Sparse Allreduce: Efficient Scalable Communication for Power-Law Data

Many large datasets exhibit power-law statistics: The web graph, social networks, text data, click through data etc. Their adjacency graphs are termed natural graphs, and are known to be difficult to partition. As a consequence most distributed algorithms on these graphs are communication intensive. Many algorithms on natural graphs involve an Allreduce: a sum or average of partitioned data which is then shared back to the cluster nodes. Examples include PageRank, spectral partitioning, and many machine learning algorithms including regression, factor (topic) models, and clustering. In this paper we describe an efficient and scalable Allreduce primitive for power-law data. We point out scaling problems with existing butterfly and round-robin networks for Sparse Allreduce, and show that a hybrid approach improves on both. Furthermore, we show that Sparse Allreduce stages should be nested instead of cascaded (as in the dense case). And that the optimum throughput Allreduce network should be a butterfly of heterogeneous degree where degree decreases with depth into the network. Finally, a simple replication scheme is introduced to deal with node failures. We present experiments showing significant improvements over existing systems such as PowerGraph and Hadoop

Pregelix: Big(ger) Graph Analytics on A Dataflow Engine

There is a growing need for distributed graph processing systems that are capable of gracefully scaling to very large graph datasets. Unfortunately, this challenge has not been easily met due to the intense memory pressure imposed by process-centric, message passing designs that many graph processing systems follow. Pregelix is a new open source distributed graph processing system that is based on an iterative dataflow design that is better tuned to handle both in-memory and out-of-core workloads. As such, Pregelix offers improved performance characteristics and scaling properties over current open source systems (e.g., we have seen up to 15x speedup compared to Apache Giraph and up to 35x speedup compared to distributed GraphLab), and makes more effective use of available machine resources to support Big(ger) Graph Analytics

PlinyCompute: A Platform for High-Performance, Distributed, Data-Intensive Tool Development

This paper describes PlinyCompute, a system for development of high-performance, data-intensive, distributed computing tools and libraries. In the large, PlinyCompute presents the programmer with a very high-level, declarative interface, relying on automatic, relational-database style optimization to figure out how to stage distributed computations. However, in the small, PlinyCompute presents the capable systems programmer with a persistent object data model and API (the "PC object model") and associated memory management system that has been designed from the ground-up for high performance, distributed, data-intensive computing. This contrasts with most other Big Data systems, which are constructed on top of the Java Virtual Machine (JVM), and hence must at least partially cede performance-critical concerns such as memory management (including layout and de/allocation) and virtual method/function dispatch to the JVM. This hybrid approach---declarative in the large, trusting the programmer's ability to utilize PC object model efficiently in the small---results in a system that is ideal for the development of reusable, data-intensive tools and libraries. Through extensive benchmarking, we show that implementing complex objects manipulation and non-trivial, library-style computations on top of PlinyCompute can result in a speedup of 2x to more than 50x or more compared to equivalent implementations on Spark.Comment: 48 pages, including references and Appendi

Apache Calcite: A Foundational Framework for Optimized Query Processing Over Heterogeneous Data Sources

Apache Calcite is a foundational software framework that provides query processing, optimization, and query language support to many popular open-source data processing systems such as Apache Hive, Apache Storm, Apache Flink, Druid, and MapD. Calcite's architecture consists of a modular and extensible query optimizer with hundreds of built-in optimization rules, a query processor capable of processing a variety of query languages, an adapter architecture designed for extensibility, and support for heterogeneous data models and stores (relational, semi-structured, streaming, and geospatial). This flexible, embeddable, and extensible architecture is what makes Calcite an attractive choice for adoption in big-data frameworks. It is an active project that continues to introduce support for the new types of data sources, query languages, and approaches to query processing and optimization.Comment: SIGMOD'1

Logic programming in the context of multiparadigm programming: the Oz experience

Oz is a multiparadigm language that supports logic programming as one of its major paradigms. A multiparadigm language is designed to support different programming paradigms (logic, functional, constraint, object-oriented, sequential, concurrent, etc.) with equal ease. This article has two goals: to give a tutorial of logic programming in Oz and to show how logic programming fits naturally into the wider context of multiparadigm programming. Our experience shows that there are two classes of problems, which we call algorithmic and search problems, for which logic programming can help formulate practical solutions. Algorithmic problems have known efficient algorithms. Search problems do not have known efficient algorithms but can be solved with search. The Oz support for logic programming targets these two problem classes specifically, using the concepts needed for each. This is in contrast to the Prolog approach, which targets both classes with one set of concepts, which results in less than optimal support for each class. To explain the essential difference between algorithmic and search programs, we define the Oz execution model. This model subsumes both concurrent logic programming (committed-choice-style) and search-based logic programming (Prolog-style). Instead of Horn clause syntax, Oz has a simple, fully compositional, higher-order syntax that accommodates the abilities of the language. We conclude with lessons learned from this work, a brief history of Oz, and many entry points into the Oz literature.Comment: 48 pages, to appear in the journal "Theory and Practice of Logic Programming

Dynamic Control Flow in Large-Scale Machine Learning

Many recent machine learning models rely on fine-grained dynamic control flow for training and inference. In particular, models based on recurrent neural networks and on reinforcement learning depend on recurrence relations, data-dependent conditional execution, and other features that call for dynamic control flow. These applications benefit from the ability to make rapid control-flow decisions across a set of computing devices in a distributed system. For performance, scalability, and expressiveness, a machine learning system must support dynamic control flow in distributed and heterogeneous environments. This paper presents a programming model for distributed machine learning that supports dynamic control flow. We describe the design of the programming model, and its implementation in TensorFlow, a distributed machine learning system. Our approach extends the use of dataflow graphs to represent machine learning models, offering several distinctive features. First, the branches of conditionals and bodies of loops can be partitioned across many machines to run on a set of heterogeneous devices, including CPUs, GPUs, and custom ASICs. Second, programs written in our model support automatic differentiation and distributed gradient computations, which are necessary for training machine learning models that use control flow. Third, our choice of non-strict semantics enables multiple loop iterations to execute in parallel across machines, and to overlap compute and I/O operations. We have done our work in the context of TensorFlow, and it has been used extensively in research and production. We evaluate it using several real-world applications, and demonstrate its performance and scalability.Comment: Appeared in EuroSys 2018. 14 pages, 16 figure

A Survey on Compiler Autotuning using Machine Learning

Since the mid-1990s, researchers have been trying to use machine-learning based approaches to solve a number of different compiler optimization problems. These techniques primarily enhance the quality of the obtained results and, more importantly, make it feasible to tackle two main compiler optimization problems: optimization selection (choosing which optimizations to apply) and phase-ordering (choosing the order of applying optimizations). The compiler optimization space continues to grow due to the advancement of applications, increasing number of compiler optimizations, and new target architectures. Generic optimization passes in compilers cannot fully leverage newly introduced optimizations and, therefore, cannot keep up with the pace of increasing options. This survey summarizes and classifies the recent advances in using machine learning for the compiler optimization field, particularly on the two major problems of (1) selecting the best optimizations and (2) the phase-ordering of optimizations. The survey highlights the approaches taken so far, the obtained results, the fine-grain classification among different approaches and finally, the influential papers of the field.Comment: version 5.0 (updated on September 2018)- Preprint Version For our Accepted Journal @ ACM CSUR 2018 (42 pages) - This survey will be updated quarterly here (Send me your new published papers to be added in the subsequent version) History: Received November 2016; Revised August 2017; Revised February 2018; Accepted March 2018

High-performance computing selection of models of DNA substitution for multicore clusters

[Abstract] This paper presents the high-performance computing (HPC) support of jModelTest2, the most popular bioinformatic tool for the statistical selection of models of DNA substitution. As this can demand vast computational resources, especially in terms of processing power, jModelTest2 implements three parallel algorithms for model selection: (1) a multithreaded implementation for shared memory architectures; (2) a message-passing implementation for distributed memory architectures, such as clusters; and (3) a hybrid shared/distributed memory implementation for clusters of multicore nodes, combining the workload distribution across cluster nodes with a multithreaded model optimization within each node. The main limitation of the shared and distributed versions is the workload imbalance that generally appears when using more than 32 cores, a direct consequence of the heterogeneity in the computational cost of the evaluated models. The hybrid shared/distributed memory version overcomes this issue reducing the workload imbalance through a thread-based decomposition of the most costly model optimization tasks. The performance evaluation of this HPC application on a 40-core shared memory system and on a 528-core cluster has shown high scalability, with speedups of the multithreaded version of up to 32, and up to 257 for the hybrid shared/distributed memory implementation. This can represent a reduction in the execution time of some analyses from 4 days down to barely 20 minutes. The implementation of the three parallel execution strategies of jModelTest2 presented in this paper are available under a GPL license at http://code.google.com/jmodeltest2.European Research Council; ERC-2007-Stg 203161-PHYGENOM to D.P.Ministerio de Ciencia y Educación; BFU2009-08611 to D.P.Ministerio de Ciencia y Educación; TIN2010-16735 to R.D