Case Studies

An optimization approach for agent-based computational models of biological development

April 9, 2018

Pablo Gonzalez-de-Aledoa, Andrey Vladimirovd, Marco Mancab, Jerry Baughc, Ryo Asaid, Marcus Kaisere,f, Roman Bauerf,e a Software Performance Optimization Group, Imperial College London, London, United Kingdom b CERN Openlab, IT Department, CERN, Switzerland c Intel Corporation, USA d Colfax International, USA e Interdisciplinary Computing and Complex BioSystems Research Group, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom f Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom A paper led by Pablo Gonzales-de-Aledo (Imperial College London) with contributions from his colleagues from CERN, Intel, Colfax and Newcastle University was published in the journal Advances in Engineering Software. This is a case study on performance optimization in a biological simulation code. The code presents a highly parallel implementation of a computer simulation that involves millions of agents interacting in a 3D environment. The paper explains the general approach to transforming a sequential code to run on modern, highly [...]

Optimization of Real-Time Object Detection on Intel® Xeon® Scalable Processors

November 11, 2017

This publication demonstrates the process of optimizing an object detection inference workload on an Intel® Xeon® Scalable processor using TensorFlow. This project pursues two objectives: Achieve object detection with real-time throughput (frame rate) and low latency Minimize the required computational resources In this case study, a model described in the “You Only Look Once” (YOLO) project is used for object detection. The model consists of two components: a convolutional neural network and a post-processing pipeline. In this work, the original Darknet model is converted to a TensorFlow model. First, the convolutional neural network is optimized for inference. Then array programming with NumPy and TensorFlow is implemented for the post-processing pipeline. Finally, environment variables and other configuration parameters are tuned to maximize the computational performance. With these optimizations, real-time object detection is achieved while using a fraction of the available processing power of an Intel Xeon Scalable processor-based system. [...]

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) [...]

FALCON Library: Fast Image Convolution in Neural Networks on Intel Architecture

November 9, 2016

We describe FALCON, an original open-source implementation of image convolution with a 3×3 filter based on Winograd’s minimal filtering algorithm. Compared to direct convolution, Winograd’s algorithm reduces the number of arithmetic operations at the cost of complicating the memory access pattern. This study is carried out in the context of image analysis in convolutional neural networks. Our implementation combines C language code with BLAS function calls for general matrix-matrix multiplication. The code is optimized for Intel Xeon Phi processors x200 (formerly Knights Landing) with Intel Math Kernel Library (MKL) used for BLAS call to the SGEMM function. To test the performance of FALCON in the context of machine learning, we benchmarked it for a set of image and filter sizes corresponding to the VGG Net architecture. In this test, FALCON achieves 10% greater overall performance than convolution from DNN primitives in Intel MKL. However, for some layers, FALCON is faster than MKL by 1.5x, but for other layers slower by as much as 4x. This indicates a possibility of a [...]

Machine Learning on 2nd Generation Intel® Xeon Phi™ Processors: Image Captioning with NeuralTalk2, Torch

June 20, 2016

In this case study, we describe a proof-of-concept implementation of a highly optimized machine learning application for Intel Architecture. Our results demonstrate the capabilities of Intel Architecture, particularly the 2nd generation Intel Xeon Phi processors (formerly codenamed Knights Landing), in the machine learning domain. Download as PDF: Colfax-NeuralTalk2-Summary.pdf (814 KB) or read online below. Code: see our branch of NeuralTalk2 for instructions on reproducing our results (in Readme.md). It uses our optimized branch of Torch to run efficiently on Intel architecture. See also: colfaxresearch.com/get-ready-for-intel-knights-landing-3-papers/ 1. Case Study It is common in the machine learning (ML) domain to see applications implemented with the use of frameworks and libraries such as Torch, Caffe, TensorFlow, and similar. This approach allows the computer scientist to focus on the learning algorithm, leaving the details of performance optimization to the framework. Similarly, the ML frameworks usually rely on a third-party library such as Atlas, CuBLAS, [...]

Optimization Techniques for the Intel MIC Architecture. Part 3 of 3: False Sharing and Padding

August 8, 2015

This is part 3 of a 3-part educational series of publications introducing select topics on optimization of applications for Intel’s multi-core and manycore architectures (Intel Xeon processors and Intel Xeon Phi coprocessors). In this paper we discuss false sharing, highlighting the situations in which it may occur, and eliminating it with the help of data container padding. For a practical illustration, we construct and optimize a micro-kernel for binning particles based on their coordinates. Similar workloads occur in Monte Carlo simulations, particle physics software, and statistical analysis. Results show that the impact of false sharing may be as high as an order of magnitude performance loss in a parallel application. On Intel Xeon processors, padding required to eliminate false sharing is greater than on Intel Xeon Phi coprocessors, so target-specific padding values may be used in real-life applications. See also: Part 1: Multi-Threading and Parallel Reduction Part 2: Strip-Mining for Vectorization Part 3: False Sharing and Padding Complete paper: [...]

Optimization Techniques for the Intel MIC Architecture. Part 2 of 3: Strip-Mining for Vectorization

June 26, 2015

This is part 2 of a 3-part educational series of publications introducing select topics on optimization of applications for Intel’s multi-core and manycore architectures (Intel Xeon processors and Intel Xeon Phi coprocessors). In this paper we discuss data parallelism. Our focus is automatic vectorization and exposing vectorization opportunities to the compiler. For a practical illustration, we construct and optimize a micro-kernel for particle binning particles. Similar workloads occur applications in Monte Carlo simulations, particle physics software, and statistical analysis. The optimization technique discussed in this paper leads to code vectorization, which results in an order of magnitude performance improvement on an Intel Xeon processor. Performance on Xeon Phi compared to that on a high-end Xeon is 1.4x greater in single precision and 1.6x greater in double precision. See also: Part 1: Multi-Threading and Parallel Reduction Part 2: Strip-Mining for Vectorization Part 3: False Sharing and Padding Complete paper: Colfax_Optimization_Techniques_2_of_3.pdf (650 KB) [...]

Optimization Techniques for the Intel MIC Architecture. Part 1 of 3: Multi-Threading and Parallel Reduction

May 29, 2015

This is part 1 of a 3-part educational series of publications introducing select topics on optimization of applications for the Intel multi-core and manycore architectures (Intel Xeon processors and Intel Xeon Phi coprocessors). In this paper we focus on thread parallelism and race conditions. We discuss the usage of mutexes in OpenMP to resolve race conditions. We also show how to implement efficient parallel reduction using thread-private storage and mutexes. For a practical illustration, we construct and optimize a micro-kernel for binning particles based on their coordinates. Workloads like this one occur in such applications as Monte Carlo simulations, particle physics software, and statistical analysis. The optimization technique discussed in this paper leads to a performance increase of 25x on a 24-core CPU and up to 100x on the MIC architecture compared to a single-threaded implementation on the same architectures. In the next publication of this series, we will demonstrate further optimization of this workload, focusing on vectorization. See also: Part 1: Multi-Threading [...]

Fine-Tuning Vectorization and Memory Traffic on Intel Xeon Phi Coprocessors: LU Decomposition of Small Matrices

January 27, 2015

Common techniques for fine-tuning the performance of automatically vectorized loops in applications for Intel Xeon Phi coprocessors are discussed. These techniques include strength reduction, regularizing the vectorization pattern, data alignment and aligned data hint, and pointer disambiguation. In addition, the loop tiling technique of memory traffic tuning is shown. The optimization methods are illustrated on an example of single-threaded LU decomposition of a single precision matrix of size 128×128. Benchmarks show that the discussed optimizations improve the performance on the coprocessor by a factor of 2.8 compared to the unoptimized code, and by a factor of 1.7 on the multi-core host system, achieving roughly the same performance on the host and on the coprocessor. The code discussed in the paper can be freely downloaded from this page. Complete paper: Colfax_LU.pdf (604 KB) Source code for Linux: colfax-lu.tgz (17 [...]

Intel Cilk Plus for Complex Parallel Algorithms: “Enormous Fast Fourier Transforms” (EFFT) Library

September 18, 2014

In this paper we demonstrate the methodology for parallelizing the computation of large one-dimensional discrete fast Fourier transforms (DFFTs) on multi-core Intel Xeon processors. DFFTs based on the recursive Cooley-Tukey method have to control cache utilization, memory bandwidth and vector hardware usage, and at the same time scale across multiple threads or compute nodes. Our method builds on single-threaded Intel Math Kernel Library (MKL) implementation of DFFT, and uses the Intel Cilk Plus framework for thread parallelism. We demonstrate the ability of Intel Cilk Plus to handle parallel recursion with nested loop-centric parallelism without tuning the code to the number of cores or cache metrics. The result of our work is a library called EFFT that performs 1D DFTs of size 2^N for N>=21 faster than the corresponding Intel MKL parallel DFT implementation by up to 1.5x, and faster than FFTW by up to 2.5x. The code of EFFT is available for free download under the GPLv3 license. This work provides a new efficient DFFT implementation, and at the same time demonstrates an [...]

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