的确会影响计算速度,但是它可以通过以下方式弥补:机器的并行性。作为测试案例,我们报告了在室温下模拟512分子液体丁烷(C_4H_(10))的结果。达到180 ps的平衡后,系统的跟踪时间总计为1.15 ns。在Torre上进行整个模拟所用的有效CPU时间(512个节点约等于25 Gigaflops)约为48小时。

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