A bibliography on parallel and vector numerical algorithms

This is a bibliography of numerical methods. It also includes a number of other references on machine architecture, programming language, and other topics of interest to scientific computing. Certain conference proceedings and anthologies which have been published in book form are listed also

A VLSI synthesis of a Reed-Solomon processor for digital communication systems

The Reed-Solomon codes have been widely used in digital communication systems such as computer networks, satellites, VCRs, mobile communications and high- definition television (HDTV), in order to protect digital data against erasures, random and burst errors during transmission. Since the encoding and decoding algorithms for such codes are computationally intensive, special purpose hardware implementations are often required to meet the real time requirements. -- One motivation for this thesis is to investigate and introduce reconfigurable Galois field arithmetic structures which exploit the symmetric properties of available architectures. Another is to design and implement an RS encoder/decoder ASIC which can support a wide family of RS codes. -- An m-programmable Galois field multiplier which uses the standard basis representation of the elements is first introduced. It is then demonstrated that the exponentiator can be used to implement a fast inverter which outperforms the available inverters in GF(2m). Using these basic structures, an ASIC design and synthesis of a reconfigurable Reed-Solomon encoder/decoder processor which implements a large family of RS codes is proposed. The design is parameterized in terms of the block length n, Galois field symbol size m, and error correction capability t for the various RS codes. The design has been captured using the VHDL hardware description language and mapped onto CMOS standard cells available in the 0.8-µm BiCMOS design kits for Cadence and Synopsys tools. The experimental chip contains 218,206 logic gates and supports values of the Galois field symbol size m = 3,4,5,6,7,8 and error correction capability t = 1,2,3, ..., 16. Thus, the block length n is variable from 7 to 255. Error correction t and Galois field symbol size m are pin-selectable. -- Since low design complexity and high throughput are desired in the VLSI chip, the algebraic decoding technique has been investigated instead of the time or transform domain. The encoder uses a self-reciprocal generator polynomial which structures the codewords in a systematic form. At the beginning of the decoding process, received words are initially stored in the first-in-first-out (FIFO) buffer as they enter the syndrome module. The Berlekemp-Massey algorithm is used to determine both the error locator and error evaluator polynomials. The Chien Search and Forney's algorithms operate sequentially to solve for the error locations and error values respectively. The error values are exclusive or-ed with the buffered messages in order to correct the errors, as the processed data leave the chip

Solution of partial differential equations on vector and parallel computers

The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed

Descriptional complexity of cellular automata and decidability questions

We study the descriptional complexity of cellular automata (CA), a parallel model of computation. We show that between one of the simplest cellular models, the realtime-OCA. and "classical" models like deterministic finite automata (DFA) or pushdown automata (PDA), there will be savings concerning the size of description not bounded by any recursive function, a so-called nonrecursive trade-off. Furthermore, nonrecursive trade-offs are shown between some restricted classes of cellular automata. The set of valid computations of a Turing machine can be recognized by a realtime-OCA. This implies that many decidability questions are not even semi decidable for cellular automata. There is no pumping lemma and no minimization algorithm for cellular automata

Modeling, Design, and Analysis of MagnetoElastic NML Circuits

With the predicted end of CMOS scaling process, researchers started to study several alternative technologies. Among them NanoMagnet Logic (NML) offers advantages complementary to MOS transistors especially for its magnetic nature. Its intrinsic memory capability makes it suitable for zero stand-by power and logic-in-memory applications. NML requires a clock system that, if based on a magnetic field, highly increases the circuit dynamic power consumption. We have recently proposed a solution based on the magnetoelastic effect (ME-NML) [1] and on currently available fabrication processes, which drastically reduces dynamic power consumption. However, many questions still remain unanswered. Which kind of applications are best suited for this technology? How can we effectively design, analyze, and compare ME-NML circuits? Does it really offer advantages over state-of-the-art CMOS transistors? In this paper, we provide answers to all these questions and the results prove that this technology offers indeed extremely good performance. We have designed a Galois field multiplier with a systolic array structure to reduce interconnection overhead. We developed a new RTL model that allows us to easily describe and simulate circuits of any complexity, evaluating at the same time the performance and keeping into account technology constraints. We approach for the first time in the NML scenario the design of ME-NML circuits adopting the standard-cell method used in standard technologies and fulfill the design down to the physical level. The same circuit is designed also with NML technology based on magnetic fields and with a 28 nm low power CMOS bulk technology for comparison. The CMOS circuit is obtained through physical place&route with a commercial tool, providing, therefore, the most accurate comparison ever presented in literature. Power analysis shows that ME-NML circuits have a considerable advantage over both NML and state-of-the-art CMOS bulk technology. As a further by-product results clearly highlight which kind of architectures can better exploit the true potential of NML technology

Architectural Solutions for NanoMagnet Logic

The successful era of CMOS technology is coming to an end. The limit on minimum fabrication dimensions of transistors and the increasing leakage power hinder the technological scaling that has characterized the last decades. In several different ways, this problem has been addressed changing the architectures implemented in CMOS, adopting parallel processors and thus increasing the throughput at the same operating frequency. However, architectural alternatives cannot be the definitive answer to a continuous increase in performance dictated by Moore’s law. This problem must be addressed from a technological point of view. Several alternative technologies that could substitute CMOS in next years are currently under study. Among them, magnetic technologies such as NanoMagnet Logic (NML) are interesting because they do not dissipate any leakage power. More- over, magnets have memory capability, so it is possible to merge logic and memory in the same device. However, magnetic circuits, and NML in this specific research, have also some important drawbacks that need to be addressed: first, the circuit clock frequency is limited to 100 MHz, to avoid errors in data propagation; second, there is a connection between circuit layout and timing, and in particular, longer wires will have longer latency. These drawbacks are intrinsic to the technology and for this reason they cannot be avoided. The only chance is to limit their impact from an architectural point of view. The first step followed in the research path of this thesis is indeed the choice and optimization of architectures able to deal with the problems of NML. Systolic Ar- rays are identified as an ideal solution for this technology, because they are regular structures with local interconnections that limit the long latency of wires; more- over they are composed of several Processing Elements that work in parallel, thus exploit parallelization to increase throughput (limiting the impact of the low clock frequency). Through the analysis of Systolic Arrays for NML, several possible im- provements have been identified and addressed: 1) it has been defined a rigorous way to increase throughput with interleaving, providing equations that allow to esti- mate the number of operations to be interleaved and the rules to provide inputs; 2) a latency insensitive circuit has been designed, that exploits a data communication protocol between processing elements to avoid data synchronization problems. This feature has been exploited to design a latency insensitive Systolic Array that is able to execute the Floyd-Steinberg dithering algorithm. All the improvements presented in this framework apply to Systolic Arrays implemented in any technology. So, they can also be exploited to increase performance of today’s CMOS parallel circuits. This research path is presented in Chapter 3. While Systolic Arrays are an interesting solution for NML, their usage could be quite limited because they are normally application-specific. The second re- search path addresses this problem. A Reconfigurable Systolic Array is presented, that can be programmed to execute several algorithms. This architecture has been tested implementing many algorithms, including FIR and IIR filters, Discrete Cosine Transform and Matrix Multiplication. This research path is presented in Chapter 4. In common Von Neumann architectures, the logic part of the circuit and the memory one are separated. Today bus communication between logic and memory represents the bottleneck of the system. This problem is addressed presenting Logic- In-Memory (LIM), an architecture where memory elements are merged in logic ones. This research path aims at defining a real LIM architectures. This has been done in two steps. The first step is represented by an architecture composed of three layers: memory, routing and logic. In the second step instead the routing plane is no more present, and its features are inherited by the memory plane. In this solution, a pyramidal memory model is used, where memories near logic elements contain the most probably used data, and other memory layers contain the remaining data and instruction set. This circuit has been tested with odd-even sort algorithms and it has been benchmarked against GPUs and ASIC. This research path is presented in Chapter 5. MagnetoElastic NML (ME-NML) is a technological improvement of the NML principle, proposed by researchers of Politecnico di Torino, where the clock system is based on the induced stretch of a piezoelectric substrate when a voltage is ap- plied to its boundaries. The main advantage of this solution is that it consumes much less power than the classic clock implementation. This technology has not yet been investigated from an architectural point of view and considering complex circuits. In this research field, a standard methodology for the design of ME-NML circuits has been proposed. It is based on a Standard Cell Library and an enhanced VHDL model. The effectiveness of this methodology has been proved designing a Galois Field Multiplier. Moreover the serial-parallel trade-off in ME-NML has been investigated, designing three different solutions for the Multiply and Accumulate structure. This research path is presented in Chapter 6. While ME-NML is an extremely interesting technology, it needs to be combined with other faster technologies to have a real competitive system. Signal interfaces between NML and other technologies (mainly CMOS) have been rarely presented in literature. A mixed-technology multiplexer is designed and presented as the basis for a CMOS to NML interface. The reverse interface (from ME-NML to CMOS) is instead based on a sensing circuit for the Faraday effect: a change in the polarization of a magnet induces an electric field that can be used to generate an input signal for a CMOS circuit. This research path is presented in Chapter 7. The research work presented in this thesis represents a fundamental milestone in the path towards nanotechnologies. The most important achievement is the de- sign and simulation of complex circuits with NML, benchmarking this technology with real application examples. The characterization of a technology considering complex functions is a major step to be performed and that has not yet been ad- dressed in literature for NML. Indeed, only in this way it is possible to intercept in advance any weakness of NanoMagnet Logic that cannot be discovered consid- ering only small circuits. Moreover, the architectural improvements introduced in this thesis, although technology-driven, can be actually applied to any technology. We have demonstrated the advantages that can derive applying them to CMOS cir- cuits. This thesis represents therefore a major step in two directions: the first is the enhancement of NML technology; the second is a general improvement of parallel architectures and the development of the new Logic-In-Memory paradigm

On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics

The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the FastFlow parallel programming framework, are shown on a simulation tool to perform the modeling, the tuning, and the sensitivity analysis of stochastic biological models. A stochastic simulation needs thousands of independent simulation trajectories turning into big data that should be analysed by statistic and data mining tools. In the considered approach the two stages are pipelined in such a way that the simulation stage streams out the partial results of all simulation trajectories to the analysis stage that immediately produces a partial result. The simulation-analysis workflow is validated for performance and effectiveness of the online analysis in capturing biological systems behavior on a multicore platform and representative proof-of-concept biological systems. The exploited methodologies include pattern-based parallel programming and data streaming that provide key features to the software designers such as performance portability and efficient in-memory (big) data management and movement. Two paradigmatic classes of biological systems exhibiting multistable and oscillatory behavior are used as a testbed