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Journal Seminar: Is Singularity-based Container Technology Ready for Running MPI Application on HPC Clouds?

Journal Seminar: Is Singularity-based Container Technology Ready for Running MPI Application on HPC Clouds?

Journal Seminar in [email protected] Tech (2018-04-19)
https://www.bi.cs.titech.ac.jp/

metaVariable

April 26, 2018
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  1. Is Singularity-based Container Technology Ready for Running MPI Applications on

    HPC Clouds? by Jie Zhang, Xiaoyi Lu, Dhabaleswar K. Panda* * The Ohio State University In Proceedings of the10th International Conference on Utility and Cloud Computing (UCC '17) pp.151-160, 2017. Kento Aoyama, Ph.D. Student Akiyama Laboratory, Dept. of Computer Science, Tokyo Institute of Technology Journal Seminar (Akiyama and Ishida Laboratory) on April 19th, 2018
  2. Self-Introduction 2 Name Aoyama Kento 青山 健人 Research Interests High

    Performance Computing, Container Virtualization, Parallel/Distributed Computing, Bioinformatics Educations WebCV https://metavariable.github.io @meta1127 富山高等専門学校 情報工学科 (A.Sc. in Eng.) 電気通信大学 電気通信学部 情報工学科 (B.Sc. in Eng.) 東京工業大学 大学院情報理工学研究科 修士課程 (M.Sc. in Eng.) (富士通株式会社 / Software Developer, Fujitsu Ltd.) 東京工業大学 情報理工学院 博士課程 (Ph.D. Student)
  3. SlideShare: https://www.slideshare.net/KentoAoyama/reproducibility-of-computational- workflows-is-automated-using-continuous-analysis Side-Story | Bioinformatics + Container 3

  4. 4 Why do we have to do the “INSTALLATION BATTLE”

    on Supercomputers ? Isn’t it a waste of time? image from Jiro Ueda, “Why don’t you do your best?”, 2004.
  5. 1. Meta-Information • Conference / Authors / Abstract 2. Background

    • Container-Virtualization 3. HPC Features • Intel Knight Landing 4. Experiments 5. Conclusion 6. (Additional Discussion) Outline 5
  6. • In Proceedings of the10th International Conference on Utility and

    Cloud Computing (UCC '17) • Place : Austin, Texas, USA • Date : December 5-8, 2017 • H5-Index : 14.00 ( https://aminer.org/ranks/conf ) Conference Information 6 http://www.depts.ttu.edu/cac/conferences/ucc2017/
  7. Jie Zhang • Ph.D Student in NOWLAB (Network Based Computing

    Lab) • Best Student Paper Award (UCC’17, this paper) Prof. Dhabaleswar K. (DK) Panda • Professor of the Ohio State University • Faculty of NOWLAB MVAPICH • famous MPI Implementation in HPC e.g.) Sunway TaihuLight, TSUBAME2.5, etc. • http://mvapich.cse.ohio-state.edu/publications/ OSU Benchmark • MPI Communication Benchmark • point-to-point, collective, non-blocking, GPU memory access, … Authors 7 “The MVAPICH Project: Evolution and Sustainability of an Open Source Production Quality MPI Library for HPC” D. Panda, K. Tomko, K. Schulz, A. Majumdar Int'l Workshop on Sustainable Software for Science: Practice and Experiences, Nov 2013. http://nowlab.cse.ohio-state.edu/people
  8. Question: “Is Singularity-based Container Technology Ready for Running MPI Applications

    on HPC Clouds?” Answer: Yes. • Singularity shows near-native performance even when running MPI (HPC) applications • Container-Technology is ready for HPC field! What’s the message? 8
  9. • Presents 4-Dimension based Evaluation Methodology for Characterizing Singularity Performance

    Contributions (1/2) 9 Singularity Omni-Path Intel KNL Intel Xeon Haswell Intel KNL - Cluster Modes - Cache/Flat Modes InfiniBand
  10. • Conducts Extensive Performance Evaluation on cutting-edge HPC technologies •

    Intel Xeon • Intel KNL • Omni-Path • InfiniBand • Provides Performance Reports and analysis of running MPI Benchmarks with Singularity on different platforms • Chameleon Cloud ( https://www.chameleoncloud.org/ ) • Local Clusters Contributions (2/2) 10
  11. Background Container Virtualization 11

  12. 12 Why do we have to do the “INSTALLATION BATTLE”

    on Supercomputers ? Because of … - Complex Library Dependencies ... - Version Mismatch of Libraries (Too old…) etc.
  13. 13 All you needs is Container-Technology … To end the

    “INSTALLATION BATTLE” image from Jiro Ueda, “Why don’t you do your best?”, 2004.
  14. Application-Centric Virtualization or “Process-Level Virtualization” Background | Container Virtualization 14

    Hardware Virtual Machine App Guest OS Bins/Libs Virtual Machine App Guest OS Bins/Libs Hypervisor Virtual Machines (Hypervisor-based Virtualization) Hardware Linux Kernel Container App Bins/Libs Container App Bins/Libs Containers (Container-based Virtualization) Fast & Lightweight
  15. Linux Container • Concept of Linux container based on Linux

    namespace. • No visibility to objects outside the container • Containers have another level of access controls namespace • namespace can isolates system resources • creates separate instances of global namespaces • process id (PID), host & domain name (UTS), inter-process communication (IPC), users (UID), … • Processes running inside the container … • shares the host Linux kernel • has its own root directory and mount table • performs to be running on a normal Linux system Background | Linux Container (namespace) 15 E. W. Biederman. “Multiple instances of the global Linux namespaces.”, In Proceedings of the 2006 Ottawa Linux Symposium, 2006. Hardware Linux Kernel Container App Bins/Libs own namespace, pid, uid, gid, hosntname, filesystem, …
  16. Background | Portability (e.g. Docker) 16 Keeping Portability & Reproducibility

    for application • Easy to port the application using Docker Hub • Easy to reproduce the Environments using Dockerfile Docker Hub Image App Bins/Libs Push Pull Dockerfile apt-get install … wget … … make Generate Share Ubuntu Docker Engine Container App Bins/Libs Image App Bins/Libs Linux Kernel Container App Bins/Libs Image App Bins/Libs CentOS Docker Engine Linux Kernel
  17. How about on Performance? • virtualization overhead • Compute, Network

    I/O, File I/O, … • Latency, Bandwidth, Throughput, … How about on Security? • requires root-daemon process (Docker) • requires SUID for binary (Shifter, Singularity) How about on Usability? • where to store container image (repository, local file, …) • affinity with user’s workflow Background | Concerns on HPC Field 17
  18. SlideShare: https://www.slideshare.net/KentoAoyama/an-updated-performance- comparison-of-virtual-machines-and-linux-containers-73758906 Side-Story | Docker Performance 18

  19. Side-Story | Docker Performance Overview (1/2) 19 Case Perf. Category

    Docker KVM A, B CPU Good Bad* C Memory Bandwidth (sequential) Good Good D Memory Bandwidth (Random) Good Good E Network Bandwidth Acceptable* Acceptable* F Network Latency Bad* Bad G Block I/O (Sequential) Good Good G Block I/O (RandomAccess) Good (with Volume Option) Bad Comparing to native performance … equal = Good a little worse = Acceptable worse = Bad *= depends case or tuning
  20. Side-Story | Docker Performance Overview (2/2) 20 [1] W. Felter,

    A. Ferreira, R. Rajamony, and J. Rubio, “An updated performance comparison of virtual machines and Linux containers,” IEEE International Symposium on Performance Analysis of Systems and Software, pp.171-172, 2015. (IBM Research Report, RC25482 (AUS1407-001), 2014.) 0.96 1.00 0.98 0.78 0.83 0.99 0.82 0.98 0.00 0.20 0.40 0.60 0.80 1.00 PXZ [MB/s] Linpack [GFLOPS] Random Access [GUPS] Performance Ratio [based Native] Native Docker KVM KVM-tuned
  21. Docker Solomon Hykes and others. “What is Docker?” - https://www.docker.com/what-docker

    Shifter W. Bhimji, S. Canon, D. Jacobsen, L. Gerhardt, M. Mustafa, and J. Porter, “Shifter : Containers for HPC,” Cray User Group, pp. 1–12, 2016. Singularity Gregory M. K., Vanessa S., Michael W. B., “Singularity: Scientific containers for mobility of compute”, PLOS ONE 12(5): e0177459. Background | Containers for HPC 21
  22. Background | Singularity (OSS) 22 Gregory M. K., Vanessa S.,

    Michael W. B., “Singularity: Scientific containers for mobility of compute”, PLOS ONE 12(5): e0177459. Linux Container OSS for HPC Workload • Developed by LBNL (Lawrence Berkeley National Laboratory, USA) Key Features • Near-native performance • Not-require the root daemon • Compatible with Docker Container Format • Support HPC Features • NVIDIA GPU, MPI, InfiniBand, etc. http://singularity.lbl.gov/
  23. Background | Singularity Workflow 23 Command privilege Functions singularity create

    required create a empty container image file singularity import required import container image from registry (e.g. Docker Hub) singularity bootstrap required build a container image from definition file singularity shell (partially) required attach interactive-shell into the container (‘--writable’ option requires privilege) singularity run run a container process from container image file singularity exec execute user-command inside the container process https://singularity.lbl.gov/
  24. • Container Virtualization is a application-centric virtualization technology • can

    packages library dependencies • can provide Application Portability & Reproducibility under the reasonable Performance • “Singularity” is a Linux Container OSS for HPC Workloads • provide near-native performance • support HPC features (GPU, MPI, InfiniBand, …) Background | Summary 24
  25. HPC Features Intel KNL: Memory Modes Intel KNL: Cluster Modes

    Intel Omni-Path 25
  26. Intel KNL (Knight Landing) 26 2nd Generation Intel® Xeon Phi

    Processor • MIC (Many Integrated Core) designed by Intel® for High-Performance Computing • covers similar HPC areas with GPU • allow use of standard programming language API such as OpenMP, MPI, … • Examples of use on Supercomputers • Oakforest-PACS by JCAHPC (Tokyo Univ., Tsukuba Univ.) • Tianhe-2A by NSCC-GZ (China) A. Sodani, “Knights landing (KNL): 2nd Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  27. Intel KNL Architecture 27 A. Sodani, “Knights landing (KNL): 2nd

    Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  28. Intel KNL Memory Modes 28 A. Sodani, “Knights landing (KNL):

    2nd Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  29. Intel KNL Cluster Modes (1/4) 29 A. Sodani, “Knights landing

    (KNL): 2nd Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  30. Intel KNL Cluster Modes (2/4) 30 A. Sodani, “Knights landing

    (KNL): 2nd Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  31. Intel KNL Cluster Modes (3/4) 31 A. Sodani, “Knights landing

    (KNL): 2nd Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  32. Intel KNL Cluster Modes (4/4) 32 A. Sodani, “Knights landing

    (KNL): 2nd Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  33. Intel KNL with Omni-Path 33 A. Sodani, “Knights landing (KNL):

    2nd Generation Intel® Xeon Phi processor,” 2015 IEEE Hot Chips 27 Symp. HCS 2015, 2016.
  34. MIC (Many Integrated Core) designed by Intel® for High-Performance Computing

    Memory Mode • Cache Mode : Automatically use MCDRAM as L3-Cache • Flat Mode : Manually allocate data onto MCDRAM Cluster Mode • All-to-All : Address uniformly hashed across all distributed directories • Quadrant : Address divided into same quadrant • SNC : Each quadrant exposed as a NUMA node (can be seen as 4 sockets) Intel KNL Summary 34
  35. Experiments MPI Point-to-Point Communication Performance MPI Collective Communication Performance HPC

    Application Performance 35
  36. case1: MPI Point-to-Point Communication Performance • MPI_Send / MPI Recv

    • measure Latency and Bandwidth • (both of MPI Intra-Node and MPI Inter-Node) case2: MPI Collective Communication Performance • MPI_Bcast / MPI_Allgather / MPI_Allreduce, MPI_Alltoall • measure Latency and Bandwidth case3: HPC Application Performance • Graph500 (https://graph500.org/) , NAS [NASA, 1991] • measure Execution Time Experiments Overview 36
  37. Chameleon Cloud (for Intel Xeon nodes) • 32 baremetal InfiniBand

    nodes • CPU: Intel Xeon E5-2670v3 (Haswell) 24 cores, 2 sockets • Memory: 128 GB • Network Card: Mellanox ConnectX-3 FDR (56Gbps) Local Cluster (for Intel KNL nodes) • Intel Xeon Phi CPU7250 (1.40 GHz) • Memory: 96 GB (host, DDR4) 16 GB (MCDRAM) • Network Card: Omni-Path HFI Silicon 100 Series fabric controller Clusters Information 37
  38. Common Software Settings • Singularity: 2.3 • gcc: 4.8.3 (used

    for compiling all application & libraries on experiments) • MPI library: MVAPICH2-2.3a • OSU micro-benchmarks v5.3 Others • Results are averaged across 5 runs • Cluster mode was set to “All-to-All” or “Quadrant” (?) • >“Since there is only one NUMA node on KNL architecture, we do not consider intra/inter-socket anymore here.” Other Settings 38
  39. case1: MPI Point-to-Point Communication Performance • Singularity’s overhead is less

    than 7% (on Haswell) • Singularity’s overhead is less than 8% (on KNL) case2: MPI Collective Communication Performance • Singularity’s overhead is less than 8% at all operations • Singularity reflects native performance characteristics case3: HPC Application Performance • Singularity’s overhead is less than 7% at all case “It reveals a promising way for efficiently running MPI applications on HPC clouds.” Results Summary (about Singularity) 39
  40. MPI Point-to-Point Communication Performance on Haswell 40 intra-socket (intra-node) case

    is better InfiniBand FDR 6.4 GB/s
  41. MPI Point-to-Point Communication Performance on KNL with Cache Mode 41

    Latency Performance: Haswell architecture is better than KNL with cache mode Omni-Path fabric controller 9.2 GB/s - complex memory access - maintaining cache coherency
  42. MPI Point-to-Point Communication Performance on KNL with Flat Mode 42

    Omni-Path fabric controller 9.2 GB/s inter-node > intra-node intra-node Bandwidth Performance: KNL with Flat mode is better than KNL with Cache mode because of cache miss penalty on MCDRAM
  43. MPI Collective Communication Performance with 512-Process (32 nodes) on Haswell

    43
  44. MPI Collective Communication Performance with 128-Process (2 nodes) on KNL

    with Cache Mode 44
  45. MPI Collective Communication Performance with 128-Process (2 nodes) on KNL

    with Flat Mode 45 over L2-cache capacity
  46. NAS Parallel Benchmarks Graph500 • Graph data-analytics workload • Heavily

    utilizes point-to-point communication (MPI_Isend, MPI_Irecv) with 4 KB messages for BFS search of random vertices • scale (x, y) = the graph has 2𝑥 vertices and 2𝑦 edges NAS, Graph500 46 CG Conjugate Gradient, irregular memory access and communication EP Embarrassingly Parallel FT discrete 3D fast Fourier Transform, all-to-all communication IS Integer Sort, random memory access LU Lower-Upper Gauss-Seidel solver MG Multi-Grid on a sequence of meshes, long- and short-distance communication, memory intensive
  47. Application Performance with 512-Process (32 nodes) on Haswell 47 Singularity-based

    container technology only introduces <7% overhead
  48. Application Performance with 128-Process (2 nodes) on KNL with Cache/Flat

    Mode 48 Singularity-based container technology only introduces <7% overhead
  49. Discussion (Personal Discussion) 49

  50. • What’s the cause of Singularity’s overhead (0-8%)? • Network?

    File I/O? Memory I/O? Compute? • What’s the cause of the performance differences on Fig.12? (e.g. Traits of Benchmarks) Where Singularity’s overhead come from? 50
  51. 1. Singularity application is invoked 2. Global options are parsed

    and activated 3. The Singularity command (subcommand) process is activated 4. Subcommand options are parsed 5. The appropriate sanity checks are made 6. Environment variables are set 7. The Singularity Execution binary is called (sexec) 8. Sexec determines if it is running privileged and calls the SUID code if necessary 9. Namespaces are created depending on configuration and process requirements 10. The Singularity image is checked, parsed, and mounted in the CLONE_NEWNS namespace 11. Bind mount points are setup so that files on the host are visible in the container 12. The namespace CLONE_FS is used to virtualize a new root file system 13. Singularity calls execvp() and Singularity process itself is replaced by the process inside the container 14. When the process inside the container exits, all namespaces collapse with that process, leaving a clean system (material) Singularity Process Flow 51
  52. Conclusion 52

  53. • proposed a 4D evaluation methodology for HPC clouds •

    conducted the comprehensive studies to evaluate the Singularity’s performance • Singularity-based container technology can achieve near-native performance on Intel Xeon/KNL • Singularity provides a promising way to build the next-generation HPC clouds Conclusion 53