A Survey on Automatic Parameter Tuning for Big Data Processing Systems

Big data processing systems (e.g., Hadoop, Spark, Storm) contain a vast number of configuration parameters controlling parallelism, I/O behavior, memory settings, and compression. Improper parameter settings can cause significant performance degradation and stability issues. However, regular users and even expert administrators grapple with understanding and tuning them to achieve good performance. We investigate existing approaches on parameter tuning for both batch and stream data processing systems and classify them into six categories: rule-based, cost modeling, simulation-based, experiment-driven, machine learning, and adaptive tuning. We summarize the pros and cons of each approach and raise some open research problems for automatic parameter tuning.Peer reviewe

Performance modelling, analysis and prediction of Spark jobs in Hadoop cluster : a thesis by publications presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Computer Science, School of Mathematical & Computational Sciences, Massey University, Auckland, New Zealand

Big Data frameworks have received tremendous attention from the industry and from academic research over the past decade. The advent of distributed computing frameworks such as Hadoop MapReduce and Spark are powerful frameworks that offer an efficient solution for analysing large-scale datasets running under the Hadoop cluster. Spark has been established as one of the most popular large-scale data processing engines because of its speed, low latency in-memory computation, and advanced analytics. Spark computational performance heavily depends on the selection of suitable parameters, and the configuration of these parameters is a challenging task. Although Spark has default parameters and can deploy applications without much effort, a significant drawback of default parameter selection is that it is not always the best for cluster performance. A major limitation for Spark performance prediction using existing models is that it requires either large input data or system configuration that is time-consuming. Therefore, an analytical model could be a better solution for performance prediction and for establishing appropriate job configurations. This thesis proposes two distinct parallelisation models for performance prediction: the 2D-Plate model and the Fully-Connected Node model. Both models were constructed based on serial boundaries for a certain arrangement of executors and size of the data. In order to evaluate the cluster performance, various HiBench workloads were used, and workload’s empirical data were fitted with the models for performance prediction analysis. The developed models were benchmarked with the existing models such as Amdahl’s, Gustafson, ERNEST, and machine learning. Our experimental results show that the two proposed models can quickly and accurately predict performance in terms of runtime, and they can outperform the accuracy of machine learning models when extrapolating predictions

Towards General and Efficient Online Tuning for Spark

The distributed data analytic system -- Spark is a common choice for processing massive volumes of heterogeneous data, while it is challenging to tune its parameters to achieve high performance. Recent studies try to employ auto-tuning techniques to solve this problem but suffer from three issues: limited functionality, high overhead, and inefficient search. In this paper, we present a general and efficient Spark tuning framework that can deal with the three issues simultaneously. First, we introduce a generalized tuning formulation, which can support multiple tuning goals and constraints conveniently, and a Bayesian optimization (BO) based solution to solve this generalized optimization problem. Second, to avoid high overhead from additional offline evaluations in existing methods, we propose to tune parameters along with the actual periodic executions of each job (i.e., online evaluations). To ensure safety during online job executions, we design a safe configuration acquisition method that models the safe region. Finally, three innovative techniques are leveraged to further accelerate the search process: adaptive sub-space generation, approximate gradient descent, and meta-learning method. We have implemented this framework as an independent cloud service, and applied it to the data platform in Tencent. The empirical results on both public benchmarks and large-scale production tasks demonstrate its superiority in terms of practicality, generality, and efficiency. Notably, this service saves an average of 57.00% memory cost and 34.93% CPU cost on 25K in-production tasks within 20 iterations, respectively

Efficient Resource Management for Deep Learning Clusters

Deep Learning (DL) is gaining rapid popularity in various domains, such as computer vision, speech recognition, etc. With the increasing demands, large clusters have been built to develop DL models (i.e., data preparation and model training). DL jobs have some unique features ranging from their hardware requirements to execution patterns. However, the resource management techniques applied in existing DL clusters have not yet been adapted to those new features, which leads to resource inefficiency and hurts the performance of DL jobs. We observed three major challenges brought by DL jobs. First, data preparation jobs, which prepare training datasets from a large volume of raw data, are memory intensive. DL clusters often over-allocate memory resource to those jobs for protecting their performance, which causes memory underutilization in DL clusters. Second, the execution time of a DL training job is often unknown before job completion. Without such information, existing cluster schedulers are unable to minimize the average Job Completion Time (JCT) of those jobs. Third, model aggregations in Distributed Deep Learning (DDL) training are often assigned with a fixed group of CPUs. However, a large portion of those CPUs are wasted because the bursty model aggregations can not saturate them all the time. In this thesis, we propose a suite of techniques to eliminate the mismatches between DL jobs and resource management in DL clusters. First, we bring the idea of memory disaggregation to enhance the memory utilization of DL clusters. The unused memory in data preparation jobs is exposed as remote memory to other machines that are running out of local memory. Second, we design a two-dimensional attained-service-based scheduler to optimize the average JCT of DL training jobs. This scheduler takes the temporal and spatial characteristics of DL training jobs into consideration and can efficiently schedule them without knowing their execution time. Third, we define a shared model aggregation service to reduce the CPU cost of DDL training. Using this service, model aggregations from different DDL training jobs are carefully packed together and use the same group of CPUs in a time-sharing manner. With these techniques, we demonstrate that huge improvements in resource efficiency and job performance can be obtained when the cluster’s resource management matches with the features of DL jobs.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169955/1/jcgu_1.pd

A Study of Scalability and Cost-effectiveness of Large-scale Scientific Applications over Heterogeneous Computing Environment

Recent advances in large-scale experimental facilities ushered in an era of data-driven science. These large-scale data increase the opportunity to answer many fundamental questions in basic science. However, these data pose new challenges to the scientific community in terms of their optimal processing and transfer. Consequently, scientists are in dire need of robust high performance computing (HPC) solutions that can scale with terabytes of data. In this thesis, I address the challenges in three major aspects of scientific big data processing as follows: 1) Developing scalable software and algorithms for data- and compute-intensive scientific applications. 2) Proposing new cluster architectures that these software tools need for good performance. 3) Transferring the big scientific dataset among clusters situated at geographically disparate locations. In the first part, I develop scalable algorithms to process huge amounts of scientific big data using the power of recent analytic tools such as, Hadoop, Giraph, NoSQL, etc. At a broader level, these algorithms take the advantage of locality-based computing that can scale with increasing amount of data. The thesis mainly addresses the challenges involved in large-scale genome analysis applications such as, genomic error correction and genome assembly which made their way to the forefront of big data challenges recently. In the second part of the thesis, I perform a systematic benchmark study using the above-mentioned algorithms on different distributed cyberinfrastructures to pinpoint the limitations in a traditional HPC cluster to process big data. Then I propose the solution to those limitations by balancing the I/O bandwidth of the solid state drive (SSD) with the computational speed of high-performance CPUs. A theoretical model has been also proposed to help the HPC system designers who are striving for system balance. In the third part of the thesis, I develop a high throughput architecture for transferring these big scientific datasets among geographically disparate clusters. The architecture leverages the power of Ethereum\u27s Blockchain technology and Swarm\u27s peer-to-peer (P2P) storage technology to transfer the data in secure, tamper-proof fashion. Instead of optimizing the computation in a single cluster, in this part, my major motivation is to foster translational research and data interoperability in collaboration with multiple institutions

High Performance Computing [electronic resource] : ISC High Performance 2016 International Workshops, ExaComm, E-MuCoCoS, HPC-IODC, IXPUG, IWOPH, P^3MA, VHPC, WOPSSS, Frankfurt, Germany, June 19–23, 2016, Revised Selected Papers /

This book constitutes revised selected papers from 7 workshops that were held in conjunction with the ISC High Performance 2016 conference in Frankfurt, Germany, in June 2016. The 45 papers presented in this volume were carefully reviewed and selected for inclusion in this book. They stem from the following workshops: Workshop on Exascale Multi/Many Core Computing Systems, E-MuCoCoS; Second International Workshop on Communication Architectures at Extreme Scale, ExaComm; HPC I/O in the Data Center Workshop, HPC-IODC; International Workshop on OpenPOWER for HPC, IWOPH; Workshop on the Application Performance on Intel Xeon Phi – Being Prepared for KNL and Beyond, IXPUG; Workshop on Performance and Scalability of Storage Systems, WOPSSS; and International Workshop on Performance Portable Programming Models for Accelerators, P3MA.E-MuCoCoS -- 2016 Workshop on Exascale Multi/Many Core Computing Systems -- Behavioral Emulation for Scalable Design-Space Exploration of Algorithms and Architectures -- Closing the Performance Gap with Modern C++ -- Energy Efficient Runtime Framework for Exascale Systems -- Extreme-Scale In-Situ Visualization of Turbulent Flows on IBM Blue Gene/Q JUQUEEN -- The EPiGRAM Project: Preparing Parallel Programming Models for Exascale -- Work Distribution of Data-parallel Applications on Heterogeneous Systems -- ExaComm -- Reducing manipulation overhead of remote data-structure by controlling remote memory access order -- SONAR: Automated Communication Characterization for HPC Applications -- HPC-IODC -- HPC I/O in the Data Center Workshop -- An Overview of the Sirocco Parallel Storage System -- Analyzing Data Properties using Statistical Sampling Techniques -- Illustrated on Scientific File Formats and Compression Features -- Delta: Data Reduction for Integrated Application Workflows and Data Storage -- Investigating Read Performance of Python and NetCDF4 when using HPC Parallel Filesystems -- IWOPH -- International Workshop on OpenPOWER for HPC -- Early Application Performance at the Hartree Centre with the OpenPOWER Architecture -- Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms -- Exploring Energy Efficiency for GPU-Accelerated POWER Servers -- First Experiences with ab initio Molecular Dynamics on OpenPOWER: The Case of CPMD -- High Performance Computing on the IBM Power8 platform -- Measuring and Managing Energy in OpenPOWER -- Performance Analysis of Spark/GraphX on POWER8 Cluster -- Performance of the 3D Combustion Simulation code RECOM-AIOLOS on IBM POWER8 architecture -- Performance-Portable Many-Core Plasma Simulations: Porting PIConGPU to OpenPower and Beyond -- IXPUG -- Application Performance on Intel Xeon Phi -- Being Prepared for KNL and Beyond -- A Comparative Study of Application Performance and Scalability on the Intel Knights Landing Processor -- Application Suitability Assessment for Many-Core Targets -- Applying the Rooine Performance Model to the Intel Xeon Phi Knights Landing Processor -- Dynamic SIMD Vector Lane Scheduling -- High performance optimizations for nuclear physics code MFDn on KNL -- Optimization of the sparse matrix-vector products of an IDR Krylov iterative solver in EMGeo for the Intel KNL manycore processor -- Optimizing a Multiple Right-hand Side Dslash Kernel for Intel Knights Corner -- Optimizing Excited-State Electronic-Structure Codes for Intel Knights Landing: a Case Study on the BerkeleyGW Software -- Optimizing Wilson-Dirac operator and linear solvers for Intel KNL -- P^3MA -- First International Workshop on Performance Portable Programming Models for Accelerators Workshop -- A C++ Programming Model for Heterogeneous System Architecture -- Battling Memory Requirements of Array Programming through Streaming -- From Describing to Prescribing Parallelism: Translating the SPEC ACCEL OpenACC Suite to OpenMP Target Directives -- GPU-STREAM v2.0: Benchmarking the achievable memory bandwidth of many-core processors across diverse parallel programming models -- Porting the MPI Parallelized LES Model PALM to Multi-GPU Systems -- an Experience Report -- Software Cost Analysis of GPU-Accelerated Aeroacoustics Simulations in C++ with OpenACC -- Task-Based Cholesky Decomposition on Knights Corner using OpenMP -- Using C++ AMP to accelerate HPC applications on Multiple Platforms -- WOPSSS -- Analysis of Memory Performance: Mixed Rank Performance across Microarchitectures -- Considering I/O Processing in CloudSim for Performance and Energy Evaluation -- Early Evaluation of the "Infinite Memory Engine" Burst Buffer Solution -- Motivation and Implementation of a Dynamic Remote Storage System for I/O demanding HPC Applications -- Parallel I/O Architecture Modelling Based on File System Counters -- User-space I/O for µs – levelstoragedevices -- Scaling Spark on Lustre.This book constitutes revised selected papers from 7 workshops that were held in conjunction with the ISC High Performance 2016 conference in Frankfurt, Germany, in June 2016. The 45 papers presented in this volume were carefully reviewed and selected for inclusion in this book. They stem from the following workshops: Workshop on Exascale Multi/Many Core Computing Systems, E-MuCoCoS; Second International Workshop on Communication Architectures at Extreme Scale, ExaComm; HPC I/O in the Data Center Workshop, HPC-IODC; International Workshop on OpenPOWER for HPC, IWOPH; Workshop on the Application Performance on Intel Xeon Phi – Being Prepared for KNL and Beyond, IXPUG; Workshop on Performance and Scalability of Storage Systems, WOPSSS; and International Workshop on Performance Portable Programming Models for Accelerators, P3MA