Python in the Hadoop Ecosystem (Rock Health presentation)

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A Guide to Python Frameworks for HadoopUri Lasersonlaserson@cloudera.com20 March 2014

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Goals for today

1. Easy to jump into Hadoop with Python2. Describe 5 ways to use Python with Hadoop, batch

and interactive3. Guidelines for choosing Python framework

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Code:https://github.com/laserson/rock-health-python

Blog post:http://blog.cloudera.com/blog/2013/01/a-guide-to-python-frameworks-for-hadoop/

Slides:http://www.slideshare.net/urilaserson/

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About the speaker

• Joined Cloudera late 2012• Focus on life sciences/medical

• PhD in BME/computational biology at MIT/Harvard (2005-2012)

• Focused on genomics• Cofounded Good Start Genetics (2007-)

• Applying next-gen DNA sequencing to genetic carrier screening

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About the speaker

• No formal training in computer science• Never touched Java• Almost all work using Python

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7

Python frameworks for Hadoop

• Hadoop Streaming• mrjob (Yelp)• dumbo• Luigi (Spotify)• hadoopy• pydoop• PySpark• happy• Disco• octopy• Mortar Data• Pig UDF/Jython• hipy• Impala + Numba

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Goals for Python framework

1. “Pseudocodiness”/simplicity2. Flexibility/generality3. Ease of use/installation4. Performance

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Python frameworks for Hadoop

• Hadoop Streaming• mrjob (Yelp)• dumbo• Luigi (Spotify)• hadoopy• pydoop• PySpark• happy• Disco• octopy• Mortar Data• Pig UDF/Jython• hipy• Impala + Numba

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Python frameworks for Hadoop

• Hadoop Streaming ✓• mrjob (Yelp) ✓• dumbo• Luigi (Spotify) ✓• hadoopy• pydoop• PySpark✓• happy abandoned? Jython-based• Disco not Hadoop• octopy not serious/not Hadoop• Mortar Data HaaS; support numpy, scipy, nltk, pip-installable in UDF• Pig UDF/Jython Pig is another talk; Jython limited• hipy Python syntactic sugar to construct Hive queries• Impala + Numba✓

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An n-gram is a tuple of n words.

Problem: aggregating the Google n-gram datahttp://books.google.com/ngrams

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An n-gram is a tuple of n words.

Problem: aggregating the Google n-gram datahttp://books.google.com/ngrams

1 2 3 4 5 6 7 8

( )

8-gram

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"A partial differential equation is an equation that contains partial derivatives."

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A partial differential equation is an equation that contains partial derivatives.

A 1partial 2differential 1equation 2is 1an 1that 1contains 1derivatives. 1

1-grams

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A partial differential equation is an equation that contains partial derivatives.

A partial 1partial differential 1differential equation 1equation is 1is an 1an equation 1equation that 1that contains 1contains partial 1partial derivatives. 1

2-grams

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A partial differential equation is an equation that contains partial derivatives.

A partial differential equation is 1partial differential equation is an 1differential equation is an equation 1equation is an equation that 1is an equation that contains 1an equation that contains partial 1equation that contains partial derivatives. 1

5-grams

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goto code

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flourished in 1993 2 2 2flourished in 1998 2 2 1flourished in 1999 6 6 4flourished in 2000 5 5 5flourished in 2001 1 1 1flourished in 2002 7 7 3flourished in 2003 9 9 4flourished in 2004 22 21 13flourished in 2005 37 37 22flourished in 2006 55 55 38flourished in 2007 99 98 76flourished in 2008 220 215 118fluid of 1899 2 2 1fluid of 2000 3 3 1fluid of 2002 2 1 1fluid of 2003 3 3 1fluid of 2004 3 3 3

2-gram year matches pages volumes

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Compute how often two words are near each other in a given year.

Two words are “near” if they are both present in a 2-, 3-, 4-, or 5-gram.

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...2-grams...(cat, the) 1999 14(the, cat) 1999 7002

...3-grams...(the, cheshire, cat) 1999 563

...4-grams...

...5-grams...(the, cat, in, the, hat) 1999 1023(the, dog, chased, the, cat) 1999 403(cat, is, one, of, the) 1999 24

(cat, the) 1999 8006(hat, the) 1999 1023

raw data

aggregated results

lexicographicordering

internal n-grams counted by smaller n-grams:• avoids double-counting• increases sensitivity (observed at least 40 times)

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What is Hadoop?

• Ecosystem of tools• Core is the HDFS file system• Downloadable set of jars that can be run on any

machine

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HDFS design assumptions

• Based on Google File System• Files are large (GBs to TBs)• Failures are common

• Massive scale means failures very likely• Disk, node, or network failures

• Accesses are large and sequential• Files are append-only

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HDFS properties

• Fault-tolerant• Gracefully responds to node/disk/network failures

• Horizontally scalable• Low marginal cost

• High-bandwidth

1

2

3

4

5

2

4

5

1

2

5

1

3

4

2

3

5

1

3

4

Input File

HDFS storage distributionNode A Node B Node C Node D Node E

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MapReduce computation

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MapReduce computation

• Structured as1. Embarrassingly parallel “map stage”2. Cluster-wide distributed sort (“shuffle”)3. Aggregation “reduce stage”

• Data-locality: process the data where it is stored• Fault-tolerance: failed tasks automatically detected

and restarted• Schema-on-read: data must not be stored conforming

to rigid schema

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Pseudocode for MapReduce

def map(record):    (ngram, year, count) = unpack(record)    // ensure word1 has the lexicographically first word:    (word1, word2) = sorted(ngram[first], ngram[last])    key = (word1, word2, year)    emit(key, count) 

def reduce(key, values):    emit(key, sum(values))

All source code available on GitHub:https://github.com/laserson/rock-health-python

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Native Java

import org.apache.hadoop.conf.Configured;import org.apache.hadoop.fs.Path;import org.apache.hadoop.io.IntWritable;import org.apache.hadoop.mapreduce.Job;import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;import org.apache.hadoop.util.Tool;import org.apache.hadoop.util.ToolRunner;

public class NgramsDriver extends Configured implements Tool {

public int run(String[] args) throws Exception { Job job = new Job(getConf()); job.setJarByClass(getClass()); FileInputFormat.addInputPath(job, new Path(args[0])); FileOutputFormat.setOutputPath(job, new Path(args[1])); job.setMapperClass(NgramsMapper.class); job.setCombinerClass(NgramsReducer.class); job.setReducerClass(NgramsReducer.class); job.setOutputKeyClass(TextTriple.class); job.setOutputValueClass(IntWritable.class); job.setNumReduceTasks(10); return job.waitForCompletion(true) ? 0 : 1; } public static void main(String[] args) throws Exception { int exitCode = ToolRunner.run(new NgramsDriver(), args); System.exit(exitCode); }}

import java.io.IOException;import java.util.ArrayList;import java.util.Collections;import java.util.List;import java.util.regex.Matcher;import java.util.regex.Pattern;

import org.apache.hadoop.io.IntWritable;import org.apache.hadoop.io.LongWritable;import org.apache.hadoop.io.Text;import org.apache.hadoop.mapreduce.Mapper;import org.apache.hadoop.mapreduce.lib.input.FileSplit;import org.apache.log4j.Logger;

public class NgramsMapper extends Mapper<LongWritable, Text, TextTriple, IntWritable> { private Logger LOG = Logger.getLogger(getClass()); private int expectedTokens; @Override protected void setup(Context context) throws IOException, InterruptedException { String inputFile = ((FileSplit) context.getInputSplit()).getPath().getName(); LOG.info("inputFile: " + inputFile); Pattern c = Pattern.compile("([\\d]+)gram"); Matcher m = c.matcher(inputFile); m.find(); expectedTokens = Integer.parseInt(m.group(1)); return; } @Override public void map(LongWritable key, Text value, Context context) throws IOException, InterruptedException { String[] data = value.toString().split("\\t"); if (data.length < 3) { return; } String[] ngram = data[0].split("\\s+"); String year = data[1]; IntWritable count = new IntWritable(Integer.parseInt(data[2])); if (ngram.length != this.expectedTokens) { return; } // build keyOut List<String> triple = new ArrayList<String>(3); triple.add(ngram[0]); triple.add(ngram[expectedTokens - 1]); Collections.sort(triple); triple.add(year); TextTriple keyOut = new TextTriple(triple); context.write(keyOut, count); }}

import java.io.IOException;

import org.apache.hadoop.io.IntWritable;import org.apache.hadoop.mapreduce.Reducer;

public class NgramsReducer extends Reducer<TextTriple, IntWritable, TextTriple, IntWritable> { @Override protected void reduce(TextTriple key, Iterable<IntWritable> values, Context context) throws IOException, InterruptedException { int sum = 0; for (IntWritable value : values) { sum += value.get(); } context.write(key, new IntWritable(sum)); }}

import java.io.DataInput;import java.io.DataOutput;import java.io.IOException;import java.util.List;

import org.apache.hadoop.io.Text;import org.apache.hadoop.io.WritableComparable;

public class TextTriple implements WritableComparable<TextTriple> { private Text first; private Text second; private Text third; public TextTriple() { set(new Text(), new Text(), new Text()); } public TextTriple(List<String> list) { set(new Text(list.get(0)), new Text(list.get(1)), new Text(list.get(2))); } public void set(Text first, Text second, Text third) { this.first = first; this.second = second; this.third = third; } public void write(DataOutput out) throws IOException { first.write(out); second.write(out); third.write(out); }

public void readFields(DataInput in) throws IOException { first.readFields(in); second.readFields(in); third.readFields(in); }

@Override public int hashCode() { return first.hashCode() * 163 + second.hashCode() * 31 + third.hashCode(); } @Override public boolean equals(Object obj) { if (obj instanceof TextTriple) { TextTriple tt = (TextTriple) obj; return first.equals(tt.first) && second.equals(tt.second) && third.equals(tt.third); } return false; } @Override public String toString() { return first + "\t" + second + "\t" + third; }

public int compareTo(TextTriple other) { int comp = first.compareTo(other.first); if (comp != 0) { return comp; } comp = second.compareTo(other.second); if (comp != 0) { return comp; } return third.compareTo(other.third); } }

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Native Java

• Maximum flexibility• Fastest performance• Native to Hadoop• Most difficult to write

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Hadoop Streaming

hadoop jar hadoop-streaming-*-.jar \ -input path/to/input -output path/to/output -mapper “grep WARN”

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Hadoop Streaming: features

• Canonical method for using any executable as mapper/reducer

• Includes shell commands, like grep• Transparent communication with Hadoop though

stdin/stdout• Key boundaries manually detected in reducer• Built-in with Hadoop: should require no additional

framework installation• Developer must decide how to encode more

complicated objects (e.g., JSON) or binary data

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Hadoop Streaming

goto code

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mrjob

class NgramNeighbors(MRJob): # specify input/intermed/output serialization # default output protocol is JSON; here we set it to text OUTPUT_PROTOCOL = RawProtocol

def mapper(self, key, line): pass def combiner(self, key, counts): pass def reducer(self, key, counts): pass

if __name__ == '__main__': # sets up a runner, based on command line options NgramNeighbors.run()

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mrjob: features

• Abstracted MapReduce interface• Handles complex Python objects• Multi-step MapReduce workflows• Extremely tight AWS integration• Easily choose to run locally, on Hadoop cluster, or on

EMR• Actively developed; great documentation

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mrjob

goto code

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mrjob: serialization

class MyMRJob(mrjob.job.MRJob): INPUT_PROTOCOL = mrjob.protocol.RawValueProtocol INTERNAL_PROTOCOL = mrjob.protocol.JSONProtocol OUTPUT_PROTOCOL = mrjob.protocol.JSONProtocol

Defaults

RawProtocol / RawValueProtocolJSONProtocol / JSONValueProtocolPickleProtocol / PickleValueProtocolReprProtocol / ReprValueProtocol

Available

Custom protocols can be written.No current support for binary serialization schemes.

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luigi

• Full-fledged workflow management, task scheduling, dependency resolution tool in Python (similar to Apache Oozie)

• Built-in support for Hadoop by wrapping Streaming• Not as fully-featured as mrjob for Hadoop, but easily

customizable• Internal serialization through repr/eval• Actively developed at Spotify• README is good but documentation is lacking

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luigi

goto code

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The cluster used for benchmarking

• 5 virtual machines• 4 CPUs• 10 GB RAM• 100 GB disk• CentOS 6.2

• CDH4 (Hadoop 2)• 20 map tasks• 10 reduce tasks

• Python 2.6

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(Unscientific) performance comparison

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(Unscientific) performance comparison

Streaming has lowest overhead

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(Unscientific) performance comparison

JSON SerDe

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Feature comparison

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Feature comparison

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Questions?

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Cloudera Hadoop Stack

Unified Scale-Out StorageFor Any Type of Data

Batch Processing

Workload Management

System

Managem

entData

Managem

ent

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Cloudera Hadoop Stack

Unified Scale-Out StorageFor Any Type of Data

Batch Processing

Workload Management

Online NoSQL

Analytic SQL Search

Machine Learning

and Streaming

3rd PartyApps

System

Managem

entData

Managem

ent

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What is Spark?

• Started in 2009 as academic project from Amplab at UCBerkeley; now ASF and >100 contributors

• In-memory distributed execution engine• Operates on Resilient Distributed Datasets (RDDs)• Provides richer distributed computing primitives for

various problems• Can support SQL, stream processing, ML, graph

computation• Supports Scala, Java, and Python

Spark uses a general DAG scheduler

• Application aware scheduler• Uses locality for both disk

and memory• Partitioning-aware

to avoid shuffles• Can rewrite and optimize

graph based on analysis

join

union

groupBy

map

Stage 3

Stage 1

Stage 2

A: B:

C: D:

E:

F:

G:

= cached data partition

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Operations on RDDs

Zaharia 2011

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Apache Spark

file = spark.textFile("hdfs://...")errors = file.filter(lambda line: "ERROR” in line)# Count all the errorserrors.count()# Count errors mentioning MySQLerrors.filter(lambda line: "MySQL” in line).count()# Fetch the MySQL errors as an array of stringserrors.filter(lambda line: "MySQL” in line).collect()

val points = spark.textFile(...).map(parsePoint).cache()var w = Vector.random(D) // current separating planefor (i <- 1 to ITERATIONS) { val gradient = points.map(p => (1 / (1 + exp(-p.y*(w dot p.x))) - 1) * p.y * p.x ).reduce(_ + _) w -= gradient}println("Final separating plane: " + w)

Log

filte

ring

(Pyt

hon)

Logi

stic

regr

essi

on(S

cala

)

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Apache Spark

goto code

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What’s Impala?

• Interactive SQL• Typically 4-65x faster than the latest Hive (observed up to 100x faster)• Responses in seconds instead of minutes (sometimes sub-second)

• ANSI-92 standard SQL queries with HiveQL• Compatible SQL interface for existing Hadoop/CDH applications• Based on industry standard SQL

• Natively on Hadoop/HBase storage and metadata• Flexibility, scale, and cost advantages of Hadoop• No duplication/synchronization of data and metadata• Local processing to avoid network bottlenecks

• Separate runtime from batch processing• Hive, Pig, MapReduce are designed and great for batch• Impala is purpose-built for low-latency SQL queries on Hadoop

Cloudera Confidential. ©2013 Cloudera, Inc. All Rights Reserved.

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Cloudera Impala

SELECT cosmic as snp_id, vcf_chrom as chr, vcf_pos as pos, sample_id as sample, vcf_call_gt as genotype, sample_affection as phenotypeFROM hg19_parquet_snappy_join_cached_partitionedWHERE COSMIC IS NOT NULL AND dbSNP IS NULL AND sample_study = ”breast_cancer" AND VCF_CHROM = "16";

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Impala Architecture: Planner

• Example: query with join and aggregationSELECT state, SUM(revenue)FROM HdfsTbl h JOIN HbaseTbl b ON (...)GROUP BY 1 ORDER BY 2 desc LIMIT 10

HbaseScan

HashJoin

HdfsScan Exch

TopN

Agg

Exch

at coordinator at DataNodes at region servers

AggTopN

Agg

HashJoin

HdfsScan

HbaseScan

Cloudera Confidential. ©2013 Cloudera, Inc. All Rights Reserved.

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Impala User-defined Functions (UDFs)

• Tuple => Scalar value• Substring• sin, cos, pow, …• Machine-learning models

• Supports Hive UDFs (Java)• Highly unpleasurable

• Impala (native) UDFs• C++ interface designed for efficiency• Similar to Postgres UDFs• Runs any LLVM-compiled code

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LLVM compiler infrastructure

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LLVM: C++ example

bool StringEq(FunctionContext* context, const StringVal& arg1, const StringVal& arg2) { if (arg1.is_null != arg2.is_null) return false; if (arg1.is_null) return true; if (arg1.len != arg2.len) return false; return (arg1.ptr == arg2.ptr) || memcmp(arg1.ptr, arg2.ptr, arg1.len) == 0;}

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LLVM: IR output; ModuleID = '<stdin>'target datalayout = "e-p:64:64:64-i1:8:8-i8:8:8-i16:16:16-i32:32:32-i64:64:64-f32:32:32-f64:64:64-v64:64:64-v128:128:128-a0:0:64-s0:64:64-f80:128:128-n8:16:32:64-S128"target triple = "x86_64-apple-macosx10.7.0"

%"class.impala_udf::FunctionContext" = type { %"class.impala::FunctionContextImpl"* }%"class.impala::FunctionContextImpl" = type opaque%"struct.impala_udf::StringVal" = type { %"struct.impala_udf::AnyVal", i32, i8* }%"struct.impala_udf::AnyVal" = type { i8 }

; Function Attrs: nounwind readonly ssp uwtabledefine zeroext i1 @_Z8StringEqPN10impala_udf15FunctionContextERKNS_9StringValES4_(%"class.impala_udf::FunctionContext"* nocapture %context, %"struct.impala_udf::StringVal"* nocapture %arg1, %"struct.impala_udf::StringVal"* nocapture %arg2) #0 {entry: %is_null = getelementptr inbounds %"struct.impala_udf::StringVal"* %arg1, i64 0, i32 0, i32 0 %0 = load i8* %is_null, align 1, !tbaa !0, !range !3 %is_null1 = getelementptr inbounds %"struct.impala_udf::StringVal"* %arg2, i64 0, i32 0, i32 0 %1 = load i8* %is_null1, align 1, !tbaa !0, !range !3 %cmp = icmp eq i8 %0, %1 br i1 %cmp, label %if.end, label %return

if.end: ; preds = %entry %tobool = icmp eq i8 %0, 0 br i1 %tobool, label %if.end7, label %return

if.end7: ; preds = %if.end %len = getelementptr inbounds %"struct.impala_udf::StringVal"* %arg1, i64 0, i32 1 %2 = load i32* %len, align 4, !tbaa !4 %len8 = getelementptr inbounds %"struct.impala_udf::StringVal"* %arg2, i64 0, i32 1 %3 = load i32* %len8, align 4, !tbaa !4 %cmp9 = icmp eq i32 %2, %3 br i1 %cmp9, label %if.end11, label %return

if.end11: ; preds = %if.end7 %ptr = getelementptr inbounds %"struct.impala_udf::StringVal"* %arg1, i64 0, i32 2 %4 = load i8** %ptr, align 8, !tbaa !5 %ptr12 = getelementptr inbounds %"struct.impala_udf::StringVal"* %arg2, i64 0, i32 2 %5 = load i8** %ptr12, align 8, !tbaa !5 %cmp13 = icmp eq i8* %4, %5 br i1 %cmp13, label %return, label %lor.rhs

lor.rhs: ; preds = %if.end11 %conv17 = sext i32 %2 to i64 %call = tail call i32 @memcmp(i8* %4, i8* %5, i64 %conv17) %cmp18 = icmp eq i32 %call, 0 br label %return

return: ; preds = %lor.rhs, %if.end11, %if.end7, %if.end, %entry %retval.0 = phi i1 [ false, %entry ], [ true, %if.end ], [ false, %if.end7 ], [ true, %if.end11 ], [ %cmp18, %lor.rhs ] ret i1 %retval.0}

; Function Attrs: nounwind readonlydeclare i32 @memcmp(i8* nocapture, i8* nocapture, i64) #1

attributes #0 = { nounwind readonly ssp uwtable "less-precise-fpmad"="false" "no-frame-pointer-elim"="true" "no-frame-pointer-elim-non-leaf"="true" "no-infs-fp-math"="false" "no-nans-fp-math"="false" "unsafe-fp-math"="false" "use-soft-float"="false" }attributes #1 = { nounwind readonly "less-precise-fpmad"="false" "no-frame-pointer-elim"="true" "no-frame-pointer-elim-non-leaf"="true" "no-infs-fp-math"="false" "no-nans-fp-math"="false" "unsafe-fp-math"="false" "use-soft-float"="false" }

!0 = metadata !{metadata !"bool", metadata !1}!1 = metadata !{metadata !"omnipotent char", metadata !2}!2 = metadata !{metadata !"Simple C/C++ TBAA"}!3 = metadata !{i8 0, i8 2}!4 = metadata !{metadata !"int", metadata !1}!5 = metadata !{metadata !"any pointer", metadata !1}

60

LLVM compiler infrastructure

NumbaPython

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Iris data and BigMLdef predict_species_orig(sepal_width=None, petal_length=None, petal_width=None): """ Predictor for species from model/52952081035d07727e01d836

Predictive model by BigML - Machine Learning Made Easy """ if (petal_width is None): return u'Iris-virginica' if (petal_width > 0.8): if (petal_width <= 1.75): if (petal_length is None): return u'Iris-versicolor' if (petal_length > 4.95): if (petal_width <= 1.55): return u'Iris-virginica' if (petal_width > 1.55): if (petal_length > 5.45): return u'Iris-virginica' if (petal_length <= 5.45): return u'Iris-versicolor' if (petal_length <= 4.95): if (petal_width <= 1.65): return u'Iris-versicolor' if (petal_width > 1.65): return u'Iris-virginica' if (petal_width > 1.75): if (petal_length is None): return u'Iris-virginica' if (petal_length > 4.85): return u'Iris-virginica' if (petal_length <= 4.85): if (sepal_width is None): return u'Iris-virginica' if (sepal_width <= 3.1): return u'Iris-virginica' if (sepal_width > 3.1): return u'Iris-versicolor' if (petal_width <= 0.8): return u'Iris-setosa'

62

Impala + Numba

goto code

63

Impala + Numba

• Still pre-alpha• Significantly faster execution thanks to native LLVM• Significantly easier to write UDFs

64

Conclusions

65

If you have access to a Hadoop cluster and you want a one-off quick-and-dirty job…

Hadoop Streaming

66

If you want an expressive Pythonic interface to build complex, regular ETL workflows…

Luigi

67

If you want to integrate Hadoop with other regular processes…

Luigi

68

If you don’t have access to Hadoop and want to try stuff out…

mrjob

69

If you’re heavily using AWS…

mrjob

70

If you want to work interactively…

PySpark

71

If you want to do in-memory analytics…

PySpark

72

If you want to do anything…*

PySpark

73

If you want ease of Python with high performance

Impala + Numba

74

If you want to write Python UDFs for SQL queries…

Impala + Numba

75

Code:https://github.com/laserson/rock-health-python

Blog post:http://blog.cloudera.com/blog/2013/01/a-guide-to-python-frameworks-for-hadoop/

Slides:http://www.slideshare.net/urilaserson/

76