Locality-Aware Dynamic Task Graph Scheduling

Dynamic task graph schedulers automatically balance work across processor cores by scheduling tasks among available threads while preserving dependences. In this paper, we design NabbitC, a provably efficient dynamic task graph scheduler that accounts for data locality on NUMA systems. NabbitC allows users to assign a color to each task representing the location (e.g., a processor core) that has the most efficient access to data needed during that node’s execution. NabbitC then automatically adjusts the scheduling so as to preferentially execute each node at the location that matches its color—leading to better locality because the node is likely to make local rather than remote accesses. At the same time, NabbitC tries to optimize load balance and not add too much overhead compared to the vanilla Nabbit scheduler that does not consider locality. We provide a theoretical analysis that shows that NabbitC does not asymptotically impact the scalability of Nabbit . We evaluated the performance of NabbitC on a suite of memory intensive benchmarks. Our experiments indicates that adding locality awareness has a considerable performance advantage compared to the vanilla Nabbit scheduler. In addition, we also compared NabbitC to OpenMP programs for both regular and irregular applications. For regular applications, OpenMP achieves perfect locality and perfect load balance statically. For these benchmarks, NabbitC has a small performance penalty compared to OpenMP due to its dynamic scheduling strategy. For irregular applications, where OpenMP can not achieve locality and load balance simultaneously, we find that NabbitC performs better. Therefore, NabbitC combines the benefits of locality- aware scheduling for regular applications (the forte of static schedulers such as those in OpenMP) and dynamically adapting to load imbalance (the forte of dynamic schedulers such as Cilk Plus, TBB, and Nabbit)

Locality-Aware Concurrency Platforms

Modern computing systems from all domains are becoming increasingly more parallel. Manufacturers are taking advantage of the increasing number of available transistors by packaging more and more computing resources together on a single chip or within a single system. These platforms generally contain many levels of private and shared caches in addition to physically distributed main memory. Therefore, some memory is more expensive to access than other and high-performance software must consider memory locality as one of the first level considerations. Memory locality is often difficult for application developers to consider directly, however, since many of these NUMA affects are invisible to the application programmer and only show up in low performance. Moreover, on parallel platforms, the performance depends on both locality and load balance and these two metrics are often at odds with each other. Therefore, directly considering locality and load balance at the application level may make the application much more complex to program. In this work, we develop locality-conscious concurrency platforms for multiple different structured parallel programming models, including streaming applications, task-graphs and parallel for loops. In all of this work, the idea is to minimally disrupt the application programming model so that the application developer is either unimpacted or must only provide high-level hints to the runtime system. The runtime system then schedules the application to provide good locality of access while, at the same time also providing good load balance. In particular, we address cache locality for streaming applications through static partitioning and developed an extensible platform to execute partitioned streaming applications. For task-graphs, we extend a task-graph scheduling library to guide scheduling decisions towards better NUMA locality with the help of user-provided locality hints. CilkPlus parallel for loops utilize a randomized dynamic scheduler to distribute work which, in many loop based applications, results in poor locality at all levels of the memory hierarchy. We address this issue with a novel parallel for loop implementation that can get good cache and NUMA locality while providing support to maintain good load balance dynamically

Multi-Path Alpha-Fair Resource Allocation at Scale in Distributed Software Defined Networks

The performance of computer networks relies on how bandwidth is shared among different flows. Fair resource allocation is a challenging problem particularly when the flows evolve over time. To address this issue, bandwidth sharing techniques that quickly react to the traffic fluctuations are of interest, especially in large scale settings with hundreds of nodes and thousands of flows. In this context, we propose a distributed algorithm based on the Alternating Direction Method of Multipliers (ADMM) that tackles the multi-path fair resource allocation problem in a distributed SDN control architecture. Our ADMM-based algorithm continuously generates a sequence of resource allocation solutions converging to the fair allocation while always remaining feasible, a property that standard primal-dual decomposition methods often lack. Thanks to the distribution of all computer intensive operations, we demonstrate that we can handle large instances at scale

Branch and Bound Based Load Balancing for Parallel Applications

Abstract. Many parallel applications are highly dynamic in nature. In some, computation and communication patterns change gradually dur-ing the run; in others those characteristics change abruptly. Such dy-namic applications require an adaptive load balancing strategy. We are exploring an adaptive approach based on multi-partition object-based decomposition, supported by object migration. For many applications, relatively infrequent load balancing is needed. In these cases it becomes economical to spend considerable computation time toward arriving at a nearly optimal mapping of objects to processors. We present an optimal-seeking branch and bound based strategy that finds nearly optimal so-lutions to such load balancing problems quickly, and can continuously improve such solutions as time permits.

Extreme Scale De Novo Metagenome Assembly

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in size. In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach. MetaHipMer leverages a specialized scaffolding algorithm that produces long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is end-to-end parallelized using the Unified Parallel C language and therefore can run seamlessly on shared and distributed-memory systems. Experimental results show that MetaHipMer matches or outperforms the state-of-the-art tools in terms of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes. We demonstrate the unprecedented capability of MetaHipMer by computing the first full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion reads - size 2.6 TBytes.Comment: Accepted to SC1

Scalable Exact Parent Sets Identification in Bayesian Networks Learning with Apache Spark

In Machine Learning, the parent set identification problem is to find a set of random variables that best explain selected variable given the data and some predefined scoring function. This problem is a critical component to structure learning of Bayesian networks and Markov blankets discovery, and thus has many practical applications, ranging from fraud detection to clinical decision support. In this paper, we introduce a new distributed memory approach to the exact parent sets assignment problem. To achieve scalability, we derive theoretical bounds to constraint the search space when MDL scoring function is used, and we reorganize the underlying dynamic programming such that the computational density is increased and fine-grain synchronization is eliminated. We then design efficient realization of our approach in the Apache Spark platform. Through experimental results, we demonstrate that the method maintains strong scalability on a 500-core standalone Spark cluster, and it can be used to efficiently process data sets with 70 variables, far beyond the reach of the currently available solutions

Supporting intra-task parallelism in real-time multiprocessor systems

Os sistemas de tempo real modernos geram, cada vez mais, cargas computacionais pesadas e dinâmicas, começando-se a tornar pouco expectável que sejam implementados em sistemas uniprocessador. Na verdade, a mudança de sistemas com um único processador para sistemas multi- processador pode ser vista, tanto no domínio geral, como no de sistemas embebidos, como uma forma eficiente, em termos energéticos, de melhorar a performance das aplicações. Simultaneamente, a proliferação das plataformas multi-processador transformaram a programação paralela num tópico de elevado interesse, levando o paralelismo dinâmico a ganhar rapidamente popularidade como um modelo de programação. A ideia, por detrás deste modelo, é encorajar os programadores a exporem todas as oportunidades de paralelismo através da simples indicação de potenciais regiões paralelas dentro das aplicações. Todas estas anotações são encaradas pelo sistema unicamente como sugestões, podendo estas serem ignoradas e substituídas, por construtores sequenciais equivalentes, pela própria linguagem. Assim, o modo como a computação é na realidade subdividida, e mapeada nos vários processadores, é da responsabilidade do compilador e do sistema computacional subjacente. Ao retirar este fardo do programador, a complexidade da programação é consideravelmente reduzida, o que normalmente se traduz num aumento de produtividade. Todavia, se o mecanismo de escalonamento subjacente não for simples e rápido, de modo a manter o overhead geral em níveis reduzidos, os benefícios da geração de um paralelismo com uma granularidade tão fina serão meramente hipotéticos. Nesta perspetiva de escalonamento, os algoritmos que empregam uma política de workstealing são cada vez mais populares, com uma eficiência comprovada em termos de tempo, espaço e necessidades de comunicação. Contudo, estes algoritmos não contemplam restrições temporais, nem outra qualquer forma de atribuição de prioridades às tarefas, o que impossibilita que sejam diretamente aplicados a sistemas de tempo real. Além disso, são tradicionalmente implementados no runtime da linguagem, criando assim um sistema de escalonamento com dois níveis, onde a previsibilidade, essencial a um sistema de tempo real, não pode ser assegurada. Nesta tese, é descrita a forma como a abordagem de work-stealing pode ser resenhada para cumprir os requisitos de tempo real, mantendo, ao mesmo tempo, os seus princípios fundamentais que tão bons resultados têm demonstrado. Muito resumidamente, a única fila de gestão de processos convencional (deque) é substituída por uma fila de deques, ordenada de forma crescente por prioridade das tarefas. De seguida, aplicamos por cima o conhecido algoritmo de escalonamento dinâmico G-EDF, misturamos as regras de ambos, e assim nasce a nossa proposta: o algoritmo de escalonamento RTWS. Tirando partido da modularidade oferecida pelo escalonador do Linux, o RTWS é adicionado como uma nova classe de escalonamento, de forma a avaliar na prática se o algoritmo proposto é viável, ou seja, se garante a eficiência e escalonabilidade desejadas. Modificar o núcleo do Linux é uma tarefa complicada, devido à complexidade das suas funções internas e às fortes interdependências entre os vários subsistemas. Não obstante, um dos objetivos desta tese era ter a certeza que o RTWS é mais do que um conceito interessante. Assim, uma parte significativa deste documento é dedicada à discussão sobre a implementação do RTWS e à exposição de situações problemáticas, muitas delas não consideradas em teoria, como é o caso do desfasamento entre vários mecanismo de sincronização. Os resultados experimentais mostram que o RTWS, em comparação com outro trabalho prático de escalonamento dinâmico de tarefas com restrições temporais, reduz significativamente o overhead de escalonamento através de um controlo de migrações, e mudanças de contexto, eficiente e escalável (pelo menos até 8 CPUs), ao mesmo tempo que alcança um bom balanceamento dinâmico da carga do sistema, até mesmo de uma forma não custosa. Contudo, durante a avaliação realizada foi detetada uma falha na implementação do RTWS, pela forma como facilmente desiste de roubar trabalho, o que origina períodos de inatividade, no CPU em questão, quando a utilização geral do sistema é baixa. Embora o trabalho realizado se tenha focado em manter o custo de escalonamento baixo e em alcançar boa localidade dos dados, a escalonabilidade do sistema nunca foi negligenciada. Na verdade, o algoritmo de escalonamento proposto provou ser bastante robusto, não falhando qualquer meta temporal nas experiências realizadas. Portanto, podemos afirmar que alguma inversão de prioridades, causada pela sub-política de roubo BAS, não compromete os objetivos de escalonabilidade, e até ajuda a reduzir a contenção nas estruturas de dados. Mesmo assim, o RTWS também suporta uma sub-política de roubo determinística: PAS. A avaliação experimental, porém, não ajudou a ter uma noção clara do impacto de uma e de outra. No entanto, de uma maneira geral, podemos concluir que o RTWS é uma solução promissora para um escalonamento eficiente de tarefas paralelas com restrições temporais.Multiple programming models are emerging to address the increased need for dynamic task-level parallelism in applications for multi-core processors and shared-memory parallel computing, presenting promising solutions from a user-level perspective. Nonetheless, while high-level parallel languages offer a simple way for application programmers to specify parallelism in a form that easily scales with problem size, they still leave the actual scheduling of tasks to be performed at runtime. Therefore, if the underlying system cannot efficiently map those tasks on the available cores, the benefits will be lost. This is particularly important in modern real-time systems as their average workload is rapidly growing more parallel, complex and computing-intensive, whilst preserving stringent timing constraints. However, as the real-time scheduling theory has mostly been focused on sequential task models, a shift to parallel task models introduces a completely new dimension to the scheduling problem. Within this context, the work presented in this thesis considers how to dynamically schedule highly heterogeneous parallel applications that require real-time performance guarantees on multi-core processors. A novel scheduling approach called RTWS is proposed. RTWS combines the G-EDF scheduler with a priority-aware work-stealing load balancing scheme, enabling parallel real-time tasks to be executed on more than one processor at a given time instant. Two stealing sub-policies have arisen from this proposal and their suitability is discussed in detail. Furthermore, this thesis describes the implementation of a new scheduling class in the Linux kernel concerning RTWS, and extensively evaluate its feasibility. Experimental results demonstrate the greater scalability and lower scheduling overhead of the proposed approach, comparatively to an existing real-time deadline-driven scheduling policy for the Linux kernel, as well as reveal its better performance when considering tasks with intra-task parallelism than without, even for short-living applications. We show that busy-aware stealing is robust to small deviations from a strict priority schedule and conclude that some priority inversion may be actually acceptable, provided it helps reduce contention, communication, synchronisation and coordination between parallel threads

Engineering MultiQueues: Fast relaxed concurrent priority queues

Priority queues with parallel access are an attractive data structure for applications like prioritized online scheduling, discrete event simulation, or greedy algorithms. However, a classical priority queue constitutes a severe bottleneck in this context, leading to very small throughput. Hence, there has been significant interest in concurrent priority queues with relaxed semantics. We investigate the complementary quality criteria rank error (how close are deleted elements to the global minimum) and delay (for each element x, how many elements with lower priority are deleted before x). In this paper, we introduce MultiQueues as a natural approach to relaxed priority queues based on multiple sequential priority queues. Their naturally high theoretical scalability is further enhanced by using three orthogonal ways of batching operations on the sequential queues. Experiments indicate that MultiQueues present a very good performance-quality tradeoff and considerably outperform competing approaches in at least one of these aspects. We employ a seemingly paradoxical technique of "wait-free locking" that might be of more general interest to convert sequential data structures to relaxed concurrent data structures