Using Spark Efficiently | Understanding Spark Event 7/29/17

This page is dedicated to resources related to the 7/29/17 Understanding Spark event presentation in Bellevue, WA.

Slides

Great [FREE!] resources on all things Spark:
https://jaceklaskowski.gitbooks.io/mastering-apache-spark/
https://spark.apache.org/docs/latest/sql-programming-guide.html

Databricks was founded by the original creators of Spark and is currently the largest contributor to Apache Spark. As such, they are a phenomenal resource for information and services relating to Spark.

Datasets: https://databricks.com/blog/2016/01/04/introducing-apache-spark-datasets.html
Catalyst: https://www.slideshare.net/databricks/a-deep-dive-into-spark-sqls-catalyst-optimizer-with-yin-huai
https://de.slideshare.net/SparkSummit/deep-dive-into-catalyst-apache-spark-20s-optimizer-63071120
Tungsten: https://databricks.com/blog/2015/04/28/project-tungsten-bringing-spark-closer-to-bare-metal.html
Matrix: https://databricks.com/blog/2016/07/14/a-tale-of-three-apache-spark-apis-rdds-dataframes-and-datasets.html

Personally curated Examples:

Create mock typed object data
import org.apache.spark.sql.functions._

case class CountryGDP(countryCode : String, countryName : String, Year : String, gdp: Double, language : Option[String])
val objects = Seq[CountryGDP](
CountryGDP("USA", "'Murica", "2014", 17393103000000f, None),
CountryGDP("USA", "'Murica", "2015", 18036648000000f, None),
CountryGDP("USA", "'Murica", "2016", 18569100000000f, None),
CountryGDP("CHE", "Switzerland", "2014", 702705544908.583, None),
CountryGDP("CHE", "Switzerland", "2015", 670789928809.882, None),
CountryGDP("CHE", "Switzerland", "2016", 659827235193.83, None)
)

Strongly typed Datasets
val objectsDS = spark.createDataset(objects)

// typed objects are evaluated at compile time (great for development in IDEs!)
val countriesWithLanguages = objectsDS.map(o => {
val lang = o.countryCode match {
case "USA" => Some("English")
case "CHE" => Some("Schweizerdeutsch")
case _ => Some("Simlish")
}
o.copy(language = lang)
})

Creating DataFrame and using UDF to transform
val rowsDF = spark.createDataFrame(objects)

def getLang(countryCode: String): Option[String] = {
countryCode match {
case "USA" => Some("English")
case "CHE" => Some("Schweizerdeutsch")
case _ => Some("Simlish")
}
}
val gl = sqlContext.udf.register("getLang", getLang _)

// String-based lookups are evaluated at Runtime
val rowsDFWithLanguage = rowsDF.withColumn("language", gl($"countryCode"))

Event link: https://www.eventbrite.com/e/understanding-spark-tickets-35440866586#

Video recording is here: https://livestream.com/metis/events/7597562

Learn more about parquet

Switching between Scala and Python on Spark tips

Switching between Scala and Python on Spark is relatively straightforward, but there are a few differences that can cause some minor frustration. Here are some of the little things I’ve run into and how to adjust for them.

  • PySpark Shell does not support code completion (autocomplete) by default.

Why? PySpark uses the basic Python interpreter REPL, so you get the same REPL you’d get by calling python at the command line.

Fix: Use the iPython REPL by specifying the environment variable
PYSPARK_PYTHON=ipython3 before the pyspark command.

Before:
pyspark

After:
PYSPARK_PYTHON=ipython3 pyspark

  • val and var are not python keywords!

This is silly, but I catch myself trying to create variables in python regularly with the val df = spark.read... style.

Before:
>>> val df = spark.range(100)
File "", line 1
val df = spark.range(100)
^
SyntaxError: invalid syntax

After:
>>> df = spark.range(100)

  • It’s print not println

Just like the val/var conundrum, println is not a valid keyword in python, but print is!

Before:
In [5]: df.foreach(println)
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-5-3d51e5dc3e2b> in <module>()
----> 1 df.foreach(println)

NameError: name ‘println’ is not defined

After:
In [6]: df.foreach(print)
Row(id=3)
Row(id=4)
Row(id=2)
Row(id=1)
Row(id=0)

  • All function calls need parentheses in Python

Yep, this is one of those frustrating gifts that just keeps on giving [pain].

Scala:
scala> df.groupBy("element").count.collect.foreach(println)
[bar,1]
[qux,1]
[foo,1]
[baz,1]

Python
Before:
In [15]: df.groupBy("element").count().foreach(print)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
in ()
----> 1 df.groupBy("element").count.collect.foreach(print)

AttributeError: ‘function’ object has no attribute ‘collect’

After:
In [17]: df = spark.createDataFrame([(1,"foo"), (2, "bar"), (3, "baz"), (4, "qux")]).toDF("time", "element")
In [18]: df.groupBy("element").count().foreach(print)
Row(element='bar', count=1)
Row(element='qux', count=1)
Row(element='foo', count=1)
Row(element='baz', count=1)

  • Quotes!

Python allows both single (‘) quotes and double (“) quotes for strings. Scala uses the single quote to denote more specific types.

Scala
scala> 'f
res7: Symbol = 'f

scala> 'f'
res6: Char = f

scala> 'foo'
<console>:1: error: unclosed character literal
'foo'

scala> "foo" == 'foo'
:1: error: unclosed character literal
"foo" == 'foo'

Python

In [19]: "foo" == 'foo'
Out[19]: True

Real Time Big Data analytics: Parquet (and Spark) + bonus

Apache Spark and Parquet (SParquet) are a match made in scalable data analytics and delivery heaven. Spark brings a wide ranging, powerful computing platform to the equation while Parquet offers a data format that is purpose-built for high-speed big data analytics. If this sounds like fluffy marketing talk, resist the temptation to close this tab, because what follows are substantial insights I’ve personally procured and am sharing here to help others get the most out of Parquet and Spark.

What is Parquet?

Parquet is a binary compressed columnar file format available to any project in the Hadoop ecosystem (and others outside it even). It’s a mouthful, but let’s break it down.

Binary means parquet files cannot be opened by typical text editors natively (sublime text*, vim, etc).

* My former colleague James Yu wrote a Sublime Text plugin you can find here to view parquet files.

Columnar means the data is stored as columns instead of rows as most traditional databases (MySQL, PostgreSQL, etc) and file formats (CSV, JSON, etc). This is going to be very important.

Compressed means the file footprint on disk (HDFS, S3, or local filesystem) is smaller than a typical raw uncompressed file. Parquet handles compression differently than traditional compression of a CSV file for example, but in a similar vein to Avro.

Now that the basic definition is out of the way, let’s get right to it.

How can Parquet help me?

Parquet is exceptionally good at high-speed big data analytics. It can store vast quantities of data and operate on it more quickly than many other solutions. Let’s say you have CSV files in S3 (20 TB and growing by 250GiB per day) and a use case that necessitates reporting on those files in a dashboard. A common approach to this problem is aggregating the CSV files down to a MySQL-friendly size, so that reports can be built on this aggregated data. However, this is limited in multiple ways:

  1. CSV is slow to parse because it requires reading all of the rows in the entire file, parsing each line’s columns.
  2. MySQL can only handle so much data, especially high dimensionality data where your users may want to pivot on many different attributes. Every pivot requirement is likely to be impossible to meet, so users must have their functionality restricted for the sake of tech limitations.
  3. Building many tables to support the various pivot requirements becomes onerous, because each table (and the database itself) has to be limited in both size and scope. This increases database storage costs and complexity.

If those limitations had you cringing, I’ve made my case well :). There is an alternative that utilizes SParquet…

  1. Process the CSV files into Parquet files (snappy or gzip compressed)
  2. Use Spark with those Parquet files to drive a powerful and scalable analytics solution

CSV File for Proof of Concept (PoC): NYC TLC Green Taxi for December 2016

The CSV file has 1,224,160 rows and 19 columns, coming in at 107MB uncompressed. Here’s the file schema (using header and inferSchema options in Spark 2.1.1):

 |-- VendorID: integer (nullable = true)
 |-- lpep_pickup_datetime: timestamp (nullable = true)
 |-- lpep_dropoff_datetime: timestamp (nullable = true)
 |-- store_and_fwd_flag: string (nullable = true)
 |-- RatecodeID: integer (nullable = true)
 |-- PULocationID: integer (nullable = true)
 |-- DOLocationID: integer (nullable = true)
 |-- passenger_count: integer (nullable = true)
 |-- trip_distance: nullable = true)
 |-- fare_amount: nullable = true)
 |-- extra: nullable = true)
 |-- mta_tax: nullable = true)
 |-- tip_amount: nullable = true)
 |-- tolls_amount: nullable = true)
 |-- ehail_fee: string (nullable = true)
 |-- improvement_surcharge: nullable = true)
 |-- total_amount: nullable = true)
 |-- payment_type: integer (nullable = true)
 |-- trip_type: integer (nullable = true)

Uncompressed CSV of 107MB was reduced to 24MB (Snappy Parquet) and 19MB (GZIP Parquet). But the real power comes in once the data (now in parquet format) is accessed. Parquet is exceptionally fast when accessing specific columns, which is the opposite of row-based file formats, which thrive when accessing an entire row record. Here are simple SQL examples to show the differences:

--#1
--CSV will read the entire file row-by-row
--Parquet will dump the rows based on their column values
--Winner: Parquet (minimal; because of no parsing)
SELECT *
green_tlc

--#2
--CSV will read the entire file row-by-row
--filter the PULocation column to only ones containing 226 
--and output all rows/columns that match the filter criteria as the results
--Winner: Parquet (minimal; because of no parsing and push down filtering)
SELECT *
green_tlc
<span class="hljs-keyword">WHERE PULocation = 226

--#3
--Parquet will first find only the relevant "data blocks" based on the filter criteria
--and only aggregate the rows/columns that match the filter criteria
--Winner: Parquet (huge; because of no parsing and only specific columns)
SELECT PULocation, SUM(total_amount)
green_tlc
WHERE PULocation IN (77, 102, 107, 226)
GROUP BY PULocation

#3 above is a great example of where Parquet shines, because you’re using pushdown filtering, operating on only specific columns (the rest are ignored), and do not have to parse what you don’t care about (all the other columns/rows).

What implementation strategies can I use?

Some ideas:

  1. Spark with Parquet (SParquet) on Livy to be able to cache entire datasets/queries
  2. Bonus: Impala with Parquet-backed Hive tables (also Spark compatible) to get hyperfast results available via SQL queries

By now, you have hopefully learned that Parquet is a powerful data format that facilitates big data analytics at a scale far greater than many traditional limited approaches. Go forth and play with Parquet!

Here’s my blog post for specific optimization tips: http://garrens.com/blog/2017/04/08/getting-started-and-tips-for-using-apache-parquet-with-apache-spark-2-x/

Garren Staubli is a Big Data Engineer Consultant at Blueprint Consulting Services, and formerly a big data engineer at iSpot.TV.

 

Connecting Apache Spark to External Data sources (e.g. Redshift, S3, MySQL)

Pre-requisites

AWS S3

Hadoop AWS Jar

AWS Java SDK Jar

* Note: These AWS jars should not be necessary if you’re using Amazon EMR.

Amazon Redshift

JDBC Driver

Spark-Redshift package *

* The Spark-redshift package provided by Databricks is critical particularly if you wish to WRITE to Redshift, because it does bulk file operations instead of individual insert statements. If you’re only looking to READ from Redshift, this package may not be quite as helpful.

MySQL

MySQL JDBC Connector jar

Setting your password [relatively securely]

This is not extremely secure, but is much better than putting your password directly into code.

Use a properties file:

<code>echo "spark.jdbc.password=test_pass_prop" &gt; secret_credentials.properties
spark-submit --properties-file secret_credentials.properties</code>

Examples (in Scala unless otherwise noted)

S3 (using S3A)

<code class="bash plain">spark-shell --jars hadoop-aws-2.7.3.jar,aws-java-sdk-1.7.4.jar</code>
<code>spark.conf.set("fs.s3a.access.key", "&lt;ACCESS_KEY&gt;")
spark.conf.set("fs.s3a.secret.key", "&lt;SECRET_KEY&gt;")
val d = spark.read.parquet("s3a://parquet-lab/files")
d.select("device_id").distinct().count() // =&gt; 1337</code>

* On Amazon EMR, you may be able to skip the jars and key settings.
** Also, you may also want to try using the “s3” or “s3n” protocols if s3a doesn’t work.

MySQL

<code>spark-shell --jars mysql-connector-java-5.1.40-bin.jar
val properties = new java.util.Properties()
properties.put("driver", "com.mysql.jdbc.Driver")
properties.put("url", "jdbc:mysql://mysql-host:3306")
properties.put("user", )
properties.put("password", spark.conf.get("spark.jdbc.password", "&lt;default_pass&gt;"))
// This will form a SQL query like "SELECT model_id, prediction, actual_value FROM ml_models WHERE utc_start_time BETWEEN '2017-03-31' AND '2017-04-02'"
// Using .limit(INT) will NOT work as you might expect - it will retrieve all the data first THEN limit when showing you
val models = spark.read.jdbc(properties.get("url").toString, "ml_models", Array("utc_start_time BETWEEN '2017-03-31' AND '2017-04-02'"), properties).select("model_id", "prediction", "actual_value")</code>

Redshift

Recommended approach using Databricks’ spark-redshift:

spark-shell --packages com.databricks:spark-redshift_2.11:3.0.0-preview1 --jars RedshiftJDBC42-1.2.1.1001.jar

Basic JDBC connection only:

spark-shell --jars RedshiftJDBC42-1.2.1.1001.jar
<code>
val properties = new java.util.Properties() 
properties.put("driver", "com.amazon.redshift.jdbc42.Driver") 
properties.put("url", "jdbc:redshift://redshift-host:5439/") 
properties.put("user", "&lt;username&gt;") properties.put("password",spark.conf.get("spark.jdbc.password", "&lt;default_pass&gt;")) 
val d_rs = spark.read.jdbc(properties.get("url").toString, "data_table", properties)</code>

Using the Databricks Redshift data source package – for Bulk Data WRITING to Redshift, use this package:

Reading from and writing to Redshift stages data [and doesn’t clean up after itself] in S3, so use object lifecycle management!

val devices = spark.read.format("com.databricks.spark.redshift").
option("forward_spark_s3_credentials", "true").
option("url", "jdbc:redshift://redshift-host:5439/?user=&lt;user&gt;&amp;password=&lt;password&gt;").
option("query", "SELECT * FROM devices").
option("tempdir", "s3://temporary-holding-bucket/").load()

Writing the dataframe to Redshift in the “public.temporary_devices” table:

devices_transformed.coalesce(64).write .format("com.databricks.spark.redshift") .option("forward_spark_s3_credentials", "true") .option("url", "jdbc:redshift://redshift-host:5439/?user=&amp;password=") .option("dbtable", "public.temporary_devices") .option("tempdir", "s3a://temporary-holding-bucket/") .option("tempformat", "CSV GZIP") // EXPERIMENTAL, but CSV is higher performance than AVRO for loading into redshift .mode("error") .save()

* Note: coalesce(64) is called to reduce the number of output files to the s3 staging directory, because renaming files from their temporary location in S3 can be slow. This S3Committer should help alleviate that issue.

Resources

http://deploymentzone.com/2015/12/20/s3a-on-spark-on-aws-ec2/

Tips for using Apache Parquet with Spark 2.x

What is Apache Parquet?
It is a compressable binary columnar data format used in the hadoop ecosystem. We’ll talk about it primarily with relation to the Hadoop Distributed File System (HDFS) and Spark 2.x contexts.

What role does it fill?
It is a fast and efficient data format great for scalable big data analytics.

Optimization Tips

  • Aim for around 1GB parquet output files, but experiment with other sizes for your use case and cluster setup (source)
  • Ideally store on HDFS in file sizes of at least the HDFS block size (default 128MB)
  • Storing Parquet files on S3 is also possible (side note: use amazon athena, which charges based on data read if you want Presto SQL-like queries on demand at low cost)
  • Use snappy compression if storage space is not a concern due to it being splittable, but for what should be a relatively small performance hit but much better compression, use gzip (source)
  • Continue reading “Tips for using Apache Parquet with Spark 2.x”

    Runtime Stats for Functions | Python Decorator

    In a similar vein to my prior Python decorator metadata for functions (“meta_func” => github | PyPi | blog), this decorator is intended to help illuminate the number of calls and time taken per call aggregates.

    It will keep track of each function by its uniquely assigned python object identifier, the total number of function calls, total time taken for all calls to that function, and min, max and average time for the function calls.

    Sample usage:
    @runtime_stats()
    def self_mult(n):
    sleep(0.2)
    return n*n

    print(self_mult(10)) # => 100
    print(self_mult(7)) # => 49
    print(self_mult.get_func_runtime_stats()) # => {'total_time': 401.668, 'avg': 200.834, 'func_uid': 4302206808, 'func_name': 'self_mult', 'min': 200.445, 'max': 201.223, 'total_calls': 2}

    Replace CTRL-A in a file while in a screen session

    echo -e "\u0001” | cat -v
    # ^A

    cat -v 000001 | tr '^A' '\t' | head

    Inspiration: http://stackoverflow.com/questions/31460818/creating-a-ctrl-a-delimiter-file

    Note: Within the same day, this strategy both worked then failed. YMMV

    More reliable would be to get into a non screen session and do “ctrl-v then a”

    Split file by keys

    Files sometimes come in (whether via hadoop or other processes) as big globs of data with inter-related parts. Many times I want to process these globs concurrently but see my dilemma unfolding quickly. I could a) write the code to process it serially and be done with it in 1 hour or b) write code to process it concurrently and be done in 1.5 hours because the added overhead of verifying the output, thread safety, etc exceeds the processing time serially. This made me sad, because concurrent processes are awesome. But self-managed thread safe concurrent processes are even more awesome!

    I thought, what if I could split an input file on keys and group those similarly keyed lines into separate files for processing. Aha!

    So I naturally first tried finding existing solutions and to be honest, awk has a pretty killer one liner as noted here on Stack Overflow:

    awk '{ print &gt;&gt; $5 }' yourfile

    This one liner is likely great for many folks (especially when using only small files). But for me, awk threw an error due to having “too many open files” – again, sad face :(.

    So… I wrote my own python command line utility to take an input file and split it into any number of output files by unique keys in the file. So all your input is maintained, just in different files sorted/segregated on keys you provide.

    While my naming conventions may be lacking panache, they are at least clearly intentioned utilities. (But seriously, if you have a better name, I’m all ears)

    Without further ado, I give you
    split_file_by_key

    Converting CSVs with Headers to AVRO

    Recently I wanted to quickly convert some CSV files to AVRO due to recent logging changes that meant we were receiving AVRO logs instead of CSV. I wanted to have some AVRO files to test my logic on and to get more familiar with AVRO. After looking around for a while and trying a few different CSV to AVRO conversion utilities, none of them actually worked as expected. I just wanted a simple conversion, why was this so hard to find? The closest I came to finding a working CSV2AVRO utility was avroutils.

    Unfortunately avroutils hasn’t been updated in 5 years and the code was very restrictive since it offered a command line argument for “headers.” However regardless of whether that argument was passed, it used the [in my opinion, flawed] utility “csv.Sniffer” in Python to confirm there was a header. For me, this meant even though I was explicitly telling it my file had a header it still did not convert due to the Sniffer claiming there was no header.

    To reiterate, I really just wanted a simple utility to convert CSV to AVRO if for no other reason than to some hands-on experience with the AVRO format. Why was I having such a hard time?

    So… I wrote my own [very basic] utility to handle CSV to AVRO conversions. It does no validation (re: it assumes you know what you’re doing) and is hard-coded to treat all fields as strings. Remember, this was primarily a learning exercise!

    Without further ado, I present to you csv2avro

    Questions/Comments/Bugs/Requests/etc are encouraged!

    Metadata for Functions | Python Decorator

    Often I find myself wanting more information about the Python functions I’m running, whether it’s because I want to debug, log or even time their completion. All of these are relatively well-defined problems (debugging excepted). Unfortunately no tool makes it easy enough from my research to truly see the input, output, time elapsed, errors, warnings, etc about a function in a simple interface. So I wrote a simple python decorator compatible with Python 2.7+ (and probably earlier versions), including Py3.

    What does the meta_func decorator actually do?

    It stores all arguments for every function call, both positional and keyword arguments, error information (including the ability to catch and not raise errors), warnings, time elements (time started, ended and elapsed), and the returned value as a standard python dictionary.

    What’s the point of tracking all this [meta]data?

    Debugging, Logging, Timing… The use cases are nearly endless, because it tells us a lot of what’s going on in one easily interpreted structure.

    Important Notes

    This decorator should be expected to add a good deal of overhead to many function calls due to the handling of so many dimensions.

    Arguments (Positional and Keywords), Return value, Warnings and Exceptions will be stored in their raw form, so any transformations (such as stringifying errors and traceback) would need to be done post-processing.

    The error_info field will return a tuple from sys.exc_info() with error details.

    Github Repo

    https://github.com/gstaubli/meta_func