Distributed Data Analysis with Hadoop and R - Strangeloop 2011
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This document describes a talk on interfacing Hadoop and R for distributed data analysis. It introduces Hadoop and R, discusses options for running R on Hadoop's distributed platform including the authors' prototypes, and provides an example use case of analyzing airline on-time performance data using Hadoop Streaming and R code. The authors are data engineers from Orbitz who have built prototypes for user segmentation and analyzing airline and hotel booking data on Hadoop using R.
![Airline Delay Plot: R code
> deptdelays.monthly.full <- read.delim("~/OSCON2011/Delays_by_Month.dat", header=F)
!
> View(deptdelays.monthly.full)!
> names(deptdelays.monthly.full) <- c("Year","Month","Count","Airline","Delay”)!
> Delay_by_month <- deptdelays.monthly.full[order(deptdelays.monthly.full
$Delay,decreasing=TRUE),]
> Top_10_Delay_by_Month <- Delay_by_Month[1:10,]!
> Top_10_Normal <- ((Delay - mean(Delay)) / sd(Delay))!
> symbols( Month, Delay, circles= Top_10_Normal, inches=.3, fg="white”,bg="red”,…)!
> text(Month, Delay, Airline, cex= 0.5)!
page 21](https://image.slidesharecdn.com/strangeloop2011orbitzfinal-110920084631-phpapp02/85/Distributed-Data-Analysis-with-Hadoop-and-R-Strangeloop-2011-21-320.jpg)
![RHIPE – Dataflow
Keys = […]
Values =
[1988,1,9,6,1348,1331,1458,1435,PI,942,NA,70,64,NA,23,17,SYR,BWI...
1988,1,17,7,1331,1331,1440,1435,PI,942,NA,69,64,NA,5,0,SYR,BWI…
Input to map 1987,10,14,3,741,730,912,849,PS,1451,NA,91,79,NA,23,11,SAN,SFO...
1987,10,21,3,728,730,848,849,PS,1451,NA,80,79,NA,-1,-2,SAN,SFO...
*
1987,10,23,5,731,730,902,849,PS,1451,NA,91,79,NA,13,1,SAN,SFO…
1987,10,30,5,1712,1658,1811,1800,DL,475,NA,59,62,NA,11,14,LEX,ATL...]
PI|1988|1
17
PI|1988|1
0
PS|1987|10
11
Output from map PS|1987|10
-2
PS|1987|10
1
DL|1987|10
14
* Note that Input to map is a vector of keys and a vector of values.
page 38](https://image.slidesharecdn.com/strangeloop2011orbitzfinal-110920084631-phpapp02/85/Distributed-Data-Analysis-with-Hadoop-and-R-Strangeloop-2011-38-320.jpg)
![RHIPE – Dataflow Continued
DL|1987|10
[14]
Input to reduce PI|1988|1
[0, 17]
*
PS|1987|10
[1,11,-2]
1987
10
1
DL
14
Output from reduce 1988
1987
1
10
2
3
PI
PS
8.5
3.333333
* Input to reduce is a key and a vector containing a subset of intermediate
values associated with that key. The reduce will get called until no more
values exist for the key.
page 39](https://image.slidesharecdn.com/strangeloop2011orbitzfinal-110920084631-phpapp02/85/Distributed-Data-Analysis-with-Hadoop-and-R-Strangeloop-2011-39-320.jpg)
Distributed Data Analysis with Hadoop and R - Strangeloop 2011
- 1. Distributed Data Analysis with Hadoop and R Jonathan Seidman and Ramesh Venkataramaiah, Ph. D. StrangeLoop2011 September 20 | 2011
- 2. Flow of this Talk • Introductions • Hadoop, R and Interfacing the two • Our Prototypes • A use case for interfacing Hadoop and R • Alternatives for Running R on Hadoop • Alternatives to Hadoop and R • Conclusions • References
- 3. Who We Are • Ramesh Venkataramaiah, Ph. D. – Principal Engineer, TechOps – [email protected] – @rvenkatar • Jonathan Seidman – Lead Engineer, Business Intelligence/Big Data Team – Co-founder/organizer of Chicago Hadoop User Group ( http://www.meetup.com/Chicago-area-Hadoop-User-Group-CHUG) and Chicago Big Data (http://www.meetup.com/Chicago-Big-Data/ – [email protected] – @jseidman • Orbitz Careers – http://careers.orbitz.com/ – @OrbitzTalent
- 4. Launched in 2001 Over 160 million bookings 7th Largest seller of travel in the world page 4
- 5. Hadoop and R as an analytic platform?
- 6. What is Hadoop? Distributed file system (HDFS) and parallel processing framework. Uses MapReduce programming model as the core. Provides fault tolerant and scalable storage of very large datasets across machines in a cluster.
- 7. What is R? When do we need it? Open-source stat package with visualization Vibrant community support. One-line calculations galore! Steep learning curve but worth it! Insight into statistical properties and trends… or for machine learning purposes… or Big Data to be understood well. page 7
- 8. Our Options • Data volume reduction by sampling – Very bad for long-tail data distribution – Approximation lead to bad conclusion • Scaling R – Still in-memory – But make it parallel using segue, Rhipe, R-Hive… • Use sql-like interfaces – Apache Hive with Hadoop – File sprawl and process issues • Regular DBMS – How to fit square peg in a round hole – No in-line R calls from SQL but commercial efforts are underway. • This Talk: How to bring Hadoop’s parallel processing capability to R environment. page 8
- 9. Our prototypes User segmentations Hotel bookings Airline Performance* * Public dataset page 9
- 10. We have two distinct dataspaces serving different constituents Semi-structure data Transactional data (e.g. searches) (e.g. bookings) Hadoop Cluster Data Warehouse page 10
- 11. Our Hadoop infrastructure allows us to record and process user activity at the individual level Detailed Non- Transactional Data Transactional Data (e.g. bookings) (What Each User Sees and Clicks) Data Warehouse Hadoop page 11
- 12. Getting a Buy-in presented a long-term, semi-structured data growth story and explained how this will help harness long-tail opportunities at lowest cost. - Traditional DW! - Big Data! - Classical Stats! - Specific spikes! - Sampling! - Median is not the message! - Create a universal key ! - Always keep source data! - Operationalize the infrastructure! * From a blog
- 13. An example of “median is not the message” • Positional Bias during Hotel Searches
- 14. Our Customers pick top positions the most…
- 15. Safari Users Seem to be Interested in More Expensive Hotels page 15
- 16. Seasonal variations • Customer hotel stay gets longer during summer months • Could help in designing search based on seasons. page 16
- 17. Workload and Resource Partition � � � � � � � � � � � � � � � � � � � � � � � � � � page 17
- 18. Airline Performance page 18
- 19. Description of Use Case • Analyze openly available dataset: Airline on-time performance. • Dataset was used in Visualization Poster Competition 2009 – Consists of flight arrival/departure details from 1987-2008. – Approximately 120 MM records totaling 12GB. • Available at: http://stat-computing.org/dataexpo/2009/ page 19
- 20. Our dataset page 20
- 21. Airline Delay Plot: R code > deptdelays.monthly.full <- read.delim("~/OSCON2011/Delays_by_Month.dat", header=F) ! > View(deptdelays.monthly.full)! > names(deptdelays.monthly.full) <- c("Year","Month","Count","Airline","Delay”)! > Delay_by_month <- deptdelays.monthly.full[order(deptdelays.monthly.full $Delay,decreasing=TRUE),] > Top_10_Delay_by_Month <- Delay_by_Month[1:10,]! > Top_10_Normal <- ((Delay - mean(Delay)) / sd(Delay))! > symbols( Month, Delay, circles= Top_10_Normal, inches=.3, fg="white”,bg="red”,…)! > text(Month, Delay, Airline, cex= 0.5)! page 21
- 22. Airline delay page 22
- 23. Multiple Distributions: R code > library(lattice)! > deptdelays.monthly.full$Year <- as.character(deptdelays.monthly.full$Year)! > h <- histogram(~Delay|Year,data=deptdelays.monthly.full,layout=c(5,5))! > update(h)! page 23
- 24. Running R on Hadoop: Hadoop Streaming page 24
- 25. Hadoop Streaming – Overview • An alternative to the Java MapReduce API which allows you to write jobs in any language supporting stdin/stdout. • Limited to text data in current versions of Hadoop. Support for binary streams added in 0.21.0. • Requires installation of R on all DataNodes. page 25
- 26. Hadoop Streaming – Dataflow 1988,1,9,6,1348,1331,1458,1435,PI,942,NA,70,64,NA,23,17,SYR,BWI... 1988,1,17,7,1331,1331,1440,1435,PI,942,NA,69,64,NA,5,0,SYR,BWI… Input to map 1987,10,14,3,741,730,912,849,PS,1451,NA,91,79,NA,23,11,SAN,SFO... 1987,10,21,3,728,730,848,849,PS,1451,NA,80,79,NA,-1,-2,SAN,SFO... 1987,10,23,5,731,730,902,849,PS,1451,NA,91,79,NA,13,1,SAN,SFO… * 1987,10,30,5,1712,1658,1811,1800,DL,475,NA,59,62,NA,11,14,LEX,ATL... PI|1988|1 17 PI|1988|1 0 PS|1987|10 11 Output from map PS|1987|10 -2 PS|1987|10 1 DL|1987|10 14 * Map function receives input records line-by-line via standard input. page 26
- 27. Hadoop Streaming – Dataflow Continued DL|1987|10 14 PI|1988|1 0 Input to reduce PI|1988|1 17 PS|1987|10 PS|1987|10 1 11 * PS|1987|10 -2 1987 10 1 DL 14 Output from reduce 1988 1987 1 10 2 3 PI PS 8.5 3.333333 * Reduce receives map output key/value pairs sorted by key, line-by-line. page 27
- 28. Hadoop Streaming Example – map.R page 28
- 29. Hadoop Streaming Example – reduce.R page 29
- 30. Running R on Hadoop: Hadoop Interactive page 30
- 31. Hadoop Interactive (hive) – Overview • Very unfortunate acronym. • Provides an interface to Hadoop from the R environment. – Functions to access HDFS – Control Hadoop – And run streaming jobs directly from R • Allows HDFS data, including the output from MapReduce processing, to be manipulated and analyzed directly from R. • Seems to still have some rough edges. page 31
- 32. Hadoop Interactive – Example page 32
- 33. Running R on Hadoop: RHIPE page 33
- 34. RHIPE – Overview • Active project with frequent updates and active community. • RHIPE is based on Hadoop streaming source, but provides some significant enhancements, such as support for binary files (sort of). • Developed to provide R users with access to same Hadoop functionality available to Java developers. – For example, provides rhcounter() and rhstatus(), analagous to counters and the reporter interface in the Java API. page 34
- 35. RHIPE – Overview • Can be somewhat confusing and intimidating. – Then again, the same can be said for the Java API. – Worth taking the time to get comfortable with. page 35
- 36. RHIPE – Overview • Allows developers to work directly on data stored in HDFS in the R environment. • Also allows developers to write MapReduce jobs in R and execute them on the Hadoop cluster. • RHIPE uses Google protocol buffers to serialize data. Most R data types are supported. – Using protocol buffers increases efficiency and provides interoperability with other languages. • Must be installed on all DataNodes. page 36
- 37. RHIPE – MapReduce map <- expression({}) ! reduce <- expression( ! pre = {…},! reduce = {…}, ! post = {…}! ) ! z <- rhmr(map=map,reduce=reduce,! inout=c("text","sequence ), ! ifolder=INPUT_PATH ,! ofolder=OUTPUT_PATH,! …)! rhex(z) ! page 37
- 38. RHIPE – Dataflow Keys = […] Values = [1988,1,9,6,1348,1331,1458,1435,PI,942,NA,70,64,NA,23,17,SYR,BWI... 1988,1,17,7,1331,1331,1440,1435,PI,942,NA,69,64,NA,5,0,SYR,BWI… Input to map 1987,10,14,3,741,730,912,849,PS,1451,NA,91,79,NA,23,11,SAN,SFO... 1987,10,21,3,728,730,848,849,PS,1451,NA,80,79,NA,-1,-2,SAN,SFO... * 1987,10,23,5,731,730,902,849,PS,1451,NA,91,79,NA,13,1,SAN,SFO… 1987,10,30,5,1712,1658,1811,1800,DL,475,NA,59,62,NA,11,14,LEX,ATL...] PI|1988|1 17 PI|1988|1 0 PS|1987|10 11 Output from map PS|1987|10 -2 PS|1987|10 1 DL|1987|10 14 * Note that Input to map is a vector of keys and a vector of values. page 38
- 39. RHIPE – Dataflow Continued DL|1987|10 [14] Input to reduce PI|1988|1 [0, 17] * PS|1987|10 [1,11,-2] 1987 10 1 DL 14 Output from reduce 1988 1987 1 10 2 3 PI PS 8.5 3.333333 * Input to reduce is a key and a vector containing a subset of intermediate values associated with that key. The reduce will get called until no more values exist for the key. page 39
- 40. RHIPE – Example page 40
- 41. RHIPE – Example page 41
- 42. RHIPE – Example page 42
- 43. Running R on Hadoop: rmr page 43
- 44. rmr Overview • New project from Revolution Analytics introduced August 2011. • Part of RHadoop, a suite of open-source projects which also includes: – rhdfs – functions to access and manage HDFS from within R. – rhbase – functions providing basic connectivity to HBase. • Goals are to provide productive environment for MapReduce programming in an R-like way - “…stay true to map reduce and true to R …” • Reduce gets all intermediate values for each key (yay!). • Like RHIPE, based on streaming source. page 44
- 45. rmr – Example page 45
- 46. Running R on Hadoop: Segue page 46
- 47. Segue – Overview • Intended to work around single-threading in R by taking advantage of Hadoop streaming to provide simple parallel processing. – For example, running multiple simulations in parallel. • Suitable for embarrassingly pleasantly parallel problems – big CPU, not big data. • Runs on Amazon’s Elastic Map Reduce (EMR). – Not intended for internal clusters. • Provides emrlapply(), a parallel version of lapply()! page 47
- 48. Segue – Example page 48
- 49. Performance Comparison: Streaming and RHIPE page 49
- 50. Performance Testing – Environment and Setup • Twenty-eight DataNodes: – Dual hex-core – 24GB RAM – Shared cluster. • Data – Airline dataset – 22 input files – About 12GB uncompressed data page 50
- 51. Performance Comparison Number of Reducers Streaming RHIPE 264 246 seconds* 96 seconds* *All numbers are an average of 3 runs. page 51
- 52. Alternatives Alternate languages/libraries: • Apache Mahout – Scalable machine learning library. – Offers clustering, classification, collaborative filtering on Hadoop. • Python – Many modules available to support scientific and statistical computing. page 52
- 53. Alternatives Alternative parallel processing frameworks: • Revolution Analytics – Provides commercial packages to support processing big data with R. • Other HPC/parallel processing packages for R, e.g. Rmpi or snow. page 53
- 54. Alternatives Apache Hive + RJDBC? • We haven t been able to get it to work yet. • You can however wrap calls to the Hive client in R to return R objects. See https://github.com/satpreetsingh/rDBwrappers/wiki page 54
- 55. Alternatives Interesting solutions that you can t have: • Ricardo – Developed as part of a research project at IBM. – Interesting paper published, but apparently no plans to make available. page 55
- 56. Conclusions • If practical, consider using Hadoop to aggregate data for input to R analyses. • Avoid using R for general purpose MapReduce use. page 56
- 57. Conclusions • For simple MapReduce jobs, or embarrassingly parallel jobs on a local cluster, consider Hadoop streaming. – Limited to processing text only. – But easy to test at the command line outside of Hadoop: • $ cat DATAFILE |./map.R |sort |./reduce.R! • To run compute-bound analyses with relatively small amount of data on the cloud look at Segue. page 57
- 58. Conclusions • Otherwise, your best bet is RHIPE, but definitely check out rmr. • Also consider alternatives – Mahout, Python, etc. page 58
- 59. Conclusions On an operational note: • Make sure your cluster nodes are consistent – same version of R installed, required libraries are installed on each node, etc. page 59
- 60. Example Code • https://github.com/jseidman/hadoop-R page 60
- 61. References • Hadoop – Apache Hadoop project: http://hadoop.apache.org/ – Hadoop The Definitive Guide, Tom White, O Reilly Press, 2011 • R – R Project for Statistical Computing: http://www.r-project.org/ – R Cookbook, Paul Teetor, O Reilly Press, 2011 – Getting Started With R: Some Resources: http://quanttrader.info/public/gettingStartedWithR.html page 61
- 62. References • Hadoop Streaming – Documentation on Apache Hadoop Wiki: http://hadoop.apache.org/mapreduce/docs/current/ streaming.html – Word count example in R : https://forums.aws.amazon.com/thread.jspa? messageID=129163 page 62
- 63. References • Hadoop InteractiVE – Project page on CRAN: http://cran.r-project.org/web/packages/hive/index.html – Simple Parallel Computing in R Using Hadoop: http://www.rmetrics.org/Meielisalp2009/Presentations/ Theussl1.pdf page 63
- 64. References • RHIPE – RHIPE - R and Hadoop Integrated Processing Environment: http://www.stat.purdue.edu/~sguha/rhipe/ – Code: http://code.google.com/p/rhipe/ – Wiki: http://code.google.com/p/rhipe/w/list – Installing RHIPE on CentOS: https://groups.google.com/forum/#!topic/brumail/ qH1wjtBgwYI – Introduction to using RHIPE: http://ml.stat.purdue.edu/rhafen/rhipe/ – RHIPE combines Hadoop and the R analytics language, SD Times: http://www.sdtimes.com/link/34792 page 64
- 65. References • RHIPE – Using R and Hadoop to Analyze VoIP Network Data for QoS, Hadoop World 2010: • video: http://www.cloudera.com/videos/ hw10_video_using_r_and_hadoop_to_analyze_voip_net work_data_for_qos • slides: http://www.cloudera.com/resource/ hw10_voice_over_ip_studying_traffic_characteristics_for _quality_of_service – RHIPE examples (k-means, etc.): http://groups.google.com/group/brumail/browse_thread/ thread/e403db404f039e31?pli=1 page 65
- 66. References • RHadoop (including rmr) – Github: https://github.com/RevolutionAnalytics/RHadoop – Advanced Big Data Analytics with R and Hadoop whitepaper: http://info.revolutionanalytics.com/R-and-Hadoop-Big-Data- Analytics-White-Paper.html page 66
- 67. References • Segue – Project page: http://code.google.com/p/segue/ – Google Group:http://groups.google.com/group/segue-r – Abusing Amazon s Elastic MapReduce Hadoop service… easily, from R, Jefferey Breen: http://jeffreybreen.wordpress.com/2011/01/10/segue-r-to- amazon-elastic-mapreduce-hadoop/ – Presentation at Chicago Hadoop Users Group March 23, 2011: http://files.meetup.com/1634302/segue-presentation- RUG.pdf page 67
- 68. References • Sawmill (A framework for integrating a PMML-compliant Scoring Engine with Hadoop). – More information: • Open Data Group www.opendatagroup.com • [email protected] – Augustus, an open source system for building & scoring statistical models • augustus.googlecode.com – PMML • Data Mining Group: dmg.org – Analytics over Clouds using Hadoop, presentation at Chicago Hadoop User Group: http://files.meetup.com/1634302/CHUG 20100721 Sawmill.pdf page 68
- 69. References • Ricardo – Ricardo: Integrating R and Hadoop, paper: http://www.cs.ucsb.edu/~sudipto/papers/sigmod2010- das.pdf – Ricardo: Integrating R and Hadoop, Powerpoint presentation: http://www.uweb.ucsb.edu/~sudipto/talks/Ricardo- SIGMOD10.pptx page 69
- 70. References • General references on Hadoop and R – Pete Skomoroch s R and Hadoop bookmarks: http://www.delicious.com/pskomoroch/R+hadoop – Pigs, Bees, and Elephants: A Comparison of Eight MapReduce Languages: http://www.dataspora.com/2011/04/pigs-bees-and- elephants-a-comparison-of-eight-mapreduce-languages/ – Quora – How can R and Hadoop be used together?: http://www.quora.com/How-can-R-and-Hadoop-be-used- together page 70
- 71. References • Mahout – Mahout project: http://mahout.apache.org/ – Mahout in Action, Owen, et. al., Manning Publications, 2011 • Python – Think Stats, Probability and Statistics for Programmers, Allen B. Downey, O Reilly Press, 2011 • CRAN Task View: High-Performance and Parallel Computing with R, a set of resources compiled by Dirk Eddelbuettel: http://cran.r-project.org/web/views/ HighPerformanceComputing.html page 71
- 72. References • Other examples of airline data analysis with R: – A simple Big Data analysis using the RevoScaleR package in Revolution R: http://www.r-bloggers.com/a-simple-big-data-analysis-using- the-revoscaler-package-in-revolution-r/ page 72
- 73. And finally… Parallel R (working title), Q Ethan McCallum, Stephen Weston, O Reilly Press, due autumn 2011 R meets Big Data - a basket of strategies to help you use R for large-scale analysis and computation. page 73