Computer-aided programming for multiprocessing systems

As both the number of processors and the complexity of problems to be solved increase, programming multiprocessing systems becomes more difficult and error-prone. This report discusses parallel models of computation and tools for computer-aided programming (CAP). Program development tools are necessary since programmers are not able to develop complex parallel programs efficiently. In particular, a CAP tool, named Hypertool, is described here. It performs scheduling and handles the communication primitive insertion automatically so that many errors are eliminated. It also generates the performance estimates and other program quality measures to help programmers in improving their algorithms and programs. Experiments have shown that up to a 300% performance improvement can be achieved by computer-aided programming

AutoParallel: A Python module for automatic parallelization and distributed execution of affine loop nests

The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax, automatic memory management and garbage collection, which simplifies code re-usage through library packages, and easily configurable tools for deployment. For instance, Python has risen to the top of the list of the programming languages due to the simplicity of its syntax, while still achieving a good performance even being an interpreted language. Moreover, the community has helped to develop a large number of libraries and modules, tuning them to obtain great performance. However, there is still room for improvement when preventing users from dealing directly with distributed and parallel computing issues. This paper proposes and evaluates AutoParallel, a Python module to automatically find an appropriate task-based parallelization of affine loop nests to execute them in parallel in a distributed computing infrastructure. This parallelization can also include the building of data blocks to increase task granularity in order to achieve a good execution performance. Moreover, AutoParallel is based on sequential programming and only contains a small annotation in the form of a Python decorator so that anyone with little programming skills can scale up an application to hundreds of cores.Comment: Accepted to the 8th Workshop on Python for High-Performance and Scientific Computing (PyHPC 2018

GPU acceleration for statistical gene classification

The use of Bioinformatic tools in routine clinical diagnostics is still facing a number of issues. The more complex and advanced bioinformatic tools become, the more performance is required by the computing platforms. Unfortunately, the cost of parallel computing platforms is usually prohibitive for both public and small private medical practices. This paper presents a successful experience in using the parallel processing capabilities of Graphical Processing Units (GPU) to speed up bioinformatic tasks such as statistical classification of gene expression profiles. The results show that using open source CUDA programming libraries allows to obtain a significant increase in performances and therefore to shorten the gap between advanced bioinformatic tools and real medical practic

Experimenting with independent and-parallel prolog using standard prolog

This paper presents an approximation to the study of parallel systems using sequential tools. The Independent And-parallelism in Prolog is an example of parallel processing paradigm in the framework of logic programming, and implementations like <fc-Prolog uncover the potential performance of parallel processing. But this potential can also be explored using only sequential systems. Being the spirit of this paper to show how this can be done with a standard system, only standard Prolog will be used in the implementations included. Such implementations include tests for parallelism in And-Prolog, a correctnesschecking meta-interpreter of <fc-Prolog and a simulator of parallel execution for <fc-Prolog

Dataflow development of medium-grained parallel software

PhD ThesisIn the 1980s, multiple-processor computers (multiprocessors) based on conven- tional processing elements emerged as a popular solution to the continuing demand for ever-greater computing power. These machines offer a general-purpose parallel processing platform on which the size of program units which can be efficiently executed in parallel - the "grain size" - is smaller than that offered by distributed computing environments, though greater than that of some more specialised architectures. However, programming to exploit this medium-grained parallelism remains difficult. Concurrent execution is inherently complex, yet there is a lack of programming tools to support parallel programming activities such as program design, implementation, debugging, performance tuning and so on. In helping to manage complexity in sequential programming, visual tools have often been used to great effect, which suggests one approach towards the goal of making parallel programming less difficult. This thesis examines the possibilities which the dataflow paradigm has to offer as the basis for a set of visual parallel programming tools, and presents a dataflow notation designed as a framework for medium-grained parallel programming. The implementation of this notation as a programming language is discussed, and its suitability for the medium-grained level is examinedScience and Engineering Research Council of Great Britain EC ERASMUS schem

GPU cards as a low cost solution for efficient and fast classification of high dimensional gene expression datasets

The days when bioinformatics tools will be so reliable to become a standard aid in routine clinical diagnostics are getting very close. However, it is important to remember that the more complex and advanced bioinformatics tools become, the more performances are required by the computing platforms. Unfortunately, the cost of High Performance Computing (HPC) platforms is still prohibitive for both public and private medical practices. Therefore, to promote and facilitate the use of bioinformatics tools it is important to identify low-cost parallel computing solutions. This paper presents a successful experience in using the parallel processing capabilities of Graphical Processing Units (GPU) to speed up classification of gene expression profiles. Results show that using open source CUDA programming libraries allows to obtain a significant increase in performances and therefore to shorten the gap between advanced bioinformatics tools and real medical practic

Experiences on the characterization of parallel applications in embedded systems with Extrae/Paraver

Cutting-edge functionalities in embedded systems require the use of parallel architectures to meet their performance requirements. This imposes the introduction of a new layer in the software stacks of embedded systems: the parallel programming model. Unfortunately, the tools used to analyze embedded systems fall short to characterize the performance of parallel applications at a parallel programming model level, and correlate this with information about non-functional requirements such as real-time, energy, memory usage, etc. HPC tools, like Extrae, are designed with that level of abstraction in mind, but their main focus is on performance evaluation. Overall, providing insightful information about the performance of parallel embedded applications at the parallel programming model level, and relate it to the non-functional requirements, is of paramount importance to fully exploit the performance capabilities of parallel embedded architectures. This paper contributes to the state-of-the-art of analysis tools for embedded systems by: (1) analyzing the particular constraints of embedded systems compared to HPC systems (e.g., static setting, restricted memory, limited drivers) to support HPC analysis tools; (2) porting Extrae, a powerful tracing tool from the HPC domain, to the GR740 platform, a SoC used in the space domain; and (3) augmenting Extrae with new features needed to correlate the parallel execution with the following non-functional requirements: energy, temperature and memory usage. Finally, the paper presents the usefulness of Extrae to characterize OpenMP applications and its non-functional requirements, evaluating different aspects of the applications running in the GR740.This work has been partially funded from the HP4S (High Performance Parallel Payload Processing for Space) project under the ESA-ESTEC ITI contract № 4000124124/18/NL/CRS.Peer ReviewedPostprint (author's final draft

Parallel Computing in Java

The Java programming language and environment is inspiring new research activities in many areas of computing, of which parallel computing is one of the major interests. Parallel techniques are themselves finding new uses in cluster computing systems. Although there are excellent software tools for scheduling, monitoring and message-based programming on parallel clusters, these systems are not yet well integrated and do not provide very high-level parallel programming support. This research presents a number of issues which are considered to be key to the suitability of Java for HPC (High Performance Computing) applications and then explore the support for concurrency in the current Java 1.8 specification. We further present various relatively recent parallel Java models which support HPC for both shared and distributed memory programming paradigms. Finally, we attempt to evaluate the performance of discussed Java HPC models by comparing the same with the relative traditional native C implementations, where appropriate. The analysis of the results suggest that Java can achieve near similar performance to natively compiled languages, both for sequential and parallel applications, thus making it a viable alternative for HPC programming