MC64-ClustalWP2: A Highly-Parallel Hybrid Strategy to Align Multiple Sequences in Many-Core Architectures

We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification/traceability), including the protected designation of origin, among other applications

An Efficient NoC-based Framework To Improve Dataflow Thread Management At Runtime

This doctoral thesis focuses on how the application threads that are based on dataflow execution model can be managed at Network-on-Chip (NoC) level. The roots of the dataflow execution model date back to the early 1970’s. Applications adhering to such program execution model follow a simple producer-consumer communication scheme for synchronising parallel thread related activities. In dataflow execution environment, a thread can run if and only if all its required inputs are available. Applications running on a large and complex computing environment can significantly benefit from the adoption of dataflow model. In the first part of the thesis, the work is focused on the thread distribution mechanism. It has been shown that how a scalable hash-based thread distribution mechanism can be implemented at the router level with low overheads. To enhance the support further, a tool to monitor the dataflow threads’ status and a simple, functional model is also incorporated into the design. Next, a software defined NoC has been proposed to manage the distribution of dataflow threads by exploiting its reconfigurability. The second part of this work is focused more on NoC microarchitecture level. Traditional 2D-mesh topology is combined with a standard ring, to understand how such hybrid network topology can outperform the traditional topology (such as 2D-mesh). Finally, a mixed-integer linear programming based analytical model has been proposed to verify if the application threads mapped on to the free cores is optimal or not. The proposed mathematical model can be used as a yardstick to verify the solution quality of the newly developed mapping policy. It is not trivial to provide a complete low-level framework for dataflow thread execution for better resource and power management. However, this work could be considered as a primary framework to which improvements could be carried out

Efficient Adaptive Hard Real-time Multi-processor Systems

Modern computing systems are based on multi-processor systems, i.e. multiple cores on the same chip. Hard real-time systems are required to perform particular tasks within certain amount of time; failure to do so characterises an unaccepted behavior. Hard real-time systems are found in safety-critical applications, e.g. airbag control software, flight control software, etc. In safety-critical applications, failure to meet the real-time constraints can have catastrophic effects. The safe and, at the same time, efficient deployment of applications, with hard real-time constraints, on multi-processors is a challenging task. Scheduling methods and Models of Computation, that provide safe deployments, require a realistic estimation of the Worst-Case Execution Time (WCET) of tasks. The simultaneous access of shared resources by parallel tasks, causes interference delays due to hardware arbitration. Interference delays can be accounted for, with the pessimistic assumption that all possible interference can happen. The resulting schedules would be exceedingly conservative, thus the benefits of multi-processor would be significantly negated. Producing less pessimistic schedules is challenging due to the inter-dependency between WCET estimation and deployment optimisation. Accurate estimation of interference delays -and thus estimation of task WCET- depends on the way an application is deployed; deployment is an optimisation problem that depends on the estimation of task WCET. Another efficiency gap, which is of consequence in several systems (e.g. airbag control), stems from the fact that rarely tasks execute with their WCET. Safe runtime adaptation based on the Actual Execution Times, can yield additional improvements in terms of latency (more responsive systems). To achieve efficiency and retain adaptability, we propose that interference analysis should be coupled with the deployment process. The proposed interference analysis method estimates the possible amount of interference, based on an architecture and an application model. As more information is provided, such as scheduling, memory mapping, etc, the per-task interference estimation becomes more accurate. Thus, the method computes interference-sensitive WCET estimations (isWCET). Based on the isWCET method, we propose a method to break the inter-dependency between WCET estimation and deployment optimisation. Initially, the isWCETs are over-approximated, by assuming worst-case interference, and a safe deployment is derived. Subsequently, the proposed method computes accurate isWCETs by spatio-temporal exclusion, i.e. excluding interferences from non-overlapping tasks that share resources (space). Based on accurate isWCETs, the deployment solution is improved to provide better latency guarantees. We also propose a distributed runtime adaptation technique, that aims to improve run-time latency. Using isWCET estimations restricts the possible adaptations, as an adaptation might increase the interference and violate the safety guarantees. The proposed technique introduces statically scheduling dependencies between tasks that prevent additional interference. At runtime, a self-timed scheduling policy that respects these dependencies, is applied, proven to be safe, and with minimal overhead. Experimental evaluation on Kalray MPPA-256 shows that our methods improve isWCET up to 36%, guaranteed latency up to 46%, runtime performance up to 42%, with a consolidated performance gain of 50%

Embedded Machine-Learning For Variable-Rate Fertiliser Systems: A Model-Driven Approach To Precision Agriculture

Efficient use of fertilisers, in particular the use of Nitrogen (N), is one of the rate-limiting factors in meeting global food production requirements. While N is a key driver in increasing crop yields, overuse can also lead to negative environmental and health impacts. It has been suggested that Variable-Rate Fertiliser (VRF) techniques may help to reduce excessive N applications. VRF seeks to spatially vary fertiliser input based on estimated crop requirements, however a major challenge in the operational deployment of VRF systems is the automated processing of large amounts of sensor data in real-time. Machine Learning (ML) algorithms have shown promise in their ability to process these large, high-velocity data streams, and to produce accurate predictions. The newly developed Fuzzy Boxes (FB) algorithm has been designed with VRF applications in mind, however no publicly available software implementation currently exists. Therefore, development of a prototype implementation of FB forms a component of this work. This thesis will also employ a Hardware-in-the-Loop (HWIL) testing methodology using a potential target device in order to simulate a real-world VRF deployment environment. By using this environment simulation, two existing ML algorithms (Artificial Neural Network (ANN) and Support Vector Machine (SVM)) can be compared against the prototype implementation of FB for applicability to VRF applications. It will be shown that all tested algorithms could potentially be suitable for high-speed VRF when measured on prediction time and various accuracy metrics. All algorithms achieved higher than 84.5% accuracy, with FB20 reaching 87.21%. Prediction times were highly varied; the fastest average predictor was an ANN (16.64μs), while the slowest was FB20(502.77μs). All average prediction times were fast enough to achieve a spatial resolution of 31 mm when operating at 60 m/s, making all tested algorithms fast enough predictors for VRF applications

Reconfigurable Antenna Systems: Platform implementation and low-power matters

Antennas are a necessary and often critical component of all wireless systems, of which they share the ever-increasing complexity and the challenges of present and emerging trends. 5G, massive low-orbit satellite architectures (e.g. OneWeb), industry 4.0, Internet of Things (IoT), satcom on-the-move, Advanced Driver Assistance Systems (ADAS) and Autonomous Vehicles, all call for highly flexible systems, and antenna reconfigurability is an enabling part of these advances. The terminal segment is particularly crucial in this sense, encompassing both very compact antennas or low-profile antennas, all with various adaptability/reconfigurability requirements. This thesis work has dealt with hardware implementation issues of Radio Frequency (RF) antenna reconfigurability, and in particular with low-power General Purpose Platforms (GPP); the work has encompassed Software Defined Radio (SDR) implementation, as well as embedded low-power platforms (in particular on STM32 Nucleo family of micro-controller). The hardware-software platform work has been complemented with design and fabrication of reconfigurable antennas in standard technology, and the resulting systems tested. The selected antenna technology was antenna array with continuously steerable beam, controlled by voltage-driven phase shifting circuits. Applications included notably Wireless Sensor Network (WSN) deployed in the Italian scientific mission in Antarctica, in a traffic-monitoring case study (EU H2020 project), and into an innovative Global Navigation Satellite Systems (GNSS) antenna concept (patent application submitted). The SDR implementation focused on a low-cost and low-power Software-defined radio open-source platform with IEEE 802.11 a/g/p wireless communication capability. In a second embodiment, the flexibility of the SDR paradigm has been traded off to avoid the power consumption associated to the relevant operating system. Application field of reconfigurable antenna is, however, not limited to a better management of the energy consumption. The analysis has also been extended to satellites positioning application. A novel beamforming method has presented demonstrating improvements in the quality of signals received from satellites. Regarding those who deal with positioning algorithms, this advancement help improving precision on the estimated position

Systematic Design Space Exploration of Dynamic Dataflow Programs for Multi-core Platforms

The limitations of clock frequency and power dissipation of deep sub-micron CMOS technology have led to the development of massively parallel computing platforms. They consist of dozens or hundreds of processing units and offer a high degree of parallelism. Taking advantage of that parallelism and transforming it into high program performances requires the usage of appropriate parallel programming models and paradigms. Currently, a common practice is to develop parallel applications using methods evolving directly from sequential programming models. However, they lack the abstractions to properly express the concurrency of the processes. An alternative approach is to implement dataflow applications, where the algorithms are described in terms of streams and operators thus their parallelism is directly exposed. Since algorithms are described in an abstract way, they can be easily ported to different types of platforms. Several dataflow models of computation (MoCs) have been formalized so far. They differ in terms of their expressiveness (ability to handle dynamic behavior) and complexity of analysis. So far, most of the research efforts have focused on the simpler cases of static dataflow MoCs, where many analyses are possible at compile-time and several optimization problems are greatly simplified. At the same time, for the most expressive and the most difficult to analyze dynamic dataflow (DDF), there is still a dearth of tools supporting a systematic and automated analysis minimizing the programming efforts of the designer. The objective of this Thesis is to provide a complete framework to analyze, evaluate and refactor DDF applications expressed using the RVC-CAL language. The methodology relies on a systematic design space exploration (DSE) examining different design alternatives in order to optimize the chosen objective function while satisfying the constraints. The research contributions start from a rigorous DSE problem formulation. This provides a basis for the definition of a complete and novel analysis methodology enabling systematic performance improvements of DDF applications. Different stages of the methodology include exploration heuristics, performance estimation and identification of refactoring directions. All of the stages are implemented as appropriate software tools. The contributions are substantiated by several experiments performed with complex dynamic applications on different types of physical platforms

Improving Model-Based Software Synthesis: A Focus on Mathematical Structures

Computer hardware keeps increasing in complexity. Software design needs to keep up with this. The right models and abstractions empower developers to leverage the novelties of modern hardware. This thesis deals primarily with Models of Computation, as a basis for software design, in a family of methods called software synthesis. We focus on Kahn Process Networks and dataflow applications as abstractions, both for programming and for deriving an efficient execution on heterogeneous multicores. The latter we accomplish by exploring the design space of possible mappings of computation and data to hardware resources. Mapping algorithms are not at the center of this thesis, however. Instead, we examine the mathematical structure of the mapping space, leveraging its inherent symmetries or geometric properties to improve mapping methods in general. This thesis thoroughly explores the process of model-based design, aiming to go beyond the more established software synthesis on dataflow applications. We starting with the problem of assessing these methods through benchmarking, and go on to formally examine the general goals of benchmarks. In this context, we also consider the role modern machine learning methods play in benchmarking. We explore different established semantics, stretching the limits of Kahn Process Networks. We also discuss novel models, like Reactors, which are designed to be a deterministic, adaptive model with time as a first-class citizen. By investigating abstractions and transformations in the Ohua language for implicit dataflow programming, we also focus on programmability. The focus of the thesis is in the models and methods, but we evaluate them in diverse use-cases, generally centered around Cyber-Physical Systems. These include the 5G telecommunication standard, automotive and signal processing domains. We even go beyond embedded systems and discuss use-cases in GPU programming and microservice-based architectures

An automated OpenCL FPGA compilation framework targeting a configurable, VLIW chip multiprocessor

Modern system-on-chips augment their baseline CPU with coprocessors and accelerators to increase overall computational capacity and power efficiency, and thus have evolved into heterogeneous systems. Several languages have been developed to enable this paradigm shift, including CUDA and OpenCL. This thesis discusses a unified compilation environment to enable heterogeneous system design through the use of OpenCL and a customised VLIW chip multiprocessor (CMP) architecture, known as the LE1. An LLVM compilation framework was researched and a prototype developed to enable the execution of OpenCL applications on the LE1 CPU. The framework fully automates the compilation flow and supports work-item coalescing to better utilise the CPU cores and alleviate the effects of thread divergence. This thesis discusses in detail both the software stack and target hardware architecture and evaluates the scalability of the proposed framework on a highly precise cycle-accurate simulator. This is achieved through the execution of 12 benchmarks across 240 different machine configurations, as well as further results utilising an incomplete development branch of the compiler. It is shown that the problems generally scale well with the LE1 architecture, up to eight cores, when the memory system becomes a serious bottleneck. Results demonstrate superlinear performance on certain benchmarks (x9 for the bitonic sort benchmark with 8 dual-issue cores) with further improvements from compiler optimisations (x14 for bitonic with the same configuration