Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

We describe LLVM (low level virtual machine), a compiler framework designed to support transparent, lifelong program analysis and transformation for arbitrary programs, by providing high-level information to compiler transformations at compile-time, link-time, run-time, and in idle time between runs. LLVM defines a common, low-level code representation in static single assignment (SSA) form, with several novel features: a simple, language-independent type-system that exposes the primitives commonly used to implement high-level language features; an instruction for typed address arithmetic; and a simple mechanism that can be used to implement the exception handling features of high-level languages (and setjmp/longjmp in C) uniformly and efficiently. The LLVM compiler framework and code representation together provide a combination of key capabilities that are important for practical, lifelong analysis and transformation of programs. To our knowledge, no existing compilation approach provides all these capabilities. We describe the design of the LLVM representation and compiler framework, and evaluate the design in three ways: (a) the size and effectiveness of the representation, including the type information it provides; (b) compiler performance for several interprocedural problems; and (c) illustrative examples of the benefits LLVM provides for several challenging compiler problems.

/pdf/llvm-a-compilation-framework-for-lifelong-program-analysis-2e1wwcps42.pdf

LLVM: a compilation framework for lifelong program analysis & transformation

The Internet has led to the creation of a digital society, where (almost) everything is connected and is accessible from anywhere. However, despite their widespread adoption, traditional IP networks are complex and very hard to manage. It is both difficult to configure the network according to predefined policies, and to reconfigure it to respond to faults, load, and changes. To make matters even more difficult, current networks are also vertically integrated: the control and data planes are bundled together. Software-defined networking (SDN) is an emerging paradigm that promises to change this state of affairs, by breaking vertical integration, separating the network's control logic from the underlying routers and switches, promoting (logical) centralization of network control, and introducing the ability to program the network. The separation of concerns, introduced between the definition of network policies, their implementation in switching hardware, and the forwarding of traffic, is key to the desired flexibility: by breaking the network control problem into tractable pieces, SDN makes it easier to create and introduce new abstractions in networking, simplifying network management and facilitating network evolution. In this paper, we present a comprehensive survey on SDN. We start by introducing the motivation for SDN, explain its main concepts and how it differs from traditional networking, its roots, and the standardization activities regarding this novel paradigm. Next, we present the key building blocks of an SDN infrastructure using a bottom-up, layered approach. We provide an in-depth analysis of the hardware infrastructure, southbound and northbound application programming interfaces (APIs), network virtualization layers, network operating systems (SDN controllers), network programming languages, and network applications. We also look at cross-layer problems such as debugging and troubleshooting. In an effort to anticipate the future evolution of this new paradigm, we discuss the main ongoing research efforts and challenges of SDN. In particular, we address the design of switches and control platforms—with a focus on aspects such as resiliency, scalability, performance, security, and dependability—as well as new opportunities for carrier transport networks and cloud providers. Last but not least, we analyze the position of SDN as a key enabler of a software-defined environment.

https://publications.uni.lu/bitstream/10993/20596/1/survey_on_SDN.pdf

Software-Defined Networking: A Comprehensive Survey

Aspect] is a simple and practical aspect-oriented extension to Java With just a few new constructs, AspectJ provides support for modular implementation of a range of crosscutting concerns. In AspectJ's dynamic join point model, join points are well-defined points in the execution of the program; pointcuts are collections of join points; advice are special method-like constructs that can be attached to pointcuts; and aspects are modular units of crosscutting implementation, comprising pointcuts, advice, and ordinary Java member declarations. AspectJ code is compiled into standard Java bytecode. Simple extensions to existing Java development environments make it possible to browse the crosscutting structure of aspects in the same kind of way as one browses the inheritance structure of classes. Several examples show that AspectJ is powerful, and that programs written using it are easy to understand.

An overview of AspectJ

A type system is a syntactic method for automatically checking the absence of certain erroneous behaviors by classifying program phrases according to the kinds of values they compute. The study of type systems -- and of programming languages from a type-theoretic perspective -- has important applications in software engineering, language design, high-performance compilers, and security.This text provides a comprehensive introduction both to type systems in computer science and to the basic theory of programming languages. The approach is pragmatic and operational; each new concept is motivated by programming examples and the more theoretical sections are driven by the needs of implementations. Each chapter is accompanied by numerous exercises and solutions, as well as a running implementation, available via the Web. Dependencies between chapters are explicitly identified, allowing readers to choose a variety of paths through the material.The core topics include the untyped lambda-calculus, simple type systems, type reconstruction, universal and existential polymorphism, subtyping, bounded quantification, recursive types, kinds, and type operators. Extended case studies develop a variety of approaches to modeling the features of object-oriented languages.

https://www.seas.upenn.edu/~bcpierce/tapl/contents.pdf

Types and Programming Languages

P4 is a high-level language for programming protocol-independent packet processors. P4 works in conjunction with SDN control protocols like OpenFlow. In its current form, OpenFlow explicitly specifies protocol headers on which it operates. This set has grown from 12 to 41 fields in a few years, increasing the complexity of the specification while still not providing the flexibility to add new headers. In this paper we propose P4 as a strawman proposal for how OpenFlow should evolve in the future. We have three goals: (1) Reconfigurability in the field: Programmers should be able to change the way switches process packets once they are deployed. (2) Protocol independence: Switches should not be tied to any specific network protocols. (3) Target independence: Programmers should be able to describe packet-processing functionality independently of the specifics of the underlying hardware. As an example, we describe how to use P4 to configure a switch to add a new hierarchical label.

/pdf/p4-programming-protocol-independent-packet-processors-jlla1kwsyr.pdf

P4: programming protocol-independent packet processors

From the Publisher:
Mobile systems, whose components communicate and change their structure, now pervade the informational world and the wider world of which it is a part. The science of mobile systems is as yet immature, however. This book presents the pi-calculus, a theory of mobile systems. The pi-calculus provides a conceptual framework for understanding mobility, and mathematical tools for expressing systems and reasoning about their behaviors. 
The book serves both as a reference for the theory and as an extended demonstration of how to use pi-calculus to describe systems and analyze their properties. It covers the basic theory of pi-calculus, typed pi-calculi, higher-order processes, the relationship between pi-calculus and lambda-calculus, and applications of pi-calculus to object-oriented design and programming. 
The book is written at the graduate level, assuming no prior acquaintance with the subject, and is intended for computer scientists interested in mobile systems.

/pdf/the-pi-calculus-a-theory-of-mobile-processes-v2p06ak9w5.pdf

The Pi-Calculus: A Theory of Mobile Processes

Modern networks provide a variety of interrelated services including routing, traffic monitoring, load balancing, and access control. Unfortunately, the languages used to program today's networks lack modern features - they are usually defined at the low level of abstraction supplied by the underlying hardware and they fail to provide even rudimentary support for modular programming. As a result, network programs tend to be complicated, error-prone, and difficult to maintain.This paper presents Frenetic, a high-level language for programming distributed collections of network switches. Frenetic provides a declarative query language for classifying and aggregating network traffic as well as a functional reactive combinator library for describing high-level packet-forwarding policies. Unlike prior work in this domain, these constructs are - by design - fully compositional, which facilitates modular reasoning and enables code reuse. This important property is enabled by Frenetic's novel run-time system which manages all of the details related to installing, uninstalling, and querying low-level packet-processing rules on physical switches.Overall, this paper makes three main contributions: (1) We analyze the state-of-the art in languages for programming networks and identify the key limitations; (2) We present a language design that addresses these limitations, using a series of examples to motivate and validate our choices; (3) We describe an implementation of the language and evaluate its performance on several benchmarks.

/pdf/frenetic-a-network-programming-language-xza0s2pb9i.pdf

Frenetic: a network programming language

Configuration changes are a common source of instability in networks, leading to outages, performance disruptions, and security vulnerabilities. Even when the initial and final configurations are correct, the update process itself often steps through intermediate configurations that exhibit incorrect behaviors. This paper introduces the notion of consistent network updates---updates that are guaranteed to preserve well-defined behaviors when transitioning mbetween configurations. We identify two distinct consistency levels, per-packet and per-flow, and we present general mechanisms for implementing them in Software-Defined Networks using switch APIs like OpenFlow. We develop a formal model of OpenFlow networks, and prove that consistent updates preserve a large class of properties. We describe our prototype implementation, including several optimizations that reduce the overhead required to perform consistent updates. We present a verification tool that leverages consistent updates to significantly reduce the complexity of checking the correctness of network control software. Finally, we describe the results of some simple experiments demonstrating the effectiveness of these optimizations on example applications.

/pdf/abstractions-for-network-update-3dox41dgf6.pdf

Abstractions for network update

Managing a network requires support for multiple concurrent tasks, from routing and traffic monitoring, to access control and server load balancing Software-Defined Networking (SDN) allows applications to realize these tasks directly, by installing packet-processing rules on switches However, today's SDN platforms provide limited support for creating modular applications This paper introduces new abstractions for building applications out of multiple, independent modules that jointly manage network traffic First, we define composition operators and a library of policies for forwarding and querying traffic Our parallel composition operator allows multiple policies to operate on the same set of packets, while a novel sequential composition operator allows one policy to process packets after another Second, we enable each policy to operate on an abstract topology that implicitly constrains what the module can see and do Finally, we define a new abstract packet model that allows programmers to extend packets with virtual fields that may be used to associate packets with high-level meta-data We realize these abstractions in Pyretic, an imperative, domain-specific language embedded in Python

/pdf/composing-software-defined-networks-4rosu7yjms.pdf

David Walker

Papers

P4: programming protocol-independent packet processors

The Pi-Calculus: A Theory of Mobile Processes

Frenetic: a network programming language

Abstractions for network update

Composing software-defined networks