A distributed simulation environment for multibody physics

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1998.Includes bibliographical references (leaves 128-134).A distributed simulation environment, which can be used to model multibody physics, is developed. The software design is based on the object oriented paradigm and is implemented in C++ to run on a single workstation or multiple processors in parallel. It provides facilities to set up a multibody physics simulation, including arbitrary 3D geometric representation, particle interactions such as contacts and constraints, and visualization for postprocessing. Contact detection, the process of automatic identifying the geometric overlap between objects, is generally the most time-consuming procedure in the overall discrete element analysis pipeline. The computational cost of contact detection grows as a function of both the number of particles and the complexity of the geometric representation of each body. This thesis presents algorithms that significantly reduce the computational cost of the contact detection problem. The hashtable-based spatial reasoning algorithm demonstrates an O(M) performance, where M is the number of particles in the simulation system for a restricted set of particles. The discrete function representation (DFR) scheme is employed to model the surface geometry of complex 3D objects. DFR-based contact detection between a pair of objects exhibits an O(N) running time performance, where N is the number of surface point used to represent each object. In practice this results in a significant speedup over traditional techniques. A distributed DEM simulation environment is built on top of a set of software tools which exploit the parallelism embedded in the DEM analysis and which take advantage of a high-speed communications network to achieve good parallel performance. The goal is of reducing the entire computing time of of large-scale simulation problems to order O(N) is shown to be achieveable using the algorithms described.by Jen-Diann Chiou.Ph.D

MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

Benchmarking Memory Management Capabilities within ROOT-Sim

In parallel discrete event simulation techniques, the simulation model is partitioned into objects, concurrently executing events on different CPUs and/or multiple CPUCores. In such a context, run-time supports for logical time synchronization across the different simulation objects play a central role in determining the effectiveness of the specific parallel simulation environment. In this paper we present an experimental evaluation of the memory management capabilities offered by the ROme OpTimistic Simulator (ROOT-Sim). This is an open source parallel simulation environment transparently supporting optimistic synchronization via recoverability (based on incremental log/restore techniques) of any type of memory operation affecting the state of simulation objects, i.e., memory allocation, deallocation and update operations. The experimental study is based on a synthetic benchmark which mimics different read/write patterns inside the dynamic memory map associated with the state of simulation objects. This allows sensibility analysis of time and space effects due to the memory management subsystem while varying the type and the locality of the accesses associated with event processin