BioScript: programming safe chemistry on laboratories-on-a-chip

This paper introduces BioScript, a domain-specific language (DSL) for programmable biochemistry which executes on emerging microfluidic platforms. The goal of this research is to provide a simple, intuitive, and type-safe DSL that is accessible to life science practitioners. The novel feature of the language is its syntax, which aims to optimize human readability; the technical contributions of the paper include the BioScript type system and relevant portions of its compiler. The type system ensures that certain types of errors, specific to biochemistry, do not occur, including the interaction of chemicals that may be unsafe. The compiler includes novel optimizations that place biochemical operations to execute concurrently on a spatial 2D array platform on the granularity of a control flow graph, as opposed to individual basic blocks. Results are obtained using both a cycle-accurate microfluidic simulator and a software interface to a real-world platform

A fast time-domain EM-TCAD coupled simulation framework via matrix exponential

We present a fast time-domain multiphysics simulation framework that combines full-wave electromagnetism (EM) and carrier transport in semiconductor devices (TCAD). The proposed framework features a division of linear and nonlinear components in the EM-TCAD coupled system. The former is extracted and handled independently with high efficiency by a matrix exponential approach assisted with Krylov subspace method. The latter is treated by ordinary Newton's method yet with a much sparser Jacobian matrix that leads to substantial speedup in solving the linear system of equations. More convenient error management and adaptive control are also available through the linear and nonlinear decoupling. © 2012 ACM.published_or_final_versio

Timing-Driven Macro Placement

Placement is an important step in the process of finding physical layouts for electronic computer chips. The basic task during placement is to arrange the building blocks of the chip, the circuits, disjointly within a given chip area. Furthermore, such positions should result in short circuit interconnections which can be routed easily and which ensure all signals arrive in time. This dissertation mostly focuses on macros, the largest circuits on a chip. In order to optimize timing characteristics during macro placement, we propose a new optimistic timing model based on geometric distance constraints. This model can be computed and evaluated efficiently in order to predict timing traits accurately in practice. Packing rectangles disjointly remains strongly NP-hard under slack maximization in our timing model. Despite of this we develop an exact, linear time algorithm for special cases. The proposed timing model is incorporated into BonnMacro, the macro placement component of the BonnTools physical design optimization suite developed at the Research Institute for Discrete Mathematics. Using efficient formulations as mixed-integer programs we can legalize macros locally while optimizing timing. This results in the first timing-aware macro placement tool. In addition, we provide multiple enhancements for the partitioning-based standard circuit placement algorithm BonnPlace. We find a model of partitioning as minimum-cost flow problem that is provably as small as possible using which we can avoid running time intensive instances. Moreover we propose the new global placement flow Self-Stabilizing BonnPlace. This approach combines BonnPlace with a force-directed placement framework. It provides the flexibility to optimize the two involved objectives, routability and timing, directly during placement. The performance of our placement tools is confirmed on a large variety of academic benchmarks as well as real-world designs provided by our industrial partner IBM. We reduce running time of partitioning significantly and demonstrate that Self-Stabilizing BonnPlace finds easily routable placements for challenging designs – even when simultaneously optimizing timing objectives. BonnMacro and Self-Stabilizing BonnPlace can be combined to the first timing-driven mixed-size placement flow. This combination often finds placements with competitive timing traits and even outperforms solutions that have been determined manually by experienced designers

Modeling Power Consumption and Temperature in TLM Models

International audienceMany techniques and tools exist to estimate the power consumption and the temperature map of a chip. These tools help the hardware designers develop power efficient chips in the presence of temperature constraints. For this task, the application can be ignored or at least abstracted by some high level scenarios; at this stage, the actual embedded software is generally not available yet. However, after the hardware is defined, the embedded software can still have a significant influence on the power consumption; i.e., two implementations of the same application can consume more or less power. Moreover, the actual software powe

Manticore: Hardware-Accelerated RTL Simulation with Static Bulk-Synchronous Parallelism

The demise of Moore's Law and Dennard Scaling has revived interest in specialized computer architectures and accelerators. Verification and testing of this hardware heavily uses cycle-accurate simulation of register-transfer-level (RTL) designs. The best software RTL simulators can simulate designs at 1--1000~kHz, i.e., more than three orders of magnitude slower than hardware. Faster simulation can increase productivity by speeding design iterations and permitting more exhaustive exploration. One possibility is to use parallelism as RTL exposes considerable fine-grain concurrency. However, state-of-the-art RTL simulators generally perform best when single-threaded since modern processors cannot effectively exploit fine-grain parallelism. This work presents Manticore: a parallel computer designed to accelerate RTL simulation. Manticore uses a static bulk-synchronous parallel (BSP) execution model to eliminate runtime synchronization barriers among many simple processors. Manticore relies entirely on its compiler to schedule resources and communication. Because RTL code is practically free of long divergent execution paths, static scheduling is feasible. Communication and synchronization no longer incur runtime overhead, enabling efficient fine-grain parallelism. Moreover, static scheduling dramatically simplifies the physical implementation, significantly increasing the potential parallelism on a chip. Our 225-core FPGA prototype running at 475 MHz outperforms a state-of-the-art RTL simulator on an Intel Xeon processor running at $\approx$ 3.3 GHz by up to 27.9$\times$ (geomean 5.3$\times$) in nine Verilog benchmarks

RoHNAS: A Neural Architecture Search Framework with Conjoint Optimization for Adversarial Robustness and Hardware Efficiency of Convolutional and Capsule Networks

Neural Architecture Search (NAS) algorithms aim at finding efficient Deep Neural Network (DNN) architectures for a given application under given system constraints. DNNs are computationally-complex as well as vulnerable to adversarial attacks. In order to address multiple design objectives, we propose RoHNAS , a novel NAS framework that jointly optimizes for adversarial-robustness and hardware-efficiency of DNNs executed on specialized hardware accelerators. Besides the traditional convolutional DNNs, RoHNAS additionally accounts for complex types of DNNs such as Capsule Networks. For reducing the exploration time, RoHNAS analyzes and selects appropriate values of adversarial perturbation for each dataset to employ in the NAS flow. Extensive evaluations on multi - Graphics Processing Unit (GPU) - High Performance Computing (HPC) nodes provide a set of Pareto-optimal solutions, leveraging the tradeoff between the above-discussed design objectives. For example, a Pareto-optimal DNN for the CIFAR-10 dataset exhibits 86.07% accuracy, while having an energy of 38.63 mJ, a memory footprint of 11.85 MiB, and a latency of 4.47 ms