Richard Louis Schiek

Parallel Transistor-Level Circuit Simulation

With the advent of multi-core technology, inexpensive large-scale parallel platforms are now widely available. While this presents new opportunities for the EDA community, traditional transistor-level, SPICE-style circuit simulation has unique parallel simulation challenges. Here the Xyce Parallel Circuit Simulator is described, which has been designed from the “from-the-ground-up” to be distributed memory-parallel. Xyce has demonstrated scalable circuit simulation on hundreds of processors, but doing so required a comprehensive parallel strategy. This included the development of new solver technologies, including novel preconditioned iterative solvers, as well as attention to other aspects of the simulation such as parallel file I/O, and efficient load balancing of device evaluations and linear systems. Xyce relies primarily upon a message-passing (MPI-based) implementation, but optimal scalability on multi-core platforms can require a combination of message-passing and threading. To accommodate future parallel platforms, software abstractions allowing adaptation to other parallel paradigms are part of the Xyce design.

Development of a massively-parallel, biological circuit simulator

Genetic expression and control pathways can be successfully modeled as electrical circuits. Given the vast quantity of genomic data, very large and complex genetic circuits can be constructed. To tackle such problems, the massively-parallel, electronic circuit simulator, Xyce/sup /spl trade//, is being adapted to address biological problems. Unique to this biocircuit simulator is the ability to simulate not just one or a set of genetic circuits in a cell, but many cells and their internal circuits interacting through a common environment. Currently, electric circuit analogs for common biological and chemical machinery have been created. Using such analogs, one can construct expression, regulation and reaction networks. Individual species can be connected to other networks or cells via nondiffusive or diffusive channels (i.e. regions where species diffusion limits mass transport). Within any cell, a hierarchy of networks may exist operating at different time-scales to represent different aspects of cellular processes. Though under development, this simulator can model interesting biological and chemical systems. Prokaryotic genetic and metabolic regulatory circuits have been constructed and their interactions simulated for Escherichia colis tryptophan biosynthesis pathway. Additionally, groups of cells each containing an internal reaction network and communicating via a diffusion limited environment can produce periodic concentration waves. Thus, this biological circuit simulator has the potential to explore large, complex systems and environmentally coupled problems.

BioXyce: an engineering platform for the study of cellular systems

Researchers use constructs from the field of electrical engineering for the modelling and analysis of biological systems, but few exploit parallels between electrical and biological circuits for simulation purposes. The authors discuss the development of BioXyce, a circuit-based biological simulation platform that uses Xyce, a large-scale electrical circuit simulator, as its simulation engine. BioXyce is capable of simulating whole-cell and multicellular systems. Simulation results for the central metabolism in Escherichia coli K12 and cellular differentiation in Drosophila sp. are presented.

Simulating neural systems with Xyce.

Sandias parallel circuit simulator, Xyce, can address large scale neuron simulations in a new way extending the range within which one can perform high-fidelity, multi-compartment neuron simulations. This report documents the implementation of neuron devices in Xyce, their use in simulation and analysis of neuron systems.

Parallel Algorithm Strategies for Circuit Simulation

Circuit simulation tools (e.g., SPICE) have become invaluable in the development and design of electronic circuits. However, they have been pushed to their performance limits in addressing circuit design challenges that come from the technology drivers of smaller feature scales and higher integration. Improving the performance of circuit simulation tools through exploiting new opportunities in widely-available multi-processor architectures is a logical next step. Unfortunately, not all traditional simulation applications are inherently parallel, and quickly adapting mature application codes (even codes designed to parallel applications) to new parallel paradigms can be prohibitively difficult. In general, performance is influenced by many choices: hardware platform, runtime environment, languages and compilers used, algorithm choice and implementation, and more. In this complicated environment, the use of mini-applications small self-contained proxies for real applications is an excellent approach for rapidly exploring the parameter space of all these choices. In this report we present a multi-core performance study of Xyce, a transistor-level circuit simulation tool, and describe the future development of a mini-application for circuit simulation.

Compensating for Parasitic Voltage Drops in Resistive Memory Arrays

Parasitic resistances cause devices in a resistive memory array to experience different read/write voltages depending on the device location, resulting in uneven writes and larger leakage currents. We present a new method to compensate for this by adding extra series resistance to the drivers to equalize the parasitic resistance seen by all the devices. This allows for uniform writes, enabling multi-level cells with greater numbers of distinguishable levels, and reduced write power, enabling larger arrays.

Building guide : how to build Xyce from source code.

While Xyce uses the Autoconf and Automake system to configure builds, it is often necessary to perform more than the customary %E2%80%9C./configure%E2%80%9D builds many open source users have come to expect. This document describes the steps needed to get Xyce built on a number of common platforms.

Xyce parallel electronic simulator release notes.

The Xyce Parallel Electronic Simulator has been written to support, in a rigorous manner, the simulation needs of the Sandia National Laboratories electrical designers. Specific requirements include, among others, the ability to solve extremely large circuit problems by supporting large-scale parallel computing platforms, improved numerical performance and object-oriented code design and implementation. The Xyce release notes describe: Hardware and software requirements New features and enhancements Any defects fixed since the last release Current known defects and defect workarounds For up-to-date information not available at the time these notes were produced, please visit the Xyce web page at http://www.cs.sandia.gov/xyce.

Automated Mask Creation From A 3D Model Using Faethm

We have developed and implemented a method which given a three-dimensional object can infer from topology the two-dimensional masks needed to produce that object with surface micro-machining. The masks produced by this design tool can be generic, process independent masks, or if given process constraints, specific for a target process. This design tool calculates the two-dimensional mask set required to produce a given three-dimensional model by investigating the vertical topology of the model.

Simulating metabolism in Escherichia coli K-12 — A circuit-based approach

Computational methods for describing, understanding, and manipulating biological pathways continue to be a heavily researched area. Many researchers use constructs based in electrical circuit design in the modeling and analysis of biological systems, but few draw on and exploit parallels between electrical circuits and biological circuits for simulation purposes. We develop a biological simulation framework using Xycetrade, a large-scale electrical circuit simulator, that is capable of simulating the complete metabolic system of Escherichia coli K-12. Using our framework we are able to model large-scale hybrid systems as demonstrated in successful simulation of E.coli central metabolism, a system that includes metabolic and corresponding genetic regulatory networks.