Productive Programming Systems for Heterogeneous Supercomputers

The majority of today's scientific and data analytics workloads are still run on relatively energy inefficient, heavyweight, general-purpose processing cores, often referred to in the literature as latency-oriented architectures. The flexibility of these architectures and the programmer aids included (e.g. large and deep cache hierarchies, branch prediction logic, pre-fetch logic) makes them flexible enough to run a wide range of applications fast. However, we have started to see growth in the use of lightweight, simpler, energy-efficient, and functionally constrained cores. These architectures are commonly referred to as throughput-oriented. Within each shared memory node, the computational backbone of future throughput-oriented HPC machines will consist of large pools of lightweight cores. The first wave of throughput-oriented computing came in the mid 2000's with the use of GPUs for general-purpose and scientific computing. Today we are entering the second wave of throughput-oriented computing, with the introduction of NVIDIA Pascal GPUs, Intel Knights Landing Xeon Phi processors, the Epiphany Co-Processor, the Sunway MPP, and other throughput-oriented architectures that enable pre-exascale computing. However, while the majority of the FLOPS in designs for future HPC systems come from throughput-oriented architectures, they are still commonly paired with latency-oriented cores which handle management functions and lightweight/un-parallelizable computational kernels. Hence, most future HPC machines will be heterogeneous in their processing cores. However, the heterogeneity of future machines will not be limited to the processing elements. Indeed, heterogeneity will also exist in the storage, networking, memory, and software stacks of future supercomputers. As a result, it will be necessary to combine many different programming models and libraries in a single application. How to do so in a programmable and well-performing manner is an open research question. This thesis addresses this question using two approaches. First, we explore using managed runtimes on HPC platforms. As a result of their high-level programming models, these managed runtimes have a long history of supporting data analytics workloads on commodity hardware, but often come with overheads which make them less common in the HPC domain. Managed runtimes are also not supported natively on throughput-oriented architectures. Second, we explore the use of a modular programming model and work-stealing runtime to compose the programming and scheduling of multiple third-party HPC libraries. This approach leverages existing investment in HPC libraries, unifies the scheduling of work on a platform, and is designed to quickly support new programming model and runtime extensions. In support of these two approaches, this thesis also makes novel contributions in tooling for future supercomputers. We demonstrate the value of checkpoints as a software development tool on current and future HPC machines, and present novel techniques in performance prediction across heterogeneous cores

A design method for supporting the development and integration of ARTful global schedulers into multiple programming models

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Ciência da Computação, Florianópolis, 2019.Plataformas de execução em ambientes de alto desempenho estão tornando-se cada vez mais diversas com o desenvolvimento de novas arquiteturas e ferramentas para se beneficiar do paralelismo inerente das aplicações. Estas novas opções de ferramentas oferecem possibilidades de melhoria no desempenho de aplicações científicas e de engenharia. A crescente gama de plataformas torna mais complexa a distribuição das tarefas da aplicação no ambiente, passo que deve ser gerido pelos sistemas de execução e seus balanceadores de carga, de modo a não prejudicar a portabilidade da aplicação. No entanto, o desenvolvimento e implantação de novos escalonadores de tarefas em sistemas amplamente utilizados na indústria como OpenMP e MPI sofrem com a falta de suporte de frameworks. Este trabalho propõe uma biblioteca, MOGSLib, para auxiliar o desenvolvimento e implantação de escalonadores globais em diferentes sistemas de execução de alto desempenho. MOGSLib aplica abstrações reutilizáveis, independentes e testáveis na forma de classes template em C++ para representar as políticas de escalonamento, sua relação com o sistema de execução e a taxonomia da solução de escalonamento. Nós avaliamos o sobrecusto de nossas estratégias portáveis em comparação com suas versões nativas nos sistemas de execução em dois ambientes distintos, os sistemas Charm++ e OpenMP. Em nosso experimentos, conseguimos dar suporte à definição de estratégias de escalonamento do usuário e sua implantação como escalonadores de laço na LibGOMP e balanceadores de carga no Charm++ através da seleção de implementação das abstrações que os compõem. Nós verificamos que nossas versões dos escalonadores oferecem tempos de execução de aplicação equivalentes aos balanceadores nativos para a classe de escalonadores centralizados e cientes de carga aplicados em kernels de dinâmica molecular. Por fim, a flexibilidade de incorporar funcionalidades e políticas de escalonamento do usuário em sistemas de execução com modificações limitadas nos códigos de sistemas de execução mostra que é possível construir balanceadores de carga flexíveis com pouco sobrecusto até para ambientes de alto desempenho.Abstract: Execution platforms for high performance computing are becoming diverse as a result of new architectures and tools to benefit from the parallel behavior of applications. These new options showcase performance enhancing opportunities for scientific and engineering applications. The execution platform diversity and the mapping of an application's tasks must be implicitly handled by runtime systems and their global schedulers as to enable the application performance and implementation portability. However, the development and integration of novel global schedulers into industry standards systems like OpenMP and MPI lack framework support. This work proposes a library, MOGSLib, to support the development and integration of global schedulers into different high performance runtime systems. MOGSLib employs reusable, independent and testable abstractions represented as C++ template structures to express scheduling policies, their relationship to runtime systems and the scheduling solution taxonomy. This approach allows a bottom-up development process based on the incremental composition of abstractions through template specializations. We evaluate the overhead of employing our portable policies in comparison to their system-native counterparts in two environments, the Charm++ and OpenMP systems. Throughout our experiments we achieved development support for user-defined scheduling policies that can be implanted both as loop schedulers in LibGOMP and load balancers in Charm++ through the selection of abstraction implementations. We leveraged the overhead by employing workload-aware policies on molecular dynamics kernels which resulted in equivalent application makespan for both native and the MOGSLib scheduler versions. Ultimately, the flexibility to incorporate user-defined structures and scheduling policies into runtime systems with limited alterations into runtime system code bases hint that the definition of flexible global schedulers is available with neglible overheads even for high performance environments

TEXTAROSSA: Towards EXtreme scale Technologies and Accelerators for euROhpc hw/Sw Supercomputing Applications for exascale

To achieve high performance and high energy efficiency on near-future exascale computing systems, three key technology gaps needs to be bridged. These gaps include: energy efficiency and thermal control; extreme computation efficiency via HW acceleration and new arithmetics; methods and tools for seamless integration of reconfigurable accelerators in heterogeneous HPC multi-node platforms. TEXTAROSSA aims at tackling this gap through a co-design approach to heterogeneous HPC solutions, supported by the integration and extension of HW and SW IPs, programming models and tools derived from European research.This work is supported by the TEXTAROSSA project G.A. n.956831, as part of the EuroHPC initiative.Peer ReviewedArticle signat per 51 autors/es: Giovanni Agosta, Daniele Cattaneo, William Fornaciari, Andrea Galimberti, Giuseppe Massari, Federico Reghenzani, Federico Terraneo, Davide Zoni, Carlo Brandolese (DEIB – Politecnico di Milano, Italy, [email protected]) | Massimo Celino, Francesco Iannone, Paolo Palazzari, Giuseppe Zummo (ENEA, Italy, [email protected]) | Massimo Bernaschi, Pasqua D’Ambra (Istituto per le Applicazioni del Calcolo (IAC) - CNR, Italy, [email protected]) | Sergio Saponara, Marco Danelutto, Massimo Torquati (University of Pisa, Italy, [email protected]) | Marco Aldinucci, Yasir Arfat, Barbara Cantalupo, Iacopo Colonnelli, Roberto Esposito, Alberto R. Martinelli, Gianluca Mittone (University of Torino, Italy, [email protected]) | Olivier Beaumont, Berenger Bramas, Lionel Eyraud-Dubois, Brice Goglin, Abdou Guermouche, Raymond Namyst, Samuel Thibault (Inria - France, [email protected]) | Antonio Filgueras, Miquel Vidal, Carlos Alvarez, Xavier Martorell (BSC - Spain, [email protected]) | Ariel Oleksiak, Michal Kulczewski (PSNC, Poland, [email protected], [email protected]) | Alessandro Lonardo, Piero Vicini, Francesca Lo Cicero, Francesco Simula, Andrea Biagioni, Paolo Cretaro, Ottorino Frezza, Pier Stanislao Paolucci, Matteo Turisini (INFN Sezione di Roma - Italy, [email protected]) | Francesco Giacomini (INFN CNAF - Italy, [email protected]) | Tommaso Boccali (INFN Sezione di Pisa - Italy, [email protected]) | Simone Montangero (University of Padova and INFN Sezione di Padova - Italy, [email protected]) | Roberto Ammendola (INFN Sezione di Roma Tor Vergata - Italy, [email protected])Postprint (author's final draft

TEXTAROSSA: Towards EXtreme scale Technologies and Accelerators for euROhpc hw/Sw Supercomputing Applications for exascale

International audienceTo achieve high performance and high energy efficiency on near-future exascale computing systems, three key technology gaps needs to be bridged. These gaps include: energy efficiency and thermal control; extreme computation efficiency via HW acceleration and new arithmetics; methods andtools for seamless integration of reconfigurable accelerators in heterogeneous HPC multi-node platforms. TEXTAROSSA aims at tackling this gap through a co-design approach to heterogeneous HPC solutions, supported by the integration and extension of HW and SW IPs, programming models and tools derived from European research

Performance Observability and Monitoring of High Performance Computing with Microservices

Traditionally, High Performance Computing (HPC) softwarehas been built and deployed as bulk-synchronous, parallel executables based on the message-passing interface (MPI) programming model. The rise of data-oriented computing paradigms and an explosion in the variety of applications that need to be supported on HPC platforms have forced a re-think of the appropriate programming and execution models to integrate this new functionality. In situ workflows demarcate a paradigm shift in HPC software development methodologies enabling a range of new applications --- from user-level data services to machine learning (ML) workflows that run alongside traditional scientific simulations. By tracing the evolution of HPC software developmentover the past 30 years, this dissertation identifies the key elements and trends responsible for the emergence of coupled, distributed, in situ workflows. This dissertation's focus is on coupled in situ workflows involving composable, high-performance microservices. After outlining the motivation to enable performance observability of these services and why existing HPC performance tools and techniques can not be applied in this context, this dissertation proposes a solution wherein a set of techniques gathers, analyzes, and orients performance data from different sources to generate observability. By leveraging microservice components initially designed to build high performance data services, this dissertation demonstrates their broader applicability for building and deploying performance monitoring and visualization as services within an in situ workflow. The results from this dissertation suggest that: (1) integration of performance data from different sources is vital to understanding the performance of service components, (2) the in situ (online) analysis of this performance data is needed to enable the adaptivity of distributed components and manage monitoring data volume, (3) statistical modeling combined with performance observations can help generate better service configurations, and (4) services are a promising architecture choice for deploying in situ performance monitoring and visualization functionality. This dissertation includes previously published and co-authored material and unpublished co-authored material

Platforms for deployment of scalable on- and off-line data analytics.

The ability to exploit the intelligence concealed in bulk data to generate actionable insights is increasingly providing competitive advantages to businesses, government agencies, and charitable organisations. The burgeoning field of Data Science, and its related applications in the field of Data Analytics, finds broader applicability with each passing year. This expansion of users and applications is matched by an explosion in tools, platforms, and techniques designed to exploit more types of data in larger volumes, with more techniques, and at higher frequencies than ever before. This diversity in platforms and tools presents a new challenge for organisations aiming to integrate Data Science into their daily operations. Designing an analytic for a particular platform necessarily involves “lock-in” to that specific implementation – there are few opportunities for algorithmic portability. It is increasingly challenging to find engineers with experience in the diverse suite of tools available as well as understanding the precise details of the domain in which they work: the semantics of the data, the nature of queries and analyses to be executed, and the interpretation and presentation of results. The work presented in this thesis addresses these challenges by introducing a number of techniques to facilitate the creation of analytics for equivalent deployment across a variety of runtime frameworks and capabilities. In the first instance, this capability is demonstrated using the first Domain Specific Language and associated runtime environments to target multiple best-in-class frameworks for data analysis from the streaming and off-line paradigms. This capability is extended with a new approach to modelling analytics based around a semantically rich type system. An analytic planner using this model is detailed, thus empowering domain experts to build their own scalable analyses, without any specific programming or distributed systems knowledge. This planning technique is used to assemble complex ensembles of hybrid analytics: automatically applying multiple frameworks in a single workflow. Finally, this thesis demonstrates a novel approach to the speculative construction, compilation, and deployment of analytic jobs based around the observation of user interactions with an analytic planning system

Towards a Reference Architecture with Modular Design for Large-scale Genotyping and Phenotyping Data Analysis: A Case Study with Image Data

With the rapid advancement of computing technologies, various scientific research communities have been extensively using cloud-based software tools or applications. Cloud-based applications allow users to access software applications from web browsers while relieving them from the installation of any software applications in their desktop environment. For example, Galaxy, GenAP, and iPlant Colaborative are popular cloud-based systems for scientific workflow analysis in the domain of plant Genotyping and Phenotyping. These systems are being used for conducting research, devising new techniques, and sharing the computer assisted analysis results among collaborators. Researchers need to integrate their new workflows/pipelines, tools or techniques with the base system over time. Moreover, large scale data need to be processed within the time-line for more effective analysis. Recently, Big Data technologies are emerging for facilitating large scale data processing with commodity hardware. Among the above-mentioned systems, GenAp is utilizing the Big Data technologies for specific cases only. The structure of such a cloud-based system is highly variable and complex in nature. Software architects and developers need to consider totally different properties and challenges during the development and maintenance phases compared to the traditional business/service oriented systems. Recent studies report that software engineers and data engineers confront challenges to develop analytic tools for supporting large scale and heterogeneous data analysis. Unfortunately, less focus has been given by the software researchers to devise a well-defined methodology and frameworks for flexible design of a cloud system for the Genotyping and Phenotyping domain. To that end, more effective design methodologies and frameworks are an urgent need for cloud based Genotyping and Phenotyping analysis system development that also supports large scale data processing. In our thesis, we conduct a few studies in order to devise a stable reference architecture and modularity model for the software developers and data engineers in the domain of Genotyping and Phenotyping. In the first study, we analyze the architectural changes of existing candidate systems to find out the stability issues. Then, we extract architectural patterns of the candidate systems and propose a conceptual reference architectural model. Finally, we present a case study on the modularity of computation-intensive tasks as an extension of the data-centric development. We show that the data-centric modularity model is at the core of the flexible development of a Genotyping and Phenotyping analysis system. Our proposed model and case study with thousands of images provide a useful knowledge-base for software researchers, developers, and data engineers for cloud based Genotyping and Phenotyping analysis system development