Rui's Blog
  • Rui's Blog/Paper Reading Notes - Introduction
  • Personal Blog
    • Personal Blog - Index
      • How to Create Picture-in-Picture Effect / Video Overlay for a Presentation Video
      • How to Do Your Part to Protect the Environment in Wisconsin
      • How to Get a Driver's License in Wisconsin
      • How to Travel from the U.S. to China onboard AA127 in June 2021
      • How to Transfer Credits Back to UW-Madison
      • Resources on Learning Academic Writing (for Computer Science)
    • Towards applying to CS Ph.D. programs
  • Machine Learning Systems
    • Machine Learning Systems - Index
      • MLSys Papers - Short Notes
      • [2011 NSDI] Dominant Resource Fairness: Fair Allocation of Multiple Resource Types
      • [2014 OSDI] Scaling Distributed Machine Learning with the Parameter Server
      • [2018 OSDI] Gandiva: Introspective Cluster Scheduling for Deep Learning
      • [2018 SIGCOMM] Chameleon: Scalable Adaptation of Video Analytics via Temporal and Cross-camera ...
      • [2018 NIPS] Dynamic Space-Time Scheduling for GPU Inference
      • [2019 ATC] Analysis of Large-Scale Multi-Tenant GPU Clusters for DNN Training Workloads
      • [2019 NSDI] Tiresias: A GPU Cluster Manager for Distributed Deep Learning
      • [2019 SOSP] ByteScheduler: A Generic Communication Scheduler for Distributed DNN Training ...
      • [2019 SOSP] PipeDream: Generalized Pipeline Parallelism for DNN Training
      • [2019 SOSP] Parity Models: Erasure-Coded Resilience for Prediction Serving Systems
      • [2019 NIPS] GPipe: Efficient Training of Giant Neural Networks using Pipeline Parallelism
      • [2019 SC] ZeRO: memory optimizations toward training trillion parameter models
      • [2020 OSDI] Gavel: Heterogeneity-Aware Cluster Scheduling Policies for Deep Learning Workloads
      • [2020 OSDI] AntMan: Dynamic Scaling on GPU Clusters for Deep Learning
      • [2020 OSDI] BytePS: A High Performance and Generic Framework for Distributed DNN Training
      • [2020 SIGCOMM] Reducto: On-Camera Filtering for Resource-Efficient Real-Time Video Analytics
        • [2020 MLSys] Salus: Fine-Grained GPU Sharing Primitives for Deep Learning Applications
      • [2020 EuroSys] AlloX: Compute Allocation in Hybrid Clusters
      • [2020 VLDB] PyTorch Distributed: Experiences on Accelerating Data Parallel Training
      • [2020 NetAI] Is Network the Bottleneck of Distributed Training?
      • [2020 NSDI] Themis: Fair and Efficient GPU Cluster Scheduling
      • [2021 MLSys] Accordion: Adaptive Gradient Communication via Critical Learning Regime Identification
      • [2021 VLDB] Analyzing and Mitigating Data Stalls in DNN Training
      • [2021 FAST] CheckFreq: Frequent, Fine-Grained DNN Checkpointing
      • [2021 EuroMLSys] Interference-Aware Scheduling for Inference Serving
      • [2021 OSDI] Pollux: Co-adaptive Cluster Scheduling for Goodput-Optimized Deep Learning
      • [2021 MLSys] Wavelet: Efficient DNN Training with Tick-Tock Scheduling
      • [2021 NSDI] SwitchML: Scaling Distributed Machine Learning with In-Network Aggregation
    • Big Data Systems - Index
      • Big Data Systems Papers - Short Notes
      • [2003 SOSP] The Google File System
      • [2004 OSDI] MapReduce: Simplified Data Processing on Large Clusters
      • [2010 SIGMOD] Pregel: A System for Large-Scale Graph Processing
      • [2011 NSDI] Mesos: A Platform for Fine-Grained Resource Sharing in the Data Center
      • [2012 NSDI] Resilient Distributed Datasets: A Fault-Tolerant Abstraction for In-Memory Cluster ...
      • [2012 OSDI] PowerGraph: Distributed Graph-Parallel Computation on Natural Graphs
      • [2019 FAST] DistCache: Provable Load Balancing for Large-Scale Storage Systems with Distributed...
      • [2021 HotOS] From Cloud Computing to Sky Computing
      • [2021 EuroSys] NextDoor: Accelerating graph sampling for graph machine learning using GPUs
  • Earlier Readings & Notes
    • High Performance Computing Course Notes
      • Lecture 1: Course Overview
      • Lecture 2: From Code to Instructions. The FDX Cycle. Instruction Level Parallelism.
      • Lecture 3: Superscalar architectures. Measuring Computer Performance. Memory Aspects.
      • Lecture 4: The memory hierarchy. Caches.
      • Lecture 5: Caches, wrap up. Virtual Memory.
      • Lecture 6: The Walls to Sequential Computing. Moore’s Law.
      • Lecture 7: Parallel Computing. Flynn's Taxonomy. Amdahl's Law.
      • Lecture 8: GPU Computing Intro. The CUDA Programming Model. CUDA Execution Configuration.
      • Lecture 9: GPU Memory Spaces
      • Lecture 10: GPU Scheduling Issues.
      • Lecture 11: Execution Divergence. Control Flow in CUDA. CUDA Shared Memory Issues.
      • Lecture 12: Global Memory Access Patterns and Implications.
      • Lecture 13: Atomic operations in CUDA. GPU ode optimization rules of thumb.
      • Lecture 14: CUDA Case Studies. (1) 1D Stencil Operation. (2) Vector Reduction in CUDA.
      • Lecture 15: CUDA Case Studies. (3) Parallel Prefix Scan on the GPU. Using Multiple Streams in CUDA.
      • Lecture 16: Streams, and overlapping data copy with execution.
      • Lecture 17: GPU Computing: Advanced Features.
      • Lecture 18: GPU Computing with thrust and cub.
      • Lecture 19: Hardware aspects relevant in multi-core, shared memory parallel computing.
      • Lecture 20: Multi-core Parallel Computing with OpenMP. Parallel Regions.
      • Lecture 21: OpenMP Work Sharing.
      • Lecture 22: OpenMP Work Sharing
      • Lecture 23: OpenMP NUMA Aspects. Caching and OpenMP.
      • Lecture 24: Critical Thinking. Code Optimization Aspects.
      • Lecture 25: Computing with Supercomputers.
      • Lecture 26: MPI Parallel Programming General Introduction. Point-to-Point Communication.
      • Lecture 27: MPI Parallel Programming Point-to-Point communication: Blocking vs. Non-blocking sends.
      • Lecture 28: MPI Parallel Programming: MPI Collectives. Overview of topics covered in the class.
    • Cloud Computing Course Notes
      • 1.1 Introduction to Clouds, MapReduce
      • 1.2 Gossip, Membership, and Grids
      • 1.3 P2P Systems
      • 1.4 Key-Value Stores, Time, and Ordering
      • 1.5 Classical Distributed Algorithms
      • 4.1 Spark, Hortonworks, HDFS, CAP
      • 4.2 Large Scale Data Storage
    • Operating Systems Papers - Index
      • CS 736 @ UW-Madison Fall 2020 Reading List
      • All File Systems Are Not Created Equal: On the Complexity of Crafting Crash-Consistent Applications
      • ARC: A Self-Tuning, Low Overhead Replacement Cache
      • A File is Not a File: Understanding the I/O Behavior of Apple Desktop Applications
      • Biscuit: The benefits and costs of writing a POSIX kernel in a high-level language
      • Data Domain: Avoiding the Disk Bottleneck in the Data Domain Deduplication File System
      • Disco: Running Commodity Operating Systems on Scalable Multiprocessors
      • FFS: A Fast File System for UNIX
      • From WiscKey to Bourbon: A Learned Index for Log-Structured Merge Trees
      • LegoOS: A Disseminated, Distributed OS for Hardware Resource Disaggregation
      • LFS: The Design and Implementation of a Log-Structured File System
      • Lottery Scheduling: Flexible Proportional-Share Resource Management
      • Memory Resource Management in VMware ESX Server
      • Monotasks: Architecting for Performance Clarity in Data Analytics Frameworks
      • NFS: Sun's Network File System
      • OptFS: Optimistic Crash Consistency
      • RAID: A Case for Redundant Arrays of Inexpensive Disks
      • RDP: Row-Diagonal Parity for Double Disk Failure Correction
      • Resource Containers: A New Facility for Resource Management in Server Systems
      • ReVirt: Enabling Intrusion Analysis through Virtual-Machine Logging and Replay
      • Scheduler Activations: Effective Kernel Support for the User-Level Management of Parallelism
      • SnapMirror: File-System-Based Asynchronous Mirroring for Disaster Recovery
      • The Linux Scheduler: a Decade of Wasted Cores
      • The Unwritten Contract of Solid State Drives
      • Venti: A New Approach to Archival Storage
    • Earlier Notes
      • How to read a paper
  • FIXME
    • Template for Paper Reading Notes
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On this page
  • One-line Summary
  • Paper Structure Outline
  • Background & Motivation
  • Design and Implementation
  • Layered file system
  • Summary vector (bloom filter)
  • Stream-informed layout
  • Locality-preserved caching
  • Procedures of a segment write
  • Evaluation
  • New Vocabulary
  • Links

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  1. Earlier Readings & Notes
  2. Operating Systems Papers - Index

Data Domain: Avoiding the Disk Bottleneck in the Data Domain Deduplication File System

One-line Summary

The Data Domain Deduplication File System introduces some techniques to relieve the disk bottleneck in previous works. The techniques combined can remove 99% of the disk accesses for deduplication.

Paper Structure Outline

  1. Introduction

  2. Challenges and Observations

    1. Variable vs. Fixed Length Segments

    2. Segment Size

    3. Performance-Capacity Balance

    4. Fingerprint vs. Byte Comparisons

  3. Deduplication Storage System Architecture

    1. Content Store

    2. Segment Store

    3. Container Manager

  4. Acceleration Methods

    1. Summary Vector

    2. Stream-Informed Segment Layout

    3. Locality Preserved Caching

    4. Accelerated Segment Filtering

  5. Experimental Results

    1. Results with Real World Data

    2. I/O Savings with Summary Vector and Locality Preserved Caching

    3. Throughput

    4. Discussion

  6. Related Work

  7. Conclusions

Background & Motivation

Design and Implementation

The three main performance enhancement techniques are:

  1. Summary vectors

  2. Stream-informed layout

  3. Locality-preserved caching

The Data Domain File System also featured a layered file system architecture.

Layered file system

  • Content Store: Manages data in files; Breaks data into segments; Does the fingerprinting

  • Segment Store: Maps segment descriptors (fingerprints) to data; Performs deduplication; Keeps track of references, updates segment index; Compresses segments and pushes to container layer

  • Container Manager: Provides container abstraction; Write fixed-sized containers entirely

Summary vector (bloom filter)

This avoids going to disk and writing data if the data already exists. Bloom filters are used to check the fingerprint. It may produce false positives but no false negatives (i.e. the summary vector will not tell you that an existing fingerprint doesn't exist), so it's only a slight performance problem.

Stream-informed layout

The motivation is that fingerprints are random, distributed, but the same group of fingerprints is likely to occur at the same time in the future. The idea is to dedicate containers to holding segments & fingerprints in the logical order. This improves locality and fewer number of I/Os by the container manager.

Locality-preserved caching

An extension of the idea that motivated stream-informed layout. We divide the cache into container-sized units and cache on the granularity of containers. If we need one of the items in the container, we will likely need all of them as well.

Procedures of a segment write

  1. Check if the fingerprint is in the segment cache. If yes, then we are done. Else, continue to step 2.

  2. Check the summary vector to see if the data is already written.

    1. If not (new data), then append it to the current container (for locality with the other data in the container). Once the container is full, it is passed off to the container manager.

    2. If yes (old data), it might be a false positive so we check if it really exists.

      1. Check the index, if it's really in there (duplicate), insert it into the segment cache along with all the other fingerprints in the container.

      2. Otherwise, go to step 2.1 (append to the current container).

Evaluation

New Vocabulary

Links

PreviousBiscuit: The benefits and costs of writing a POSIX kernel in a high-level languageNextDisco: Running Commodity Operating Systems on Scalable Multiprocessors

Last updated 4 years ago

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The throughput for data deduplication in was bad. This work aims to resolve those issues.

: A space-efficient probabilistic data structure that is used to test whether an element is a member of a set.

Venti
Bloom filter
Paper PDF
Presentation Video at FAST '08
Presentation Audio at FAST '08
3MB
Data deduplication.pdf
pdf
Prof. Andrea Arpaci-Dusseau's course notes on Data Deduplication
CS 736 course notes by Prof. Andrea Arpaci-Dusseau
CS 736 course notes by Prof. Andrea Arpaci-Dusseau
~100-fold performance improvement using the combination of the two techniques