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

Transformations of High-Level Synthesis Codes for High-Performance Computing

Specialized hardware architectures promise a major step in performance and energy efficiency over the traditional load/store devices currently employed in large scale computing systems. The adoption of high-level synthesis (HLS) from languages such as C/C++ and OpenCL has greatly increased programmer productivity when designing for such platforms. While this has enabled a wider audience to target specialized hardware, the optimization principles known from traditional software design are no longer sufficient to implement high-performance codes. Fast and efficient codes for reconfigurable platforms are thus still challenging to design. To alleviate this, we present a set of optimizing transformations for HLS, targeting scalable and efficient architectures for high-performance computing (HPC) applications. Our work provides a toolbox for developers, where we systematically identify classes of transformations, the characteristics of their effect on the HLS code and the resulting hardware (e.g., increases data reuse or resource consumption), and the objectives that each transformation can target (e.g., resolve interface contention, or increase parallelism). We show how these can be used to efficiently exploit pipelining, on-chip distributed fast memory, and on-chip streaming dataflow, allowing for massively parallel architectures. To quantify the effect of our transformations, we use them to optimize a set of throughput-oriented FPGA kernels, demonstrating that our enhancements are sufficient to scale up parallelism within the hardware constraints. With the transformations covered, we hope to establish a common framework for performance engineers, compiler developers, and hardware developers, to tap into the performance potential offered by specialized hardware architectures using HLS

Computer Architectures to Close the Loop in Real-time Optimization

© 2015 IEEE.Many modern control, automation, signal processing and machine learning applications rely on solving a sequence of optimization problems, which are updated with measurements of a real system that evolves in time. The solutions of each of these optimization problems are then used to make decisions, which may be followed by changing some parameters of the physical system, thereby resulting in a feedback loop between the computing and the physical system. Real-time optimization is not the same as fast optimization, due to the fact that the computation is affected by an uncertain system that evolves in time. The suitability of a design should therefore not be judged from the optimality of a single optimization problem, but based on the evolution of the entire cyber-physical system. The algorithms and hardware used for solving a single optimization problem in the office might therefore be far from ideal when solving a sequence of real-time optimization problems. Instead of there being a single, optimal design, one has to trade-off a number of objectives, including performance, robustness, energy usage, size and cost. We therefore provide here a tutorial introduction to some of the questions and implementation issues that arise in real-time optimization applications. We will concentrate on some of the decisions that have to be made when designing the computing architecture and algorithm and argue that the choice of one informs the other

The Analogue Computer as a Voltage-Controlled Synthesiser

This paper re-appraises the role of analogue computers within electronic and computer music and provides some pointers to future areas of research. It begins by introducing the idea of analogue computing and placing in the context of sound and music applications. This is followed by a brief examination of the classic constituents of an analogue computer, contrasting these with the typical modular voltage-controlled synthesiser. Two examples are presented, leading to a discussion on some parallels between these two technologies. This is followed by an examination of the current state-of-the-art in analogue computation and its prospects for applications in computer and electronic music

Why (and How) Networks Should Run Themselves

The proliferation of networked devices, systems, and applications that we depend on every day makes managing networks more important than ever. The increasing security, availability, and performance demands of these applications suggest that these increasingly difficult network management problems be solved in real time, across a complex web of interacting protocols and systems. Alas, just as the importance of network management has increased, the network has grown so complex that it is seemingly unmanageable. In this new era, network management requires a fundamentally new approach. Instead of optimizations based on closed-form analysis of individual protocols, network operators need data-driven, machine-learning-based models of end-to-end and application performance based on high-level policy goals and a holistic view of the underlying components. Instead of anomaly detection algorithms that operate on offline analysis of network traces, operators need classification and detection algorithms that can make real-time, closed-loop decisions. Networks should learn to drive themselves. This paper explores this concept, discussing how we might attain this ambitious goal by more closely coupling measurement with real-time control and by relying on learning for inference and prediction about a networked application or system, as opposed to closed-form analysis of individual protocols

Checking-in on Network Functions

When programming network functions, changes within a packet tend to have consequences---side effects which must be accounted for by network programmers or administrators via arbitrary logic and an innate understanding of dependencies. Examples of this include updating checksums when a packet's contents has been modified or adjusting a payload length field of a IPv6 header if another header is added or updated within a packet. While static-typing captures interface specifications and how packet contents should behave, it does not enforce precise invariants around runtime dependencies like the examples above. Instead, during the design phase of network functions, programmers should be given an easier way to specify checks up front, all without having to account for and keep track of these consequences at each and every step during the development cycle. In keeping with this view, we present a unique approach for adding and generating both static checks and dynamic contracts for specifying and checking packet processing operations. We develop our technique within an existing framework called NetBricks and demonstrate how our approach simplifies and checks common dependent packet and header processing logic that other systems take for granted, all without adding much overhead during development.Comment: ANRW 2019 ~ https://irtf.org/anrw/2019/program.htm

Design of a Hybrid Modular Switch

Network Function Virtualization (NFV) shed new light for the design, deployment, and management of cloud networks. Many network functions such as firewalls, load balancers, and intrusion detection systems can be virtualized by servers. However, network operators often have to sacrifice programmability in order to achieve high throughput, especially at networks' edge where complex network functions are required. Here, we design, implement, and evaluate Hybrid Modular Switch (HyMoS). The hybrid hardware/software switch is designed to meet requirements for modern-day NFV applications in providing high-throughput, with a high degree of programmability. HyMoS utilizes P4-compatible Network Interface Cards (NICs), PCI Express interface and CPU to act as line cards, switch fabric, and fabric controller respectively. In our implementation of HyMos, PCI Express interface is turned into a non-blocking switch fabric with a throughput of hundreds of Gigabits per second. Compared to existing NFV infrastructure, HyMoS offers modularity in hardware and software as well as a higher degree of programmability by supporting a superset of P4 language