Accelerating Large-Scale Data Analysis by Offloading to High-Performance Computing Libraries using Alchemist

Apache Spark is a popular system aimed at the analysis of large data sets, but recent studies have shown that certain computations---in particular, many linear algebra computations that are the basis for solving common machine learning problems---are significantly slower in Spark than when done using libraries written in a high-performance computing framework such as the Message-Passing Interface (MPI). To remedy this, we introduce Alchemist, a system designed to call MPI-based libraries from Apache Spark. Using Alchemist with Spark helps accelerate linear algebra, machine learning, and related computations, while still retaining the benefits of working within the Spark environment. We discuss the motivation behind the development of Alchemist, and we provide a brief overview of its design and implementation. We also compare the performances of pure Spark implementations with those of Spark implementations that leverage MPI-based codes via Alchemist. To do so, we use data science case studies: a large-scale application of the conjugate gradient method to solve very large linear systems arising in a speech classification problem, where we see an improvement of an order of magnitude; and the truncated singular value decomposition (SVD) of a 400GB three-dimensional ocean temperature data set, where we see a speedup of up to 7.9x. We also illustrate that the truncated SVD computation is easily scalable to terabyte-sized data by applying it to data sets of sizes up to 17.6TB.Comment: Accepted for publication in Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, London, UK, 201

MLI: An API for Distributed Machine Learning

MLI is an Application Programming Interface designed to address the challenges of building Machine Learn- ing algorithms in a distributed setting based on data-centric computing. Its primary goal is to simplify the development of high-performance, scalable, distributed algorithms. Our initial results show that, relative to existing systems, this interface can be used to build distributed implementations of a wide variety of common Machine Learning algorithms with minimal complexity and highly competitive performance and scalability

Accelerating Large-Scale Data Analysis by Offloading to High-Performance Computing Libraries using Alchemist

Apache Spark is a popular system aimed at the analysis of large data sets, but recent studies have shown that certain computations---in particular, many linear algebra computations that are the basis for solving common machine learning problems---are significantly slower in Spark than when done using libraries written in a high-performance computing framework such as the Message-Passing Interface (MPI). To remedy this, we introduce Alchemist, a system designed to call MPI-based libraries from Apache Spark. Using Alchemist with Spark helps accelerate linear algebra, machine learning, and related computations, while still retaining the benefits of working within the Spark environment. We discuss the motivation behind the development of Alchemist, and we provide a brief overview of its design and implementation. We also compare the performances of pure Spark implementations with those of Spark implementations that leverage MPI-based codes via Alchemist. To do so, we use data science case studies: a large-scale application of the conjugate gradient method to solve very large linear systems arising in a speech classification problem, where we see an improvement of an order of magnitude; and the truncated singular value decomposition (SVD) of a 400GB three-dimensional ocean temperature data set, where we see a speedup of up to 7.9x. We also illustrate that the truncated SVD computation is easily scalable to terabyte-sized data by applying it to data sets of sizes up to 17.6TB.Comment: Accepted for publication in Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, London, UK, 201

Matrix Factorization at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies

We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausability), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to TB-sized problems in particle physics, climate modeling and bioimaging. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark's data-parallel model. We perform scaling experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance

Rethinking Data-Intensive Science Using Scalable Analytics Systems

"Next generation" data acquisition technologies are allowing scientists to collect exponentially more data at a lower cost. These trends are broadly impacting many scientific fields, including genomics, astronomy, and neuroscience. We can attack the problem caused by exponential data growth by applying horizontally scalable techniques from current analytics systems to accelerate scientific processing pipelines. In this paper, we describe ADAM, an example genomics pipeline that leverages the open-source Apache Spark and Parquet systems to achieve a 28x speedup over current genomics pipelines, while reducing cost by 63%. From building this system, we were able to distill a set of techniques for implementing scientific analyses efficiently using commodity "big data" systems. To demonstrate the generality of our architecture, we then implement a scalable astronomy image processing system which achieves a 2.8--8.9x improvement over the state-of-the-art MPI-based system

A multi-platform evaluation of the randomized CX low-rank matrix factorization in Spark:

We investigate the performance and scalability of the randomized CX low-rank matrix factorization and demonstrate its applicability through the analysis of a 1TB mass spectrometry imaging (MSI) dataset, using Apache Spark on an Amazon EC2 cluster, a Cray XC40 system, and an experimental Cray cluster. We implemented this factorization both as a parallelized C implementation with hand-tuned optimizations and in Scala using the Apache Spark high-level cluster computing framework. We obtained consistent performance across the three platforms: using Spark we were able to process the 1TB size dataset in under 30 minutes with 960 cores on all systems, with the fastest times obtained on the experimental Cray cluster. In comparison, the C implementation was 21X faster on the Amazon EC2 system, due to careful cache optimizations, bandwidth-friendly access of matrices and vector computation using SIMD units. We report these results and their implications on the hardware and software issues arising in supporting data-centric workloads in parallel and distributed environments