Apache Spark<= MPI接口

随着大数据分析的重要性不断增加,对有效和可扩展的数值线性代数和机器学习实现的需求不断增长。自从Apache Spark引入以来,它已经成为这个领域中不可或缺的工具,具有易用性、与Hadoop生态系统的互操作性和容错性等吸引人的特性。然而,已经表明,使用高性能计算中常用的并行编程工具MPI实现的数值线性代数例程可以超过等效Spark例程一个数量级或更多。
展开查看详情

1.An Apache Spark ⇔ MPI Interface Kai Rothauge, Alex Gittens, Michael W. Mahoney Thanks to NERSC and Cray Inc. for help and support! #Res1SAIS

2.What is MPI? • MPI = Message Passing Interface • A specification for the developers and users of message passing libraries • Message-Passing Parallel Programming Model: • cooperative operations between processes • data moved from address space of one process to that of another • Dominant model in high-performance computing • Requires installation of MPI implementation on system • Popular implementations: MPICH, Open MPI #Res1SAIS 2

3.More on MPI • Generally regarded as “low-level” for purposes of distributed computing • Efficient implementations of collective operations • Works with distributed memory, shared memory, GPUs • Communication between MPI processes: • via TCP/IP sockets, or • optimized for underlying interconnects (InfiniBand, Cray Aries, Intel Omni-Path, etc.) • Communicator objects connect groups of MPI processors • Con: No fault tolerance or elasticity #Res1SAIS 3

4.Case Study: Spark vs. MPI • Numerical linear algebra (NLA) using Spark vs. MPI • Why do linear algebra in Spark? Spark for data-centric workloads and scientific analysis Characterization of linear algebra in Spark Customers demand Spark; want to understand performance concerns #Res1SAIS 4

5.Case Study: Spark vs. MPI • Numerical linear algebra (NLA) using Spark vs. MPI • Why do linear algebra in Spark? Pros: Faster development, easier reuse Simple dataset abstractions (RDDs, DataFrames, DataSets) An entire ecosystem that can be used before and after NLA computations Spark can take advantage of available local linear algebra codes Automatic fault-tolerance, elasticity, out-of-core support Con: Classical MPI-based linear algebra implementations will be faster and more efficient #Res1SAIS 5

6.Case Study: Spark vs. MPI • Numerical linear algebra (NLA) using Spark vs. MPI • Computations performed on NERSC supercomputer Cori Phase 1, a Cray XC40 • 2,388 compute nodes • 128 GB RAM/node, 32 2.3GHz Haswell cores/node • Lustre storage system, Cray Aries interconnect A. Gittens et al. “Matrix factorizations at scale: A comparison of scientific data analytics in Spark and C+MPI using three case studies”, 2016 IEEE International Conference on Big Data (Big Data), pages 204–213, Dec 2016. #Res1SAIS 6

7.Case Study: Spark vs. MPI • Numerical linear algebra (NLA) using Spark vs. MPI • Matrix factorizations considered include truncated Singular Value Decomposition (SVD) • Data sets include • Ocean temperature data - 2.2 TB • Atmospheric data - 16 TB A. Gittens et al. “Matrix factorizations at scale: A comparison of scientific data analytics in Spark and C+MPI using three case studies”, 2016 IEEE International Conference on Big Data (Big Data), pages 204–213, Dec 2016. #Res1SAIS 7

8.Case Study: Spark vs. MPI Rank 20 SVD of 2.2TB ocean temperature data #Res1SAIS 8

9.Case Study: Spark vs. MPI Rank 20 SVD of 16TB atmospheric data using 48K+ cores #Res1SAIS 9

10.Case Study: Spark vs. MPI Lessons learned: • With favorable data (tall and skinny) and well-adapted algorithms, linear algebra in Spark is 2x-26x slower than MPI when I/O is included • Spark’s overheads: • Can be order of magnitude higher than the actual computation times • Anti-scale • The gaps in performance suggest it may be better to interface with MPI-based codes from Spark #Res1SAIS 10

11.• Alchemist interfaces between Apache Spark and existing or custom MPI-based libraries for large-scale linear algebra, machine learning, etc. • Idea: • Use Spark for regular data analysis workflow • When computationally intensive calculations are required, call relevant MPI-based codes from Spark using Alchemist, send results to Spark • Combine high productivity of Spark with high performance of MPI #Res1SAIS 11

12.Target users: • Scientific community: Use Spark for analysis of large scientific datasets by calling existing MPI-based libraries where appropriate • Machine learning practitioners and data analysts: • Better performance of a wide range of large-scale, computationally intensive ML and data analysis algorithms • For instance, SVD for principal component analysis, recommender systems, leverage scores, etc. #Res1SAIS 12

13.Basic Framework • Alchemist: Acts as bridge between Spark and MPI-based libraries • Alchemist-Client Interface: API for user, communicates with Alchemist via TCP/IP sockets • Alchemist-Library Interface: Shared object, imports MPI library, provides generic interface for Alchemist to communicate with library #Res1SAIS 13

14.Basic Framework Basic workflow: • Spark application: • Sends distributed dataset from RDD (IndexedRowMatrix) to Alchemist • Tells Alchemist what MPI-based code should be called • Alchemist loads relevant MPI-based library, calls function, sends results to Spark #Res1SAIS 14

15.Basic Framework • Alchemist can also load data from file • Alchemist needs to store distributed data in appropriate format that can be used by MPI-based libraries: • Candidates: ScaLAPACK, Elemental, PLAPACK • Alchemist currently uses Elemental, support for ScaLAPACK under development • #Res1SAIS 15

16.Alchemist Architecture #Res1SAIS 16

17.Sample API import alchemist.{Alchemist, AlMatrix} import alchemist.libA.QRDecomposition // libA is sample MPI lib // other code here ... // sc is instance of SparkContext val ac = new Alchemist.AlchemistContext(sc, numWorkers) ac.registerLibrary("libA", ALIlibALocation) // maybe other code here ... val alA = AlMatrix(A) // A is IndexedRowMatrix // routine returns QR factors of A as AlMatrix objects val (alQ, alR) = QRDecomposition(alA) // send data from Alchemist to Spark once ready val Q = alQ.toIndexedRowMatrix() // convert AlMatrix alQ to RDD val R = alR.toIndexedRowMatrix() // convert AlMatrix alR to RDD // maybe other code here ... ac.stop() // release resources once no longer required #Res1SAIS 17

18.Example: Matrix Multiplication • Requires expensive shuffles in Spark, which is impractical: • Matrices/RDDs are row-partitioned • One matrix must be converted to be column-partitioned • Requires an all-to-all shuffle that often fails once the matrix is distributed #Res1SAIS 18

19.Example: Matrix Multiplication GB/nodes Spark+Alchemist Spark Send (s) Multiplication (s) Receive (s) Total (s) Total (s) 0.8/1 5.90±2.17 6.60±0.07 2.19±0.58 14.68±2.69 160.31±8.89 12/1 16.66±0.88 75.69±0.42 19.43±0.45 111.78±1.26 809.31±51.90 56/2 32.50±2.88 178.68±24.8 55.83±0.37 267.02±27.38 -Failed- 144/4 69.40±1.85 171.73±0.81 66.80±3.46 307.94±4.57 -Failed- • Generated random matrices and used same number of Spark and Alchemist nodes • Take-away: Spark’s matrix multiply is slow even on one executor, and unreliable once there are more #Res1SAIS 19

20.Example: Truncated SVD Use Alchemist and MLlib to get rank 20 truncated SVD Experiment Setup • Spark: 22 nodes; Alchemist: 8 nodes • A: m-by-10K, where m = 5M, 2.5M, 1.25M, 625K, 312.5K • Ran jobs for at most 30 minutes (1800 s) #Res1SAIS 20

21.Example: Truncated SVD Experiment Setup • 2.2TB (6,177,583-by-46,752) ocean • Data replicated column-wise temperature data read in from HDF5 file #Res1SAIS 21

22.Upcoming Features • PySpark, SparkR ⇔ MPI Interface • Interface for Python => PySpark support • Future work: Interface for R • More Functionality • Support for sparse matrices • Support for MPI-based libraries built on ScaLAPACK • Alchemist and Containers • Alchemist running in Docker and Kubernetes • Will enable Alchemist on clusters and the cloud #Res1SAIS 22

23.Limitations and Constraints • Two copies of data in memory, more during a relayout during computation • Data transfer overhead between Spark and Alchemist when data on different nodes • Subject to network disruptions and overload • MPI is not fault tolerant or elastic • Lack of MPI-based libraries for machine learning • No equivalent to MLlib currently available, closest is MaTEx • On Cori, need to run Alchemist and Spark on separate nodes -> more data transfer over interconnects -> larger overheads #Res1SAIS 23

24.Future Work • Apache Spark ⇔ X Interface • Interest in connecting Spark with other libraries for distributed computing (e.g. Cray Chapel, Apache REEF) • Reduce communication costs • Exploit locality • Reduce number of messages • Use communication protocols designed for underlying network infrastructure • Run as network service • MPI computations with (basic) fault tolerance and elasticity #Res1SAIS 24

25. github.com/project-alchemist/ References ● A. Gittens, K. Rothauge, M. W. Mahoney, et al., “Alchemist: Accelerating Large-Scale Data Analysis by offloading to High-Performance Computing Libraries”, 2018, Proceedings of the 24th ACM SIGKDD International Conference, Aug 2018, to appear ● A. Gittens, K. Rothauge, M. W. Mahoney, et al., “Alchemist: An Apache Spark ⇔ MPI Interface”, 2018, to appear in CCPE Special Issue on Cray User Group Conference 2018 Thanks to Cray Inc., DARPA and NSF for financial support #Res1SAIS 25