Efficient Molecular Dynamics Simulation on Reconfigurable Models with MultiGrid Method

In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N^2) for an N particle system. In this dissertation, we are proposing two research directions for the MD simulation. First, we design a new variation of Multigrid (MG) algorithm called Multi-level charge assignment (MCA) that requires O(N) time for accurate and efficient calculation of the electrostatic forces. We apply MCA and back interpolation based on the structure of molecules to enhance the accuracy of the simulation. Our second research utilizes reconfigurable models to achieve fast calculation time. We have been working on exploiting two reconfigurable models. We design FPGA-based MD simulator implementing MCA method for Xilinx Virtex-IV. It performs about 10 to 100 times faster than software implementation depending on the simulation accuracy desired. We also design fast and scalable Reconfigurable mesh (R-Mesh) algorithms for MD simulations. This work demonstrates that the large scale biological studies can be simulated in close to real time. The R-Mesh algorithms we design highlight the feasibility of these models to evaluate potentials with faster calculation times. Specifically, we develop R-Mesh algorithms for both Direct method and Multigrid method. The Direct method evaluates exact potentials and forces, but requires O(N^2) calculation time for evaluating electrostatic forces on a general purpose processor. The MG method adopts an interpolation technique to reduce calculation time to O(N) for a given accuracy. However, our R-Mesh algorithms require only O(N) or O(logN) time complexity for the Direct method on N linear R-Mesh and N¡¿N R-Mesh, respectively and O(r)+O(logM) time complexity for the Multigrid method on an X¡¿Y¡¿Z R-Mesh. r is N/M and M = X¡¿Y¡¿Z is the number of finest grid points

"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

Ultralightweight Ballute Technology Advances

Ultralightweight ballutes offer the potential to provide the deceleration for entry and aerocapture missions at a fraction of the mass of traditional methods. A team consisting of Ball Aerospace, ILC Dover, NASA Langley, NASA Johnson, and the Jet Propulsion Laboratory has been addressing the technical issues associated with ultralightweight ballutes for aerocapture at Titan. Significant progress has been made in the areas of ballute materials, aerothermal analysis, trajectory control, and aeroelastic modeling. The status and results of efforts in these areas are presented. The results indicate that an ultralightweight ballute system mass of 8 to 10 percent of the total entry mass is possible

An integrated framework for developing generic modular reconfigurable platforms for micro manufacturing and its implementation

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The continuing trends of miniaturisation, mass customisation, globalisation and wide use of the Internet have great impacts upon manufacturing in the 21st century. Micro manufacturing will play an increasingly important role in bridging the gap between the traditional precision manufacturing and the emerging technologies like MEMS/NEMS. The key requirements for micro manufacturing in this context are hybrid manufacturing capability, modularity, reconfigurability, adaptability and energy/resource efficiency. The existing design approaches tend to have narrow scope and are largely limited to individual manufacturing processes and applications. The above requirements demand a fundamentally new approach to the future applications of micro manufacturing so as to obtain producibility, predictability and productivity covering the full process chains and value chains. A novel generic modular reconfigurable platform (GMRP) is proposed in such a context. The proposed GMRP is able to offer hybrid manufacturing capabilities, modularity, reconfigurablity and adaptivity as both an individual machine tool and a micro manufacturing system, and provides a cost effective solution to high value micro manufacturing in an agile, responsive and mass customisation manner. An integrated framework has been developed to assist the design of GMRPs due to their complexity. The framework incorporates theoretical GMRP model, design support system and extension interfaces. The GMRP model covers various relevant micro manufacturing processes and machine tool elements. The design support system includes a user-friendly interface, a design engine for design process and design evaluation, together with scalable design knowledge base and database. The functionalities of the framework can also be extended through the design support system interface, the GMRP interface and the application interface, i.e. linking to external hardware and/or software modules. The design support system provides a number of tools for the analysis and evaluation of the design solutions. The kinematic simulation of machine tools can be performed using the Virtual Reality toolbox in Matlab. A module has also been developed for the multiscale modelling, simulation and results analysis in Matlab. A number of different cutting parameters can be studied and the machining performance can be subsequently evaluated using this module. The mathematical models for a non-traditional micro manufacturing process, micro EDM, have been developed with the simulation performed using FEA. Various design theories and methodologies have been studied, and the axiomatic design theory has been selected because of its great power and simplicity. It has been applied in the conceptual design of GMRP and its design support system. The implementation of the design support system is carried out using Matlab, Java and XML technologies. The proposed GMRP and framework have been evaluated through case studies and experimental results

NASA SBIR abstracts of 1991 phase 1 projects

The objectives of 301 projects placed under contract by the Small Business Innovation Research (SBIR) program of the National Aeronautics and Space Administration (NASA) are described. These projects were selected competitively from among proposals submitted to NASA in response to the 1991 SBIR Program Solicitation. The basic document consists of edited, non-proprietary abstracts of the winning proposals submitted by small businesses. The abstracts are presented under the 15 technical topics within which Phase 1 proposals were solicited. Each project was assigned a sequential identifying number from 001 to 301, in order of its appearance in the body of the report. Appendixes to provide additional information about the SBIR program and permit cross-reference of the 1991 Phase 1 projects by company name, location by state, principal investigator, NASA Field Center responsible for management of each project, and NASA contract number are included

High performance communication on reconfigurable clusters

High Performance Computing (HPC) has matured to where it is an essential third pillar, along with theory and experiment, in most domains of science and engineering. Communication latency is a key factor that is limiting the performance of HPC, but can be addressed by integrating communication into accelerators. This integration allows accelerators to communicate with each other without CPU interactions, and even bypassing the network stack. Field Programmable Gate Arrays (FPGAs) are the accelerators that currently best integrate communication with computation. The large number of Multi-gigabit Transceivers (MGTs) on most high-end FPGAs can provide high-bandwidth and low-latency inter-FPGA connections. Additionally, the reconfigurable FPGA fabric enables tight coupling between computation kernel and network interface. Our thesis is that an application-aware communication infrastructure for a multi-FPGA system makes substantial progress in solving the HPC communication bottleneck. This dissertation aims to provide an application-aware solution for communication infrastructure for FPGA-centric clusters. Specifically, our solution demonstrates application-awareness across multiple levels in the network stack, including low-level link protocols, router microarchitectures, routing algorithms, and applications. We start by investigating the low-level link protocol and the impact of its latency variance on performance. Our results demonstrate that, although some link jitter is always present, we can still assume near-synchronous communication on an FPGA-cluster. This provides the necessary condition for statically-scheduled routing. We then propose two novel router microarchitectures for two different kinds of workloads: a wormhole Virtual Channel (VC)-based router for workloads with dynamic communication, and a statically-scheduled Virtual Output Queueing (VOQ)-based router for workloads with static communication. For the first (VC-based) router, we propose a framework that generates application-aware router configurations. Our results show that, by adding application-awareness into router configuration, the network performance of FPGA clusters can be substantially improved. For the second (VOQ-based) router, we propose a novel offline collective routing algorithm. This shows a significant advantage over a state-of-the-art collective routing algorithm. We apply our communication infrastructure to a critical strong-scaling HPC kernel, the 3D FFT. The experimental results demonstrate that the performance of our design is faster than that on CPUs and GPUs by at least one order of magnitude (achieving strong scaling for the target applications). Surprisingly, the FPGA cluster performance is similar to that of an ASIC-cluster. We also implement the 3D FFT on another multi-FPGA platform: the Microsoft Catapult II cloud. Its performance is also comparable or superior to CPU and GPU HPC clusters. The second application we investigate is Molecular Dynamics Simulation (MD). We model MD on both FPGA clouds and clusters. We find that combining processing and general communication in the same device leads to extremely promising performance and the prospect of MD simulations well into the us/day range with a commodity cloud

Small business innovation research. Abstracts of completed 1987 phase 1 projects

Non-proprietary summaries of Phase 1 Small Business Innovation Research (SBIR) projects supported by NASA in the 1987 program year are given. Work in the areas of aeronautical propulsion, aerodynamics, acoustics, aircraft systems, materials and structures, teleoperators and robotics, computer sciences, information systems, spacecraft systems, spacecraft power supplies, spacecraft propulsion, bioastronautics, satellite communication, and space processing are covered