The Nitty Gritty of Advanced Analytics Using Apache Spark in Python

The Nitty Gritty of Advanced Analytics

Using Apache Spark in Python

Miklos Christine Solutions Architectmwc@databricks.com, @Miklos_C

About MeMiklos ChristineSolutions Architect @ Databricks

- mwc@databricks.com- Miklos_C@twitter

Systems Engineer @ Cloudera Supported a few of the largest clusters in the world

Software Engineer @ CiscoUC Berkeley Graduate

We are Databricks, the company behind Spark

Founded by the creators of Apache Spark in 2013

Share of Spark code contributed by Databricksin 2014

75%

3

Data Value

Created Databricks on top of Spark to make big data simple.

…

Apache Spark Engine

Spark Core

Spark StreamingSpark SQL MLlib GraphX

Unified engine across diverse workloads & environments

Scale out, fault tolerant

Python, Java, Scala, and R APIs

Standard libraries

2012

started@

Berkeley

2010

researchpaper

2013

Databricksstarted

& donatedto ASF

2014

Spark 1.0 & libraries

(SQL, ML, GraphX)

2015

DataFramesTungsten

ML Pipelines

2016

Spark 2.0

Spark Community Growth• Spark Survey 2015

Highlights• End of Year Spark Highlights

2015: A Great Year for Spark

Most active open source project in (big) data• 1000+ code contributors

New language: R

Widespread industry support & adoption

HOW RESPONDENTS ARE RUNNING SPARK

51%

on a public cloud

TOP ROLES USING SPARK

of respondents identifythemselves as Data Engineers

41%

of respondents identifythemselves as Data Scientists

22%

Spark User Highlights

NOTABLE USERS THAT PRESENTED AT SPARK SUMMIT 2015 SAN FRANCISCO

Source: Slide 5 of Spark Community Update

Large-Scale Usage

Largest cluster:8000 Nodes (Tencent)

Largest single job:1 PB (Alibaba, Databricks)

Top Streaming Intake:1 TB/hour (HHMI Janelia Farm)

2014 On-Disk Sort RecordFastest Open Source Engine for sorting a PB

Spark API Performance

History of Spark APIs

RDD(2011)

DataFrame(2013)

Distribute collection of JVM objects

Functional Operators (map, filter, etc.)

Distribute collection of Row objects

Expression-based operations and UDFs

Logical plans and optimizer

Fast/efficient internal representations

DataSet(2015)

Internally rows, externally JVM objects

Almost the “Best of both worlds”: type safe + fast

But slower than DF Not as good for interactive analysis, especially Python

Benefit of Logical Plan:Performance Parity Across Languages

DataFrame

RDD

ETL with Spark

ETL: Extract, Transform, Load

● Key factor for big data platforms

● Provides Speed Improvements in All Workloads

● Typically Executed by Data Engineers

File Formats

● Text File Formats○ CSV○ JSON

● Avro Row Format

● Parquet Columnar Format

File Formats + Compression

● File Formats○ JSON

○ CSV

○ Avro

○ Parquet

● Compression Codecs○ No compression

○ Snappy

○ Gzip

○ LZO

● Industry Standard File Format: Parquet

○ Write to Parquet:

df.write.format(“parquet”).save(“namesAndAges.parquet”)

df.write.format(“parquet”).saveAsTable(“myTestTable”)

○ For compression:

spark.sql.parquet.compression.codec = (gzip, snappy)

Spark Parquet Properties

Small Files Problem

● Small files problem still exists

● Metadata loading

● APIs:df.coalesce(N)df.repartition(N)

Ref:

http://spark.apache.org/docs/latest/api/python/pyspark.sql.html#pyspark.sql.DataFrame

● RDD / DataFrame Partitionsdf.rdd.getNumPartitions()

● SparkSQL Shuffle Partitionsspark.sql.shuffle.partitions

● Table Level Partitionsdf.write.partitionBy(“year”).\save(“data.parquet”)

All About Partitions

# CSV

df = sqlContext.read.\

format('com.databricks.spark.csv').\

options(header='true', inferSchema='true').\

load('/path/to/data')

# JSON

df = sqlContext.read.json("/tmp/test.json")

df.write.json("/tmp/test_output.json")

PySpark ETL APIs - Text Formats

PySpark ETL APIs - Container Formats

# Binary Container Formats

# Avro

df = sqlContext.read.\

format("com.databricks.spark.avro").\

load("/path/to/files/")

# Parquet

df = sqlContext.read.parquet("/path/to/files/")

df.write.parquet("/path/to/files/")

● Manage Number of Files○ APIs manage the number of files per directory

df.repartition(80).\

write.\

parquet("/path/to/parquet/")

df.repartition(80)

partitionBy("year")\

write.\

parquet("/path/to/parquet/")

PySpark ETL APIs

Common ETL Problems

● Malformed JSON RecordssqlContext.sql("SELECT _corrupt_record FROM jsonTable WHERE _corrupt_record IS NOT NULL")

● Mismatched DataFrame Schema○ Null Representation vs Schema DataType

● Many Small Files / No Partition Strategy○ Parquet Files: ~128MB - 256MB Compressed

Ref: https://databricks.gitbooks.io/databricks-spark-knowledge-base/content/best_practices/dealing_with_bad_data.html

Debugging Spark

Spark Driver Error: Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 1 in stage 362.0 failed 4 times, most recent failure: Lost task 1.3 in stage 362.0 (TID 275202, ip-10-111-225-98.ec2.internal): java.nio.channels.ClosedChannelException

Spark Executor Error:16/04/13 20:02:16 ERROR DefaultWriterContainer: Aborting task.

java.text.ParseException: Unparseable number: "\N"

at java.text.NumberFormat.parse(NumberFormat.java:385)

at com.databricks.spark.csv.util.TypeCast$$anonfun$castTo$4.apply$mcD$sp(TypeCast.scala:58)

at com.databricks.spark.csv.util.TypeCast$$anonfun$castTo$4.apply(TypeCast.scala:58)

at com.databricks.spark.csv.util.TypeCast$$anonfun$castTo$4.apply(TypeCast.scala:58)

at scala.util.Try.getOrElse(Try.scala:77)

at com.databricks.spark.csv.util.TypeCast$.castTo(TypeCast.scala:58)

Debugging Spark

SQL with Spark

SparkSQL Best Practices

● DataFrames and SparkSQL are synonyms● Use builtin functions instead of custom UDFs

○ import pyspark.sql.functions

● Examples:○ to_date()○ get_json_object() ○ regexp_extract()○ hour() / minute()

Ref:

http://spark.apache.org/docs/latest/api/python/pyspark.sql.html#module-pyspark.sql.functions

SparkSQL Best Practices

● Large Table Joins

○ Largest Table on LHS

○ Increase Spark Shuffle Partitions

○ Leverage “cluster by” API included in Spark 1.6sqlCtx.sql("select * from large_table_1 cluster by num1")

.registerTempTable("sorted_large_table_1");

sqlCtx.sql(“cache table sorted_large_table_1”);

PySpark API Best Practices● User Defined Functions (UDFs)

from pyspark.sql import functions as F

add_n = udf(lambda x, y: x + y, IntegerType())

# We register a UDF that adds a column to the DataFrame, and we cast the id column to an Integer type.

df = df.withColumn('id_offset',

add_n( F.lit(1000), df.id.cast(IntegerType())))

PySpark API Best Practices

● Built-in Functions

corpus_df = df.select( \

F.lower( F.col('body')).alias('corpus'), \

F.monotonicallyIncreasingId().alias('id'))

corpus_df = df.select( \

F.date_format( F.from_utc_timestamp( \

F.from_unixtime(F.col('created_utc'), "PST"), 'EEEE')).alias('dayofweek'))

Ref: http://spark.apache.org/docs/latest/api/python/pyspark.sql.html#module-pyspark.sql.functions

PySpark API Best Practices

● User Defined Functions (UDFs)

def squared(s):

return s * s

sqlContext.udf.register("squaredWithPython", squared)

display(df.select("id", squared_udf("id").alias("id_squared")))

ML with Spark

Data Science Time

40

Why Spark ML

Provide general purpose ML algorithms on top of Spark• Let Spark handle the distribution of data and queries; scalability• Leverage its improvements (e.g. DataFrames, Datasets, Tungsten)

Advantages of MLlib’s Design:• Simplicity• Scalability• Streamlined end-to-end• Compatibility

High-level functionality in MLlib

Learning tasksClassificationRegressionRecommendationClusteringFrequent

itemsets

42

Workflow utilities• Model import/export• Pipelines• DataFrames• Cross validation

Data utilities• Feature

extraction & selection

• Statistics• Linear algebra

Machine Learning: What and Why?

ML uses data to identify patterns and make decisions.Core value of ML is automated decision making

• Especially important when dealing with TB or PB of data

Many Use Cases including:• Marketing and advertising optimization• Security monitoring / fraud detection• Operational optimizations

Algorithm coverage in MLlibClassification• Logistic regression w/ elastic net• Naive Bayes• Streaming logistic regression• Linear SVMs• Decision trees• Random forests• Gradient-boosted trees• Multilayer perceptron• One-vs-rest

Regression• Least squares w/ elastic net• Isotonic regression• Decision trees• Random forests• Gradient-boosted trees• Streaming linear methods

Recommendation• Alternating Least Squares

Frequent itemsets• FP-growth• Prefix span

Clustering• Gaussian mixture models• K-Means• Streaming K-Means• Latent Dirichlet Allocation• Power Iteration Clustering

Statistics• Pearson correlation• Spearman correlation• Online summarization• Chi-squared test• Kernel density estimation

Linear algebra• Local dense & sparse vectors & matrices• Distributed matrices

• Block-partitioned matrix• Row matrix• Indexed row matrix• Coordinate matrix

• Matrix decompositions

Model import/exportPipelines

Feature extraction & selection• Binarizer• Bucketizer• Chi-Squared selection• CountVectorizer• Discrete cosine transform• ElementwiseProduct• Hashing term frequency• Inverse document frequency• MinMaxScaler• Ngram• Normalizer• One-Hot Encoder• PCA• PolynomialExpansion• RFormula• SQLTransformer• Standard scaler• StopWordsRemover• StringIndexer• Tokenizer• StringIndexer• VectorAssembler• VectorIndexer• VectorSlicer• Word2Vec List based on Spark

1.5 44

Spark ML Best Practices

● Spark MLLib vs SparkML ○ Understand the differences

● Don’t Pipeline Too Many Stages ○ Check Results Between Stages

PySpark ML API Best Practices

PySpark ML API Best Practices

● DataFrame to RDD Mapping

def tokenize(text):

tokens = word_tokenize(text)

lowercased = [t.lower() for t in tokens]

no_punctuation = []

for word in lowercased:

punct_removed = ''.join([letter for letter in word if not letter in PUNCTUATION])

no_punctuation.append(punct_removed)

no_stopwords = [w for w in no_punctuation if not w in STOPWORDS]

stemmed = [STEMMER.stem(w) for w in no_stopwords]

return [w for w in stemmed if w]

rdd = wordsDataFrame.map(lambda x: (x.__getitem__('id'), tokenize(x.__getitem__('corpus'))))

PySpark ML API Best Practices

Learning more about MLlibGuides & examples• Example workflow using ML Pipelines (Python)• The above 2 links are part of the Databricks Guide, which contains many more

examples and references.References• Apache Spark MLlib User Guide

• The MLlib User Guide contains code snippets for almost all algorithms, as well as links to API documentation.

• Meng et al. “MLlib: Machine Learning in Apache Spark.” 2015. http://arxiv.org/abs/1505.06807 (academic paper)

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Spark Demo

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