Articles by Ryo

Canonical Stratification for Non-Mathematicians

October 17, 2018

Our recent publication “Algorithmic Canonical Stratifications of Simplicial Complexes” proposes a new algorithm for data analysis that offers a topology-aware path towards explainable artificial intelligence. Despite (or, perhaps, due to) being mathematically rigorous, the text of the original work is virtually impenetrable for readers not familiar with the concepts, tools, and notation of topology. In order to convey our ideas to a wider audience, we present this supplemental introduction. Here, we summarize and explain in plain English the motivation, reasoning, and methods of our new topological data analysis algorithm that we term “canonical stratification”. Canonical-Stratification-for-Non-Mathematicians.pdf (38 KB) Table of Contents 1. Motivation 2. More on Canonical Stratification 3. Conclusion 1. Motivation Machine learning has advanced significantly in recent years and has proven itself to be a powerful and versatile tool in a variety of data-driven disciplines. Machine learning algorithms are now being used to make decisions in numerous areas [...]

Optimization of Hamerly’s K-Means Clustering Algorithm: CFXKMeans Library

July 21, 2017

This publication describes the application of performance optimizations techniques to Hamerly’s K-means clustering algorithm. Starting with an unoptimized implementation of the algorithm, we discuss: Thread scheduling Reduction patterns SIMD reduction Unroll and jam Presented optimizations aggregate to 85.6x speedup compared to the original unoptimized implementation. Resulting implementation is packaged into a library named CFXKMeans with interfaces for C/C++ and Python. The Python interface is benchmarked using the MNIST 784 data set. The result for K=64 is compared to the performance of K-means clustering implementation in a popular machine learning framework, scikit-learn, from the Intel distribution for Python. CFXKMeans performed our benchmark tests faster than scikit-learn by a factor of 4.68x on an Intel Xeon processor E5-2699 v4 and 5.54x on an Intel Xeon Phi 7250 processor. The CFXKMeans library has C/C++ and Python API and is available under the MIT license at https://github.com/ColfaxResearch/CFXKMeans. Colfax-Kmeans-Clustering-Optimization.pdf (365 KB) [...]

Optimizing Torch Performance for Intel Xeon Phi Processors

November 18, 2016

In this 1-hour webinar, Ryo Asai (Colfax) discusses how machine learning applications can benefit from code modernization. He begins by exploring the parallelism that gives modern computer architecture its performance, and how it can be leveraged. Then he applies code modernization techniques live on-screen to the Torch machine learning framework. Specifically, he optimizes image recognition through a deep convolutional neural network that uses the VGG-net architecture. For each code modernization technique, he explains why it works, and how to apply it in practice. What you will learn: What code modernization is, and its importance for machine learning Practical knowledge of modern computer architectures Code modernization techniques for leveraging parallelism Slides: Colfax-Torch-VGG-Webinar.pdf (2 [...]

Intel® Python* on 2nd Generation Intel® Xeon Phi™ Processors: Out-of-the-Box Performance

June 20, 2016

This paper reports on the value and performance for computational applications of the Intel® distribution for Python* 2017 Beta on 2nd generation Intel® Xeon Phi™ processors (formerly codenamed Knights Landing). Benchmarks of LU decomposition, Cholesky decomposition, singular value decomposition and double precision general matrix-matrix multiplication routines in the SciPy and NumPy libraries are presented, and tuning methodology for use with high-bandwidth memory (HBM) is laid out. Download as PDF: Colfax-Intel-Python.pdf (1 MB) or read online below. Code: coming soon, check back later. See also: colfaxresearch.com/get-ready-for-intel-knights-landing-3-papers/ 1. A Case for Python in Computing Python is a popular scripting language in computational applications. Empowered with the fundamental tools for scientific computing, NumPy and SciPy libraries, Python applications can express in brief and convenient form basic linear algebra subroutines (BLAS) and linear algebra package (LAPACK) functions for operations on matrices and systems of linear algebraic [...]

Knights Landing Webinar Slides Translated to Japanese

May 13, 2016

日XLsoft社の協力で、弊社の “Introduction to Next-Generation Intel® Xeon Phi™ Processor: Developer’s Guide to Knights Landing” で使われているスライド集が日本語に翻訳されました。 With the help of our partners at XLsoft, the slide deck for the webinar “Introduction to Next-Generation Intel® Xeon Phi™ Processor: Developer’s Guide to Knights Landing” has been translated to the Japanese language. XLsoft社のウェブサイト/XLsoft website Download here: JP-Colfax-Programmers-Guide-to-KNL.pdf (5 MB) For more information, and to register for the webinar, please visit: Webinar [...]

MCDRAM as High-Bandwidth Memory (HBM) in Knights Landing Processors: Developer’s Guide

May 11, 2016

This publication is part of a developer guide focusing on the new features in 2nd generation Intel® Xeon Phi™ processors code-named Knights Landing (KNL). In this document we discuss the on-package high-bandwidth memory (HBM) based on the multi-channel dynamic random access memory (MCDRAM) technology: Three configuration modes of HBM: Flat mode, Cache mode and Hybrid mode Utilization of the HBM as addressable memory using two methods: by setting affinity policy with the numactl tool and through the usage of special allocators in the memkind library Guidelines for determining the optimal usage model for applications running on bootable Knights Landing. Colfax_KNL_MCDRAM_Guide.pdf (255 KB) See also: colfaxresearch.com/get-ready-for-intel-knights-landing-3-papers/ Table of Contents 1. MCDRAM in KNL 2.1. Cache Mode 2.2. Flat Mode 2.3. Hybrid Mode 3. Using HBM as addressable memory 3.1. numactl 3.2. Memkind Library 3.3. Fortran 4. Choosing Memory and Programming Model 4.1. Programming with HBM… 4.2. …and Programming without HBM Appendix A: Application Memory [...]

Guided Code Vectorization with Intel® Advisor XE

April 12, 2016

Early Stage Application Optimization made Easy with Step-by-Step Guide In this publication we discuss the usage of an optimization tool called Intel® Advisor. The discussion is illustrated with an example workload that computes the electric potential in a set of points in 3-D space produced by a group of charged particles. The example workload runs on a multi-core Intel Xeon processor with Intel AVX2 instructions. The application was originally parallelized across cores, but otherwise neither optimized nor vectorized. In the publication, we discuss three performance issues that the Intel Advisor detected: vector dependence, type conversion and inefficient memory access pattern. For each issue, we discuss how to interpret the data presented by the Intel Advisor, and also how to to optimize the application to resolve these issues. After the optimization, we observed a 16x performance boost compared to the original, non-optimized implementation. Complete paper: Colfax_Advisor_Vectorization.pdf (1 MB) Sample code for Linux: Colfax_Advisor_Vectorization_Code.zip (50 [...]

Introduction to Intel DAAL, Part 2: Distributed Variance-Covariance Matrix Computation

March 28, 2016

This is the part 2 of 3 of an introductory series of publications on the Intel® Data Analytics Acceleration Library (DAAL). DAAL is a data analytics library optimized for modern highly parallel computer architectures such as Intel Xeon and Intel Xeon Phi processors. The goal of this series is to provide developers a technical overview for developing applications using DAAL. In part 1 of the series we discussed how to implement batch mode computation on a single node. In the present publication, we discuss the distributed mode computation. Our discussion will focus both on how and when to implement distributed mode computation with Intel DAAL. As an example workload, we implement an application that uses DAAL to compute a covariance matrix of a set of vectors. We first demonstrate how to use distributed mode with this example. Then, using this example application, we scan the parameter space to determine what parameter ranges benefit from distributed computation. We also demonstrate how the output of this computation may be used in image processing to compute the eigenvectors of [...]

Introduction to Intel DAAL, Part 1: Polynomial Regression with Batch Mode Computation

October 28, 2015

This is the part 1 of 3 of an introductory series of publications on the Intel Data Analytics Acceleration Library (DAAL). DAAL is a data analytics library optimized for modern highly parallel computer architectures such as Intel Xeon and Intel Xeon Phi processors. The goal of this series is to provide developers a technical overview for developing applications using DAAL. In this paper we focus on two aspects of developing an application with Intel DAAL: data management and computation. As a practical example, we implement a simple machine learning application with polynomial regression using the library in the batch computation mode. We demonstrate using this application for data-based prediction of hydrodynamics properties of yachts. The source code and data for the sample application are available for free download. The second and third part of the series will discuss other aspects of data analysis with DAAL. In part 2, we discuss distributed data and computation in conjunction with MPI. In the third part, we discuss the case with multiple data sets and interfacing with a [...]

Software Developer’s Introduction to the HGST Ultrastar Archive Ha10 SMR Drives

July 31, 2015

In this paper we will discuss the new HGST Shingled Magnetic Recording (SMR) drives, Ultrastar Archive Ha10, which offers storage capacities of 10 TB and beyond. With their high-density storage capacities, these drives are well suited for large “active archive” applications. In an active archive application, the data is frequently read but seldom modified. The SMR drives are host managed, meaning that the developer must manage the data storage on the drives. In this publication we introduce an open source library, libzbc, which was developed by the HGST team to assist developers who use SMR drives. The discussions cover topics from the very basics like opening a device, to more advanced topics like data padding. The goal of this paper is to give readers the necessary knowledge and tools to develop applications with libzbc. We will present an example, and then report several benchmarks of I/O operations on the HGST SMR drives, and discuss the SMR drive’s effectiveness as an active archive solution. Complete paper: HGST_Introduction_to_libzbc.pdf (361 KB) Sample codes [...]

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