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

One of the greatest challenges faced by designers of digital systems is optimizing the communication and interconnection between system components. Interconnection networks offer an attractive and economical solution to this communication crisis and are fast becoming pervasive in digital systems. Current trends suggest that this communication bottleneck will be even more problematic when designing future generations of machines. Consequently, the anatomy of an interconnection network router and science of interconnection network design will only grow in importance in the coming years.

This book offers a detailed and comprehensive presentation of the basic principles of interconnection network design, clearly illustrating them with numerous examples, chapter exercises, and case studies. It incorporates hardware-level descriptions of concepts, allowing a designer to see all the steps of the process from abstract design to concrete implementation.

·Case studies throughout the book draw on extensive author experience in designing interconnection networks over a period of more than twenty years, providing real world examples of what works, and what doesn't.

·Tightly couples concepts with implementation costs to facilitate a deeper understanding of the tradeoffs in the design of a practical network.

·A set of examples and exercises in every chapter help the reader to fully understand all the implications of every design decision.

Table of Contents


Chapter 1 Introduction to Interconnection Networks 
1.1 Three Questions About Interconnection Networks 
1.2 Uses of Interconnection Networks 
1.3 Network Basics 
1.4 History 
1.5 Organization of this Book 

Chapter 2 A Simple Interconnection Network 
2.1 Network Specifications and Constraints 
2.2 Topology 
2.3 Routing 
2.4 Flow Control 
2.5 Router Design 
2.6 Performance Analysis 
2.7 Exercises 

Chapter 3 Topology Basics 
3.1 Nomenclature 
3.2 Traffic Patterns 
3.3 Performance 
3.4 Packaging Cost 
3.5 Case Study: The SGI Origin 2000 
3.6 Bibliographic Notes 
3.7 Exercises 

Chapter 4 Butterfly Networks 
4.1 The Structure of Butterfly Networks 
4.2 Isomorphic Butterflies 
4.3 Performance and Packaging Cost 
4.4 Path Diversity and Extra Stages 
4.5 Case Study: The BBN Butterfly 
4.6 Bibliographic Notes 
4.7 Exercises 

Chapter 5 Torus Networks 
5.1 The Structure of Torus Networks 
5.2 Performance 
5.3 Building Mesh and Torus Networks 
5.4 Express Cubes 
5.5 Case Study: The MIT J-Machine 
5.6 Bibliographic Notes 
5.7 Exercises 
Chapter 6 Non-Blocking Networks 
6.1 Non-Blocking vs. Non-Interfering Networks 
6.2 Crossbar Networks 
6.3 Clos Networks 
6.4 Benes Networks 
6.5 Sorting Networks 
6.6 Case Study: The Velio VC2002 (Zeus) Grooming Switch 
6.7 Bibliographic Notes 
6.8 Exercises 

Chapter 7 Slicing and Dicing 
7.1 Concentrators and Distributors 
7.2 Slicing and Dicing 
7.3 Slicing Multistage Networks 
7.4 Case Study: Bit Slicing in the Tiny Tera 
7.5 Bibliographic Notes 
7.6 Exercises 

Chapter 8 Routing Basics 
8.1 A Routing Example 
8.2 Taxonomy of Routing Algorithms 
8.3 The Routing Relation 
8.4 Deterministic Routing 
8.5 Case Study: Dimension-Order Routing in the Cray T3D 
8.6 Bibliographic Notes 
8.7 Exercises 

Chapter 9 Oblivious Routing 
9.1 Valiant's Randomized Routing Algorithm 
9.2 Minimal Oblivious Routing 
9.3 Load-Balanced Oblivious Routing 
9.4 Analysis of Oblivious Routing 
9.5 Case Study: Oblivious Routing in the
Avici Terabit Switch Router(TSR) 
9.6 Bibliographic Notes 
9.7 Exercises 

Chapter 10 Adaptive Routing 
10.1 Adaptive Routing Basics 
10.2 Minimal Adaptive Routing 
10.3 Fully Adaptive Routing 
10.4 Load-Balanced Adaptive Routing 
10.5 Search-Based Routing 
10.6 Case Study: Adaptive Routing in the
Thinking Machines CM-5 
10.7 Bibliographic Notes 
10.8 Exercises 

Chapter 11 Routing Mechanics 
11.1 Table-Based Routing 
11.2 Algorithmic Routing 
11.3 Case Study: Oblivious Source Routing in the
IBM Vulcan Network 
11.4 Bibliographic Notes 
11.5 Exercises 

Chapter 12 Flow Control Basics 
12.1 Resources and Allocation Units 
12.2 Bufferless Flow Control 
12.3 Circuit Switching 
12.4 Bibliographic Notes 
12.5 Exercises 

Chapter 13 Buffered Flow Control 
13.1 Packet-Buffer Flow Control 
13.2 Flit-Buffer Flow Control 
13.3 Buffer Management and Backpressure 
13.4 Flit-Reservation Flow Control 
13.5 Bibliographic Notes 
13.6 Exercises 

Chapter 14 Deadlock and Livelock 
14.1 Deadlock 
14.2 Deadlock Avoidance 
14.3 Adaptive Routing 
14.4 Deadlock Recovery 
14.5 Livelock 
14.6 Case Study: Deadlock Avoidance in the Cray T3E 
14.7 Bibliographic Notes 
14.8 Exercises 

Chapter 15 Quality of Service 
15.1 Service Classes and Service Contracts 
15.2 Burstiness and Network Delays 
15.3 Implementation of Guaranteed Services 
15.4 Implementation of Best-Effort Services 
15.5 Separation of Resources 
15.6 Case Study: ATM Service Classes 
15.7 Case Study: Virtual Networks in the Avici TSR 
15.8 Bibliographic Notes 
15.9 Exercises 

Chapter 16 Router Architecture 
16.1 Basic Router Architecture 
16.2 Stalls 
16.3 Closing the Loop with Credits 
16.4 Reallocating a Channel 
16.5 Speculation and Lookahead 
16.6 Flit and Credit Encoding 
16.7 Case Study: The Alpha 21364 Router 
16.8 Bibliographic Notes 
16.9 Exercises 

Chapter 17 Router Datapath Components 
17.1 Input Buffer Organization 
17.2 Switches 
17.3 Output Organization 
17.4 Case Study: The Datapath of the IBM Colony
Router 
17.5 Bibliographic Notes 
17.6 Exercises 

Chapter 18 Arbitration 
18.1 Arbitration Timing 
18.2 Fairness 
18.3 Fixed Priority Arbiter 
18.4 Variable Priority Iterative Arbiters 
18.5 Matrix Arbiter 
18.6 Queuing Arbiter 
18.7 Exercises 

Chapter 19 Allocation 
19.1 Representations
19.2 Exact Algorithms
19.3 Separable Allocators 
19.4 Wavefront Allocator 
19.5 Incremental vs. Batch Allocation 
19.6 Multistage Allocation 
19.7 Performance of Allocators 
19.8 Case Study: The Tiny Tera Allocator 
19.9 Bibliographic Notes 
19.10 Exercises

Chapter 20 Network Interfaces 
20.1 Processor-Network Interface 
20.2 Shared-Memory Interface 
20.3 Line-Fabric Interface 
20.4 Case Study: The MIT M-Machine Network Interface 
20.5 Bibliographic Notes 
20.6 Exercises 

Chapter 21 Error Control 411
21.1 Know Thy Enemy: Failure Modes and Fault Models 
21.2 The Error Control Process: Detection, Containment,
and Recovery 
21.3 Link Level Error Control 
21.4 Router Error Control 
21.5 Network-Level Error Control 
21.6 End-to-end Error Control 
21.7 Bibliographic Notes 
21.8 Exercises 

Chapter 22 Buses 
22.1 Bus Basics 
22.2 Bus Arbitration 
22.3 High Performance Bus Protocol 
22.4 From Buses to Networks 
22.5 Case Study: The PCI Bus 
22.6 Bibliographic Notes 
22.7 Exercises 

Chapter 23 Performance Analysis 
23.1 Measures of Interconnection Network Performance 
23.2 Analysis 
23.3 Validation
23.4 Case Study: Efficiency and Loss in the
BBN Monarch Network 
23.5 Bibliographic Notes 
23.6 Exercises 

Chapter 24 Simulation 
24.1 Levels of Detail 
24.2 Network Workloads 
24.3 Simulation Measurements 
24.4 Simulator Design 
24.5 Bibliographic Notes 
24.6 Exercises 

Chapter 25 Simulation Examples 495
25.1 Routing
25.2 Flow Control Performance 
25.3 Fault Tolerance 

Appendix A Nomenclature 
Appendix B Glossary 
Appendix C Network Simulator

Principles and Practices of Interconnection Networks

Information Theory and Reliable Communication

Wireless sensor network applications, similarly to other distributed systems, often require a scalable time synchronization service enabling data consistency and coordination. This paper describes the Flooding Time Synchronization Protocol (FTSP), especially tailored for applications requiring stringent precision on resource limited wireless platforms. The proposed time synchronization protocol uses low communication bandwidth and it is robust against node and link failures. The FTSP achieves its robustness by utilizing periodic flooding of synchronization messages, and implicit dynamic topology update. The unique high precision performance is reached by utilizing MAC-layer time-stamping and comprehensive error compensation including clock skew estimation. The sources of delays and uncertainties in message transmission are analyzed in detail and techniques are presented to mitigate their effects. The FTSP was implemented on the Berkeley Mica2 platform and evaluated in a 60-node, multi-hop setup. The average per-hop synchronization error was in the one microsecond range, which is markedly better than that of the existing RBS and TPSN algorithms.

/pdf/the-flooding-time-synchronization-protocol-2j5x8h86k4.pdf

The flooding time synchronization protocol

The objective of this paper is to give a comprehensive introduction to applied cryptography with an engineer or computer scientist in mind. The emphasis is on the knowledge needed to create practical systems which supports integrity, confidentiality, or authenticity. Topics covered includes an introduction to the concepts in cryptography, attacks against cryptographic systems, key use and handling, random bit generation, encryption modes, and message authentication codes. Recommendations on algorithms and further reading is given in the end of the paper. This paper should make the reader able to build, understand and evaluate system descriptions and designs based on the cryptographic components described in the paper.

[서평]「Applied Cryptography」

Implanted biomedical devices have the potential to revolutionize medicine. Smart sensors, which are created by combining sensing materials with integrated circuitry, are being considered for several biomedical applications such as a glucose level monitor or a retina prosthesis. These devices require the capability to communicate with an external computer system (base station) via a wireless interface. The limited power and computational capabilities of smart sensor based biological implants present research challenges in several aspects of wireless networking due to the need for having a bio-compatible, fault-tolerant, energy-efficient, and scalable design. Further, em bedding thesesensors in humans add additional requirements. For example, the wireless networking solutions should be ultra-safe and reliable, work trouble-free in different geographical locations (although implants are typically not expected to move; they shouldn't restrict the movements of their human host), and require minimal maintenance. This necessitates application-specific solutions which are vastly different from traditional solutions.In this paper, we describe the potential of biomedical smart sensors. We then explain the challenges for wireless networking of human-embedded smart sensor arrays and our preliminary approach for wireless networking of a retina prosthesis. Our aim is to motivate vigorous research in this area by illustrating the need for more application-specific and novel approaches toward developing wireless networking solutions for human-implanted smart sensors.

/pdf/research-challenges-in-wireless-networks-of-biomedical-1h60wksedg.pdf

Research challenges in wireless networks of biomedical sensors

While a wireless sensor network is deployed to monitor certain events and pinpoint their locations, the location information is intended only for legitimate users. However, an eavesdropper can monitor the traffic and deduce the approximate location of monitored objects in certain situations. We first describe a successful attack against the flooding-based phantom routing, proposed in the seminal work by Celal Ozturk, Yanyong Zhang, and Wade Trappe. Then, we propose GROW (Greedy Random Walk), a two-way random walk, i.e., from both source and sink, to reduce the chance an eavesdropper can collect the location information. We improve the delivery rate by using local broadcasting and greedy forwarding. Privacy protection is verified under a backtracking attack model. The message delivery time is a little longer than that of the broadcasting-based approach, but it is still acceptable if we consider the enhanced privacy preserving capability of this new approach. At the same time, the energy consumption is less than half the energy consumption of flooding-base phantom routing, which is preferred in a low duty cycle, environmental monitoring sensor network.

/pdf/preserving-source-location-privacy-in-monitoring-based-4p7oz8dviz.pdf

Preserving source location privacy in monitoring-based wireless sensor networks

Wireless sensor networks have become possible because of the on-going improvements in sensor technology and VLSI. One issue in smart sensor networks is achieving efficient operation because of the limited available power. For important classes of sensor networks, such as biomedical sensors, the locations of the sensing nodes are fixed and the placement can be pre-determined. In this paper, we consider the topology that best supports communication among these sensor nodes. We propose a power-aware routing protocol and simulate the performance, showing that our routing protocol adapts routes to the available power. This leads to a reduction in the total power used as well as more even power usage across nodes. We consider different routes and topologies, demonstrating the difference in performance and explaining the underlying causes.

/pdf/power-efficient-topologies-for-wireless-sensor-networks-53etwrvhp8.pdf

Power efficient topologies for wireless sensor networks

A network of biosensors can be implanted in a human body for health monitoring, diagnostics, or as a prosthetic device. Biosensors can be organized into clusters where most of the communication takes place within the clusters, and long range transmissions to the base station are performed by the cluster leader to reduce the energy cost. In some applications, the tissues are sensitive to temperature increase and may be damaged by the heat resulting from normal operations and the recharging of sensor nodes. Our work is the first to consider rotating the cluster leadership to minimize the heating effects on human tissues. We explore the factors that lead to temperature increase, and the process for calculating the specific absorption rate (SAR) and temperature increase of implanted biosensors by using the finite-difference time-domain (FDTD) method. We improve performance by rotating the cluster leader based on the leadership history and the sensor locations. We propose a simplified scheme, temperature increase potential, to efficiently predict the temperature increase in tissues surrounding implanted sensors. Finally, a genetic algorithm is proposed to exploit the search for an optimal temperature increase sequence.

Communication scheduling to minimize thermal effects of implanted biosensor networks in homogeneous tissue

A wireless sensor network (WSN) consists of sensors implanted in an environment for collecting and transmitting data regarding changes in the environment based on the requests from a controlling device (called base station) using wireless communication. WSNs are being used in medical, military, and environment monitoring applications. Broadcast (dissemination of information from a central node) and convergecast (gathering of information towards a central node) are important communication paradigms across all application domains. Most sensor applications involve both convergecasting and broadcasting. The time taken to complete either of them has to be kept minimal. This can be accomplished by constructing an efficient tree for both broadcasting as well as convergecasting and allocating wireless communication channels to ensure collision-free communication. There exist several works on broadcasting in multihop radio networks (a.k.a. ad hoc networks), which can also be used for broadcasting in WSNs. These algorithms construct a broadcast tree and compute a schedule for transmitting and receiving for each node to achieve collision-free broadcasting. In this paper, we show that we need a new algorithm for applications, which involve both convergecasting and broadcasting since the broadcast tree may not be efficient for convergecasting. So we propose a heuristic algorithm (convergecasting tree construction and channel allocation algorithm (CTCCAA)), which constructs a tree with schedules assigned to nodes for collision free convergecasting. The algorithm is capable of code allocation (direct sequence spread spectrum (DSSS)/ frequency hopping spread spectrum (FHSS)), in case multiple codes are available, to minimize the total duration required for convergecasting. We also show that the same tree can be used for broadcasting and is as efficient as a tree exclusively constructed for broadcasting.

Loren Schwiebert

Papers

Research challenges in wireless networks of biomedical sensors

Preserving source location privacy in monitoring-based wireless sensor networks

Power efficient topologies for wireless sensor networks

Communication scheduling to minimize thermal effects of implanted biosensor networks in homogeneous tissue

On tree-based convergecasting in wireless sensor networks