Metacomputing on clusters augmented with reconfigurable hardware

Accepted Version

Hardware design of cryptographic accelerators

With the rapid growth of the Internet and digital communications, the volume of sensitive electronic transactions being transferred and stored over and on insecure media has increased dramatically in recent years. The growing demand for cryptographic systems to secure this data, across a multitude of platforms, ranging from large servers to small mobile devices and smart cards, has necessitated research into low cost, flexible and secure solutions. As constraints on architectures such as area, speed and power become key factors in choosing a cryptosystem, methods for speeding up the development and evaluation process are necessary. This thesis investigates flexible hardware architectures for the main components of a cryptographic system. Dedicated hardware accelerators can provide significant performance improvements when compared to implementations on general purpose processors. Each of the designs proposed are analysed in terms of speed, area, power, energy and efficiency. Field Programmable Gate Arrays (FPGAs) are chosen as the development platform due to their fast development time and reconfigurable nature. Firstly, a reconfigurable architecture for performing elliptic curve point scalar multiplication on an FPGA is presented. Elliptic curve cryptography is one such method to secure data, offering similar security levels to traditional systems, such as RSA, but with smaller key sizes, translating into lower memory and bandwidth requirements. The architecture is implemented using different underlying algorithms and coordinates for dedicated Double-and-Add algorithms, twisted Edwards algorithms and SPA secure algorithms, and its power consumption and energy on an FPGA measured. Hardware implementation results for these new algorithms are compared against their software counterparts and the best choices for minimum area-time and area-energy circuits are then identified and examined for larger key and field sizes. Secondly, implementation methods for another component of a cryptographic system, namely hash functions, developed in the recently concluded SHA-3 hash competition are presented. Various designs from the three rounds of the NIST run competition are implemented on FPGA along with an interface to allow fair comparison of the different hash functions when operating in a standardised and constrained environment. Different methods of implementation for the designs and their subsequent performance is examined in terms of throughput, area and energy costs using various constraint metrics. Comparing many different implementation methods and algorithms is nontrivial. Another aim of this thesis is the development of generic interfaces used both to reduce implementation and test time and also to enable fair baseline comparisons of different algorithms when operating in a standardised and constrained environment. Finally, a hardware-software co-design cryptographic architecture is presented. This architecture is capable of supporting multiple types of cryptographic algorithms and is described through an application for performing public key cryptography, namely the Elliptic Curve Digital Signature Algorithm (ECDSA). This architecture makes use of the elliptic curve architecture and the hash functions described previously. These components, along with a random number generator, provide hardware acceleration for a Microblaze based cryptographic system. The trade-off in terms of performance for flexibility is discussed using dedicated software, and hardware-software co-design implementations of the elliptic curve point scalar multiplication block. Results are then presented in terms of the overall cryptographic system.

permGPU: Using graphics processing units in RNA microarray association studies.

BACKGROUND: Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. RESULTS: We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. CONCLUSIONS: permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

Efficient FPGA Hardware Development: A Multi-Language Approach

This paper presents a multi-language framework to FPGA hardware development which aims to satisfy the dual requirement of high-level hardware design and efficient hardware implementation. The central idea of this framework is the integration of different hardware languages in a way that harnesses the best features of each language. This is illustrated in this paper by the integration of two hardware languages in the form of HIDE: a structured hardware language which provides more abstract and elegant hardware descriptions and compositions than are possible in traditional hardware description languages such as VHDL or Verilog, and Handel-C: an ANSI C-like hardware language which allows software and hardware engineers alike to target FPGAs from high-level algorithmic descriptions. On the one hand, HIDE has proven to be very successful in the description and generation of highly optimised parameterisable FPGA circuits from geometric descriptions. On the other hand, Handel-C has also proven to be very successful in the rapid design and prototyping of FPGA circuits from algorithmic application descriptions. The proposed integrated framework hence harnesses HIDE for the generation of highly optimised circuits for regular parts of algorithms, while Handel-C is used as a top-level design language from which HIDE functionality is dynamically invoked. The overall message of this paper posits that there need not be an exclusive choice between different hardware design flows. Rather, an integrated framework where different design flows can seamlessly interoperate should be adopted. Although the idea might seem simple prima facie, it could have serious implications on the design of future generations of hardware languages.

BSP -Style Computation: A Semantic Investigation

A BSP (Bulk Synchronous Parallelism) computation is characterized by the generation of asynchronous messages in packages during independent execution of a number of processes and their subsequent delivery at synchronization points. Bundling messages together represents a significant departure from the traditional ‘one communication at a time’ approach. In this paper the semantic consequences of communication packaging are explored. In particular, the BSP communication structure is identified with a general form of substitution—predicate substitution. Predicate substitution provides a means of reasoning about the synchronized delivery of asynchronous communications when the immediate programming context does not explicitly refer to the variables that are to be updated (unlike traditional operations, such as the assignment $x := e$, where the names of the updated variables can be extracted from the context). Proofs of implementations of Newton's root finding method and prefix sum are used to illustrate the practical application of the proposed approach.

Hardware Performance Analysis of the SHACAL-2 Encryption Algorithm

A hardware performance analysis of the SHACAL-2 encryption algorithm is presented in this paper. SHACAL-2 was one of four symmetric key algorithms chosen in the New European Schemes for Signatures, Integrity and Encryption (NESSIE) initiative in 2003. The paper describes a fully pipelined encryption SHACAL-2 architecture implemented on a Xilinx Field Programmable Gate Array (FPGA) device that achieves a throughput of over 25 Gbps. This is the fastest private key encryption algorithm architecture currently available. The SHACAL-2 decryption algorithm is also defined in the paper as it was not provided in the NESSIE submission.