Big Data Processing using Apache Spark and Clojure

Talk given at ClojureD conference, Berlin

Apache Spark is an engine for efficiently processing large amounts of data. We show how to apply the elegance of Clojure to Spark - fully exploiting the REPL and dynamic typing. There will be live coding using our gorillalabs/sparkling API.

In the presentation, we will of course introduce the core concepts of Spark, like resilient distributed data sets (RDD). And you will learn how the Spark concepts resembles those well-known from Clojure, like persistent data structures and functional programming.

Finally, we will provide some Do’s and Don’ts for you to kick off your Spark program based upon our experience.

About Paulus Esterhazy and Christian Betz
Being a LISP hacker for several years, and a Java-guy for some more, Chris turned to Clojure for production code in 2011. He’s been Project Lead, Software Architect, and VP Tech in the meantime, interested in AI and data-visualization.

Now, working on the heart of data driven marketing for Performance Media in Hamburg, he turned to Apache Spark for some Big Data jobs. Chris released the API-wrapper ‘chrisbetz/sparkling’ to fully exploit the power of his compute cluster.

Paulus Esterhazy
Paulus is a philosophy PhD turned software engineer with an interest in functional programming and a penchant for hammock-driven development.

He currently works as Senior Web Developer at Red Pineapple Media in Berlin.

Transcript

1. Big Data Processing using Apache Spark and Clojure Dr. Paulus Esterhazy and Dr. Christian Betz January 2015 https://github.com/pesterhazy/, @pesterhazy https://github.com/chrisbetz/, @chris_betz
2. Who uses Clojure?
3. Who's getting paid to use Clojure?
4. Who uses BigData?
5. Who uses Hadoop?
6. Who uses Spark?
7. About us
8. Paulus red pinapple media GmbH
9. Chris
10. WTF is Spark? Patrick Wendell Databricks Spark Performance Common Patterns and Pitfalls for Implementing Algorithms in Spark Hossein Falaki @mhfalaki hossein@databricks.com Advanced Spark Reynold Xin, July 2, 2014 @ Spark Summit Training Disclaimer: We reuse stuff
11. Apache Spark - an Overview "Apache Spark™ is a fast and general engine for large-scale data processing." Value proposition? Spark keeps stuff in memory where possible, so intermediate results do not need I/O. Spark allows quicker development cycle with proper unit tests (see later) Spark allows to define your own data sources (JDBC in our case). Spark allows you to work with any data structures (so some are better than others).
12. Two Questions “I like Clojure, why might I be interested in Spark?” “Granted that Spark is useful, why program it in Clojure?”
13. Two Questions “I like Clojure, why might I be interested in Spark?” “Granted that Spark is useful, why program it in Clojure?” That's you!
14. How Big Data is processed today large amounts of data to process Hadoop is the de-facto standard Hadoop = MapReduce + HDFS
15. However, Hadoop has some limitations Pain point: performance Writing to disk after each map-/reduce step That's esp. bad for chains of map-/reduce steps and iterative algorithms (machine learning, PageRank) Identified Bottleneck: HDD I/O
16. Spark's Answer Major innovation: data sharing between processing steps In-memory processing
17. Resilient Distributed Datasets (RDDs) Datasets: Collection of elements Distributed: Could be an on any node in the cluster. Resilient: Could get lost (or partially lost), doesn't matter. Spark will recompute.
18. Different types of RDDs, all the same interface Scientific Answer: RDD is an Interface! 1.  Set of partitions (“splits” in Hadoop) 2.  List of dependencies on parent RDDs 3.  Function to compute a partition" (as an Iterator) given its parent(s) 4.  (Optional) partitioner (hash, range) 5.  (Optional) preferred location(s)" for each partition “lineage” optimized execution
19. Different types of RDDs, all the same interface Scientific Answer: RDD is an Interface! 1.  Set of partitions (“splits” in Hadoop) 2.  List of dependencies on parent RDDs 3.  Function to compute a partition" (as an Iterator) given its parent(s) 4.  (Optional) partitioner (hash, range) 5.  (Optional) preferred location(s)" for each partition “lineage” optimized execution Example: HadoopRDD partitions = one per HDFS block dependencies = none compute(part) = read corresponding block preferredLocations(part) = HDFS block location partitioner = none
20. Different types of RDDs, all the same interface Scientific Answer: RDD is an Interface! 1.  Set of partitions (“splits” in Hadoop) 2.  List of dependencies on parent RDDs 3.  Function to compute a partition" (as an Iterator) given its parent(s) 4.  (Optional) partitioner (hash, range) 5.  (Optional) preferred location(s)" for each partition “lineage” optimized execution Example: HadoopRDD partitions = one per HDFS block dependencies = none compute(part) = read corresponding block preferredLocations(part) = HDFS block location partitioner = none Example: Filtered RDD partitions = same as parent RDD dependencies = “one-to-one” on parent compute(part) = compute parent and filter it preferredLocations(part) = none (ask parent) partitioner = none
21. How are RDDs handled? You create an RDD from a data source, e.g. an HDFS file, a Cassandra DB query, or from a JDBC-Query. You transform RDDs (with map, filter, ...), which gives you new RDDs You perform an action on one RDD to get the results from that RDD into your "driver". (like first, take, collect, count, ...)
22. Basic Building Blocks: RDDs Resilient Distributed Datasets Spark follows a function approach: You define collections (RDDs) and functions on collections Sources for RDDs: • Local collections parallelized • HDFS files • Your own (e.g. JDBC-RDD) Transformations (only a selection) • map • filter Actions (only a selection) • reduce (fn) • count
23. Basic Building Blocks: RDDs Resilient Distributed Datasets Spark follows a function approach: You define collections (RDDs) and functions on collections Sources for RDDs: • Local collections parallelized • HDFS files • Your own (e.g. JDBC-RDD) Transformations (only a selection) • map • filter Actions (only a selection) • reduce (fn) • count JdbcRDD (Query) HDFS-File (Path) Sources define the basic RDDs
 you're working on
24. Basic Building Blocks: RDDs Resilient Distributed Datasets Spark follows a function approach: You define collections (RDDs) and functions on collections Sources for RDDs: • Local collections parallelized • HDFS files • Your own (e.g. JDBC-RDD) Transformations (only a selection) • map • filter Actions (only a selection) • reduce (fn) • count JdbcRDD (Query) HDFS-File (Path) map filter Sources define the basic RDDs
 you're working on Transformations create new RDDs
25. Basic Building Blocks: RDDs Resilient Distributed Datasets Spark follows a function approach: You define collections (RDDs) and functions on collections Sources for RDDs: • Local collections parallelized • HDFS files • Your own (e.g. JDBC-RDD) Transformations (only a selection) • map • filter Actions (only a selection) • reduce (fn) • count JdbcRDD (Query) HDFS-File (Path) map filter join Sources define the basic RDDs
 you're working on Transformations create new RDDs
26. Basic Building Blocks: RDDs Resilient Distributed Datasets Spark follows a function approach: You define collections (RDDs) and functions on collections Sources for RDDs: • Local collections parallelized • HDFS files • Your own (e.g. JDBC-RDD) Transformations (only a selection) • map • filter Actions (only a selection) • reduce (fn) • count JdbcRDD (Query) HDFS-File (Path) map filter join filter You provide your own functions in here! Sources define the basic RDDs
 you're working on Transformations create new RDDs
27. Basic Building Blocks: RDDs Resilient Distributed Datasets Spark follows a function approach: You define collections (RDDs) and functions on collections Sources for RDDs: • Local collections parallelized • HDFS files • Your own (e.g. JDBC-RDD) Transformations (only a selection) • map • filter Actions (only a selection) • reduce (fn) • count JdbcRDD (Query) HDFS-File (Path) map filter join filter reduce You provide your own functions in here! Sources define the basic RDDs
 you're working on Transformations create new RDDs Actions spit a
 result to the Driver
28. RDDs in Practice Example code: https://github.com/gorillalabs/ClojureD
29. In Practice 1: line count (defn line-count [lines] (->> lines count)) (defn process [f] (with-open [rdr (clojure.java.io/reader "in.log")] (let [result (f (line-seq rdr))] (if (seq? result) (doall result) result)))) (process line-count)
30. In Practice 2: line count cont'd (defn line-count* [lines] (->> lines s/count)) (defn new-spark-context [] (let [c (-> (s-conf/spark-conf) (s-conf/master "local[*]") (s-conf/app-name "sparkling") (s-conf/set "spark.akka.timeout" "300") (s-conf/set conf) (s-conf/set-executor-env { "spark.executor.memory" "4G", "spark.files.overwrite" "true"}))] (s/spark-context c) )) (defonce sc (delay (new-spark-context))) (defn process* [f] (let [lines-rdd (s/text-file @sc "in.log")] (f lines-rdd))) (defn line-count [lines] (->> lines count)) (defn process [f] (with-open [rdr (clojure.java.io/reader "in.log")] (let [result (f (line-seq rdr))] (if (seq? result) (doall result) result)))) (process line-count)
31. Only go on when your tests are green! (deftest test-line-count*
 (let [conf (test-conf)]
 (spark/with-context
 sc conf
 (testing
 "no lines return 0"
 (is (= 0 (line-count* (spark/parallelize sc [])))))
 
 (testing
 "a single line returns 1"
 (is (= 1 (line-count* (spark/parallelize sc ["this is a single line"])))))
 
 (testing
 "multiple lines count correctly"
 (is (= 10 (line-count* (spark/parallelize sc (repeat 10 "this is a single line"))))))
 )))
32. What's an RDD? What's in it? Take e.g. an JdbcRDD (we all know relational databases...):
33. What's an RDD? What's in it? Take e.g. an JdbcRDD (we all know relational databases...): campaign_id from to active 1 123 2014-01-01 2014-01-31 true 2 234 2014-01-06 2014-01-14 true 3 345 2014-02-01 2014-03-31 false 4 456 2014-02-10 2014-03-09 true
34. What's an RDD? What's in it? Take e.g. an JdbcRDD (we all know relational databases...): campaign_id from to active 1 123 2014-01-01 2014-01-31 true 2 234 2014-01-06 2014-01-14 true 3 345 2014-02-01 2014-03-31 false 4 456 2014-02-10 2014-03-09 true That's your table
35. What's an RDD? What's in it? Take e.g. an JdbcRDD (we all know relational databases...): campaign_id from to active 1 123 2014-01-01 2014-01-31 true 2 234 2014-01-06 2014-01-14 true 3 345 2014-02-01 2014-03-31 false 4 456 2014-02-10 2014-03-09 true That's your table [ {:campaign-id 123 :active true} {:campaign-id 234 :active true} {:campaign-id 345 :active false} {:campaign-id 456 :active true}]
36. What's an RDD? What's in it? Take e.g. an JdbcRDD (we all know relational databases...): campaign_id from to active 1 123 2014-01-01 2014-01-31 true 2 234 2014-01-06 2014-01-14 true 3 345 2014-02-01 2014-03-31 false 4 456 2014-02-10 2014-03-09 true That's your table [ {:campaign-id 123 :active true} {:campaign-id 234 :active true} {:campaign-id 345 :active false} {:campaign-id 456 :active true}] RDDs are lists of objects
37. What's an RDD? What's in it? Take e.g. an JdbcRDD (we all know relational databases...): campaign_id from to active 1 123 2014-01-01 2014-01-31 true 2 234 2014-01-06 2014-01-14 true 3 345 2014-02-01 2014-03-31 false 4 456 2014-02-10 2014-03-09 true That's your table [ {:campaign-id 123 :active true} {:campaign-id 234 :active true} {:campaign-id 345 :active false} {:campaign-id 456 :active true}] RDDs are lists of objects [ #t[123 {:campaign-id 123 :active true}] #t[234 {:campaign-id 234 :active true}]] [ #t[345 {:campaign-id 345 :active false}] #t[456 {:campaign-id 456 :active true}]
38. What's an RDD? What's in it? Take e.g. an JdbcRDD (we all know relational databases...): campaign_id from to active 1 123 2014-01-01 2014-01-31 true 2 234 2014-01-06 2014-01-14 true 3 345 2014-02-01 2014-03-31 false 4 456 2014-02-10 2014-03-09 true That's your table [ {:campaign-id 123 :active true} {:campaign-id 234 :active true} {:campaign-id 345 :active false} {:campaign-id 456 :active true}] RDDs are lists of objects [ #t[123 {:campaign-id 123 :active true}] #t[234 {:campaign-id 234 :active true}]] [ #t[345 {:campaign-id 345 :active false}] #t[456 {:campaign-id 456 :active true}] PairRDDs handle key-value pairs, may have partitioners assigned, keys not necessarily unique!
39. In Practice 3: status codes (defn parse-line [line] (some->> line (re-matches common-log-regex) rest (zipmap [:ip :timestamp :request :status :length :referer :ua :duration]) transform-log-entry)) (defn group-by-status-code [lines] (->> lines (map parse-line) (map (fn [entry] [(:status entry) 1])) (reduce (fn [a [k v]] (update-in a [k] #((fnil + 0) % v))) {}) (map identity)))
40. In Practice 4: status codes cont'd (defn parse-line [line] (some->> line (re-matches common-log-regex) rest (zipmap [:ip :timestamp :request :status :length :referer :ua :duration]) transform-log-entry)) (defn group-by-status-code [lines] (->> lines (map parse-line) (map (fn [entry] [(:status entry) 1])) (reduce (fn [a [k v]] (update-in a [k] #((fnil + 0) % v))) {}) (map identity))) (defn group-by-status-code* [lines] (-> lines (s/map parse-line) (s/map-to-pair (fn [entry] (s/tuple (:status entry) 1))) (s/reduce-by-key +) (s/map (sd/key-value-fn vector)) (s/collect)))
41. In Practice 5: details RDD • Lazy evaluation is explicitly forced • Transformation vs actions • Serialization of Clojure functions
42. In Practice 6: data sources and destinations • Writing to HDFS • Reading from HDFS • HDFS is versatile: text files, S3, Cassandra • Parallelizing regular Clojure collections
43. In Practice 7: top errors (defn top-errors [lines] (->> lines (map parse-line) (filter (fn [entry] (not= "200" (:status entry)))) (map (fn [entry] [(:uri entry) 1])) (reduce (fn [a [k v]] (update-in a [k] #((fnil + 0) % v))) {}) (sort-by val >) (take 10)))
44. In Practice 8: top errors cont'd (defn top-errors* [lines] (-> lines (s/map parse-line) (s/filter (fn [entry] (not= "200" (:status entry)))) s/cache (s/map-to-pair (fn [entry] (s/tuple (:uri entry) 1))) (s/reduce-by-key +) ;; flip (s/map-to-pair (sd/key-value-fn (fn [a b] (s/tuple b a)))) (s/sort-by-key false) ;; descending order ;; flip (s/map-to-pair (sd/key-value-fn (fn [a b] (s/tuple b a)))) (s/map (sd/key-value-fn vector)) (s/take 10)))
45. In Practice 9: caching • enables data sharing • avoiding data (de)serialization • performance degrades gracefully
46. Why Use Clojure to Write Spark Jobs?
47. Spark and Functional Programming • Spark is inspired by FP • Not surprising – Scala is a functional programming language • RDDs are immutable values • Resilience: caches can be discarded • DAG of transformations • Philosophically close to Clojure
48. Processing RDDs So your application • defines (source) RDDs, • transforms them (which creates new RDDs with dependencies on the source RDDs) • and runs actions on them to get results back to the driver. This defines a Directed Acyclic Graph (DAG) of operators. Spark compiles this DAG of operators into a set of stages, where the boundary between two stages is a shuffle phase. Each stage contains tasks, working on one partition each.
49. Processing RDDs So your application • defines (source) RDDs, • transforms them (which creates new RDDs with dependencies on the source RDDs) • and runs actions on them to get results back to the driver. This defines a Directed Acyclic Graph (DAG) of operators. Spark compiles this DAG of operators into a set of stages, where the boundary between two stages is a shuffle phase. Each stage contains tasks, working on one partition each. Example sc.textFile("/some-hdfs-data") map# map# reduceByKey# collect# textFile# .map(line => line.split("\t")) .map(parts => (parts[0], int(parts[1]))) .reduceByKey(_ + _, 3) .collect() RDD[String] RDD[List[String]] RDD[(String, Int)] Array[(String, Int)] RDD[(String, Int)]
50. Processing RDDs So your application • defines (source) RDDs, • transforms them (which creates new RDDs with dependencies on the source RDDs) • and runs actions on them to get results back to the driver. This defines a Directed Acyclic Graph (DAG) of operators. Spark compiles this DAG of operators into a set of stages, where the boundary between two stages is a shuffle phase. Each stage contains tasks, working on one partition each. Example sc.textFile("/some-hdfs-data") map# map# reduceByKey# collect# textFile# .map(line => line.split("\t")) .map(parts => (parts[0], int(parts[1]))) .reduceByKey(_ + _, 3) .collect() RDD[String] RDD[List[String]] RDD[(String, Int)] Array[(String, Int)] RDD[(String, Int)] Execution Graph map# map# reduceByKey# collect# textFile# map# Stage#2# Stage#1# map# reduceByKey# collect# textFile#
51. Processing RDDs So your application • defines (source) RDDs, • transforms them (which creates new RDDs with dependencies on the source RDDs) • and runs actions on them to get results back to the driver. This defines a Directed Acyclic Graph (DAG) of operators. Spark compiles this DAG of operators into a set of stages, where the boundary between two stages is a shuffle phase. Each stage contains tasks, working on one partition each. Example sc.textFile("/some-hdfs-data") map# map# reduceByKey# collect# textFile# .map(line => line.split("\t")) .map(parts => (parts[0], int(parts[1]))) .reduceByKey(_ + _, 3) .collect() RDD[String] RDD[List[String]] RDD[(String, Int)] Array[(String, Int)] RDD[(String, Int)] Execution Graph map# map# reduceByKey# collect# textFile# map# Stage#2# Stage#1# map# reduceByKey# collect# textFile# Execution Graph map# Stage#2# Stage#1# map# reduceByKey# collect# textFile# Stage#2# Stage#1# read HDFS split apply both maps partial reduce write shuffle data read shuffle data final reduce send result to driver
52. Dynamic Types for Data Processing • Clojure's strength: developer-friendly wrapper for a complex interior • Static types everywhere • Imperfect data • For this use case, static typing can get in the way • Jobs naturally represented as transformations of Clojure data structures
53. Data Exploration • Working in real time with big datasets • Great for data mining • Clojure's powerful REPL • Gorilla REPL for live plotting?
54. Summary: Why Spark(ling) Data sharing: Hadoop is for a single map-reduce pass, it needs to write out intermediate result to HDFS. Interactive data exploration: Spark keeps data in memory, opening the possibility of interactively working with TBs of data Hadoop (and HIVE and Pig) lacks an (easy) way to implement unit tests. So writing your own code is also error-prone and development cycle is slooooow.
55. Practical tips
56. Running your spark code Run locally: e.g. inside tests. Use "local" or "local[*]" as SparkMaster. Run on cluster: either directly addressing Spark or (our case): run on top of YARN Both open a Web interface on http://host:4040/. Using the REPL: Open a SparkContext, define RDDs and store them in vars, perform transformations on these. Develop stuff in the REPL transfer your REPL stuff into tests. Run inside of tests: Open local SparcContext, feed mock data, run jobs. Therefore: design for testability! Submit a Spark Job using "spark-submit" with proper arguments (see upload.sh, run.sh).
57. Best Practices / Dos and Don'ts Shuffling is very expensive, so try to avoid it: • Never, ever, let go of your Partitioner - this has huuuuuuge performance impact. Use map-values instead of map, keep partition when re-keying for join, etc. • This equals: Keep your execution plan slim. There are some tricks for this, all boiling down to proper design of your data models. Use broadcasting where necessary. You need to monitor memory usage, as the inability to store stuff in memory will cause spills to disc (e.g. while shuffling). This will kill you. Tune total memory and/or cache/shuffle ratios.
58. Example
59. Example Matrix Multiplication • Repeatedly multiply sparse matrix and vector 24 Links (url, neighbors) Ranks (url, rank) … iteration 1 iteration 2 iteration 3 Same file read over and over
60. Example Matrix Multiplication • Repeatedly multiply sparse matrix and vector 24 Links (url, neighbors) Ranks (url, rank) … iteration 1 iteration 2 iteration 3 Same file read over and over Spark can do much better 25 • Using cache(), keep neighbors in memory • Do not write intermediate results on disk Links (url, neighbors) Ranks (url, rank) join join join … Grouping same RDD over and over
61. Example Matrix Multiplication • Repeatedly multiply sparse matrix and vector 24 Links (url, neighbors) Ranks (url, rank) … iteration 1 iteration 2 iteration 3 Same file read over and over Spark can do much better 25 • Using cache(), keep neighbors in memory • Do not write intermediate results on disk Links (url, neighbors) Ranks (url, rank) join join join … Grouping same RDD over and over Spark can do much better 26 • Do not partition neighbors every time Links (url, neighbors) Ranks (url, rank) join join join … partitionBy Same node
62. Some anecdotes
63. Why did I start gorillalabs/sparkling? first, there was clj-spark from The Climate Corporation. Very basic, not maintained anymore. Then, I found out about flambo from yieldbot. Looked promising at first, fresh release, maybe used in production at yieldbot. Small jobs were developed fast with Spark. I ran into sooooo many problems (running on Spark Standalone, moving to YARN, fighting with low memory). Nothing to do with flambo, but with understanding the nuts and bolts of Spark, YARN and other elements of my infrastructure. Ok, some with serializing my Clojure data structures. Scaling up the amount of data led me directly into hell. My system was way slower than our existing solution. Was Spark the wrong way? I was completely like this guy: http:// blog.explainmydata.com/2014/05/spark-should-be-better-than-mapreduce.html: „Spark should be better than MapReduce (if only it worked)“ After some thinking, I found out what happend: flambo promised to keep me in Clojure-land. Therefore, it uses a map operation to convert Scala Tuple2 to Clojure vector and back again where necessary. But map looses your Partitioner information. Remember my point? So, flambo broke Einstein’s „as simple as possible but no simpler“ I fixed the library, I incorporated a different take on serializing functions (without reflection). That’s where I released gorillalabs/sparkling. I needed to tweak the Data Model to have the same partitioner all over the place or use hand-crafted data structures and broadcasts for those not fitting my model. I now ended up with code generating an index-structure from an RDD, sorted-tree-sets for date-ranged data, and so forth. And everything is fully unit-tested, cause that’s the only way to go. Now, my system outperforms a much bigger MySQL-based system on a local master, scales almost linearly wrt cores on a cluster. HURRAY!
64. Having nrepl / GorillaREPL is so nice! Having an nrepl open on my Cluster is so nice, since I can inspect stuff in my computation. Ever wondered, what that intermediate RDD contains? Just (spark/take rdd 10) it. Using GorillaREPL, it’s like a visual workbench for big data analysis. See for yourself: http://bit.ly/1C7sSK4
65. References
66. Online Sparkling: https://github.com/gorillalabs/sparkling Flambo: https://github.com/yieldbot/flambo flambo-example: https://github.com/pesterhazy/flambo-example
67. References http://lintool.github.io/SparkTutorial/ (where you can find the slides used in this presentation) https://speakerdeck.com/ecepoi/apache-spark-at-viadeo https://speakerdeck.com/ecepoi/viadeos-segmentation-platform-with-spark-on-mesos https://speakerdeck.com/rxin/advanced-spark-at-spark-summit-2014
68. Sources Dean, J., & Ghemawat, S. (2008). MapReduce: simplified data processing on large clusters. Communications of the ACM, 51(1), 107-113. Zaharia, M., Chowdhury, M., Das, T., Dave, A., Ma, J., McCauley, M., ... & Stoica, I. (2012, April). Resilient distributed datasets: A fault-tolerant abstraction for in- memory cluster computing. In Proceedings of the 9th USENIX conference on Networked Systems Design and Implementation (pp. 2-2). USENIX Association. (Both available as PDFs)
69. Questions?