Posts Tagged PySpark
Getting Started with Spark Structured Streaming and Kafka on AWS using Amazon MSK and Amazon EMR
Posted by Gary A. Stafford in Analytics, AWS, Big Data, Build Automation, Cloud, Software Development on September 9, 2021
Exploring Apache Spark with Apache Kafka using both batch queries and Spark Structured Streaming
Introduction
Structured Streaming is a scalable and fault-tolerant stream processing engine built on the Spark SQL engine. Using Structured Streaming, you can express your streaming computation the same way you would express a batch computation on static data. In this post, we will learn how to use Apache Spark and Spark Structured Streaming with Apache Kafka. Specifically, we will utilize Structured Streaming on Amazon EMR (fka Amazon Elastic MapReduce) with Amazon Managed Streaming for Apache Kafka (Amazon MSK). We will consume from and publish to Kafka using both batch and streaming queries. Spark jobs will be written in Python with PySpark for this post.
Apache Spark
According to the documentation, Apache Spark is a unified analytics engine for large-scale data processing. It provides high-level APIs in Java, Scala, Python (PySpark), and R, and an optimized engine that supports general execution graphs. In addition, Spark supports a rich set of higher-level tools, including Spark SQL for SQL and structured data processing, MLlib for machine learning, GraphX for graph processing, and Structured Streaming for incremental computation and stream processing.
Spark Structured Streaming
According to the documentation, Spark Structured Streaming is a scalable and fault-tolerant stream processing engine built on the Spark SQL engine. You can express your streaming computation the same way you would express a batch computation on static data. The Spark SQL engine will run it incrementally and continuously and update the final result as streaming data continues to arrive. In short, Structured Streaming provides fast, scalable, fault-tolerant, end-to-end, exactly-once stream processing without the user having to reason about streaming.
Amazon EMR
According to the documentation, Amazon EMR (fka Amazon Elastic MapReduce) is a cloud-based big data platform for processing vast amounts of data using open source tools such as Apache Spark, Hadoop, Hive, HBase, Flink, and Hudi, and Presto. Amazon EMR is a fully managed AWS service that makes it easy to set up, operate, and scale your big data environments by automating time-consuming tasks like provisioning capacity and tuning clusters.
A deployment option for Amazon EMR since December 2020, Amazon EMR on EKS, allows you to run Amazon EMR on Amazon Elastic Kubernetes Service (Amazon EKS). With the EKS deployment option, you can focus on running analytics workloads while Amazon EMR on EKS builds, configures, and manages containers for open-source applications.
If you are new to Amazon EMR for Spark, specifically PySpark, I recommend an earlier two-part series of posts, Running PySpark Applications on Amazon EMR: Methods for Interacting with PySpark on Amazon Elastic MapReduce.
Apache Kafka
According to the documentation, Apache Kafka is an open-source distributed event streaming platform used by thousands of companies for high-performance data pipelines, streaming analytics, data integration, and mission-critical applications.
Amazon MSK
Apache Kafka clusters are challenging to set up, scale, and manage in production. According to the documentation, Amazon MSK is a fully managed AWS service that makes it easy for you to build and run applications that use Apache Kafka to process streaming data. With Amazon MSK, you can use native Apache Kafka APIs to populate data lakes, stream changes to and from databases, and power machine learning and analytics applications.
Prerequisites
This post will focus primarily on configuring and running Apache Spark jobs on Amazon EMR. To follow along, you will need the following resources deployed and configured on AWS:
- Amazon S3 bucket (holds Spark resources and output);
- Amazon MSK cluster (using IAM Access Control);
- Amazon EKS container or an EC2 instance with the Kafka APIs installed and capable of connecting to Amazon MSK;
- Connectivity between the Amazon EKS cluster or EC2 and Amazon MSK cluster;
- Ensure the Amazon MSK Configuration has
auto.create.topics.enable=true; this setting isfalseby default;
As shown in the architectural diagram above, the demonstration uses three separate VPCs within the same AWS account and AWS Region, us-east-1, for Amazon EMR, Amazon MSK, and Amazon EKS. The three VPCs are connected using VPC Peering. Ensure you expose the correct ingress ports and the corresponding CIDR ranges within your Amazon EMR, Amazon MSK, and Amazon EKS Security Groups. For additional security and cost savings, use a VPC endpoint for private communications between Amazon EMR and Amazon S3.
Source Code
All source code for this post and the two previous posts in the Amazon MSK series, including the Python/PySpark scripts demonstrated here, are open-sourced and located on GitHub.
PySpark Scripts
According to the Apache Spark documentation, PySpark is an interface for Apache Spark in Python. It allows you to write Spark applications using Python API. PySpark supports most of Spark’s features such as Spark SQL, DataFrame, Streaming, MLlib (Machine Learning), and Spark Core.
There are nine Python/PySpark scripts covered in this post:
- Initial sales data published to Kafka
01_seed_sales_kafka.py - Batch query of Kafka
02_batch_read_kafka.py - Streaming query of Kafka using grouped aggregation
03_streaming_read_kafka_console.py - Streaming query using sliding event-time window
04_streaming_read_kafka_console_window.py - Incremental sales data published to Kafka
05_incremental_sales_kafka.py - Streaming query from/to Kafka using grouped aggregation
06_streaming_read_kafka_kafka.py - Batch query of streaming query results in Kafka
07_batch_read_kafka.py - Streaming query using static join and sliding window
08_streaming_read_kafka_join_window.py - Streaming query using static join and grouped aggregation
09_streaming_read_kafka_join.py
Amazon MSK Authentication and Authorization
Amazon MSK provides multiple authentication and authorization methods to interact with the Apache Kafka APIs. For this post, the PySpark scripts use Kafka connection properties specific to IAM Access Control. You can use IAM to authenticate clients and to allow or deny Apache Kafka actions. Alternatively, you can use TLS or SASL/SCRAM to authenticate clients and Apache Kafka ACLs to allow or deny actions. In a recent post, I demonstrated the use of SASL/SCRAM and Kafka ACLs with Amazon MSK:Securely Decoupling Applications on Amazon EKS using Kafka with SASL/SCRAM.
Language Choice
According to the latest Spark 3.1.2 documentation, Spark runs on Java 8/11, Scala 2.12, Python 3.6+, and R 3.5+. The Spark documentation contains code examples written in all four languages and provides sample code on GitHub for Scala, Java, Python, and R. Spark is written in Scala.
There are countless posts and industry opinions on choosing the best language for Spark. Taking no sides, I have selected the language I use most frequently for data analytics, Python using PySpark. Compared to Scala, these two languages exhibit some of the significant differences: compiled versus interpreted, statically-typed versus dynamically-typed, JVM- versus non-JVM-based, Scala’s support for concurrency and true multi-threading, and Scala’s 10x raw performance versus the perceived ease-of-use, larger community, and relative maturity of Python.
Preparation
Amazon S3
We will start by gathering and copying the necessary files to your Amazon S3 bucket. The bucket will serve as the location for the Amazon EMR bootstrap script, additional JAR files required by Spark, PySpark scripts, CSV-format data files, and eventual output from the Spark jobs.
There are a small set of additional JAR files required by the Spark jobs we will be running. Download the JARs from Maven Central and GitHub, and place them in the emr_jars project directory. The JARs will include AWS MSK IAM Auth, AWS SDK, Kafka Client, Spark SQL for Kafka, Spark Streaming, and other dependencies.
cd ./pyspark/emr_jars/
wget https://github.com/aws/aws-msk-iam-auth/releases/download/1.1.0/aws-msk-iam-auth-1.1.0-all.jar
wget https://repo1.maven.org/maven2/software/amazon/awssdk/bundle/2.17.28/bundle-2.17.28.jar
wget https://repo1.maven.org/maven2/org/apache/commons/commons-pool2/2.11.0/commons-pool2-2.11.0.jar
wget https://repo1.maven.org/maven2/org/apache/kafka/kafka-clients/2.8.0/kafka-clients-2.8.0.jar
wget https://repo1.maven.org/maven2/org/apache/spark/spark-sql-kafka-0-10_2.12/3.1.2/spark-sql-kafka-0-10_2.12-3.1.2.jar
wget https://repo1.maven.org/maven2/org/apache/spark/spark-streaming_2.12/3.1.2/spark-streaming_2.12-3.1.2.jar
wget https://repo1.maven.org/maven2/org/apache/spark/spark-tags_2.12/3.1.2/spark-tags_2.12-3.1.2.jar
wget https://repo1.maven.org/maven2/org/apache/spark/spark-token-provider-kafka-0-10_2.12/3.1.2/spark-token-provider-kafka-0-10_2.12-3.1.2.jar
Next, update the SPARK_BUCKET environment variable, then upload the JARs and all necessary project files from your copy of the GitHub project repository to your Amazon S3 bucket using the AWS s3 API.
cd ./pyspark/
export SPARK_BUCKET="<your-bucket-111222333444-us-east-1>"
aws s3 cp emr_jars/ \
"s3://${SPARK_BUCKET}/jars/" --recursive
aws s3 cp pyspark_scripts/ \
"s3://${SPARK_BUCKET}/spark/" --recursive
aws s3 cp emr_bootstrap/ \
"s3://${SPARK_BUCKET}/spark/" --recursive
aws s3 cp data/ \
"s3://${SPARK_BUCKET}/spark/" --recursive
Amazon EMR
The GitHub project repository includes a sample AWS CloudFormation template and an associated JSON-format CloudFormation parameters file. The template, stack.yml, accepts several parameters. To match your environment, you will need to update the parameter values such as SSK key, Subnet, and S3 bucket. The template will build a minimally-sized Amazon EMR cluster with one master and two core nodes in an existing VPC. The template can be easily modified to meet your requirements and budget.
aws cloudformation deploy \
--stack-name spark-kafka-demo-dev \
--template-file ./cloudformation/stack.yml \
--parameter-overrides file://cloudformation/dev.json \
--capabilities CAPABILITY_NAMED_IAM
Whether you decide to use the CloudFormation template, two essential Spark configuration items in the EMR template are the list of applications to install and the bootstrap script deployment.
Below, we see the EMR bootstrap shell script, bootstrap_actions.sh, deployed and executed on the cluster’s nodes.
The script performed several tasks, including deploying the additional JAR files we copied to Amazon S3 earlier.
AWS Systems Manager Parameter Store
The PySpark scripts in this demonstration will obtain two parameters from the AWS Systems Manager (AWS SSM) Parameter Store. They include the Amazon MSK bootstrap brokers and the Amazon S3 bucket that contains the Spark assets. Using the Parameter Store ensures that no sensitive or environment-specific configuration is hard-coded into the PySpark scripts. Modify and execute the ssm_params.sh script to create two AWS SSM Parameter Store parameters.
aws ssm put-parameter \
--name /kafka_spark_demo/kafka_servers \
--type String \
--value "<b-1.your-brokers.kafka.us-east-1.amazonaws.com:9098,b-2.your-brokers.kafka.us-east-1.amazonaws.com:9098>" \
--description "Amazon MSK Kafka broker list" \
--overwrite
aws ssm put-parameter \
--name /kafka_spark_demo/kafka_demo_bucket \
--type String \
--value "<your-bucket-111222333444-us-east-1>" \
--description "Amazon S3 bucket" \
--overwrite
Spark Submit Options with Amazon EMR
Amazon EMR provides multiple options to run Spark jobs. The recommended method for PySpark scripts is to use Amazon EMR Steps from the EMR console or AWS CLI to submit work to Spark installed on an EMR cluster. In the console and CLI, you do this using a Spark application step, which runs the spark-submit script as a step on your behalf. With the API, you use a Step to invoke spark-submit using command-runner.jar. Alternately, you can SSH into the EMR cluster’s master node and run spark-submit. We will employ both techniques to run the PySpark jobs.
Securely Accessing Amazon MSK from Spark
Each of the PySpark scripts demonstrated in this post uses a common pattern for accessing Amazon MSK from Amazon EMR using IAM Authentication. Whether producing or consuming messages from Kafka, the same security-related options are used to configure Spark (starting at line 10, below). The details behind each option are outlined in the Security section of the Spark Structured Streaming + Kafka Integration Guide and the Configure clients for IAM access control section of the Amazon MSK IAM access control documentation.
Data Source and Analysis Objective
For this post, we will continue to use data from PostgreSQL’s sample Pagila database. The database contains simulated movie rental data. The dataset is fairly small, making it less than ideal for ‘big data’ use cases but small enough to quickly install and minimize data storage and analytical query costs.
According to mastersindatascience.org, data analytics is “…the process of analyzing raw data to find trends and answer questions…” Using Spark, we can analyze the movie rental sales data as a batch or in near-real-time using Structured Streaming to answer different questions. For example, using batch computations on static data, we could answer the question, how do the current total all-time sales for France compare to the rest of Europe? Or, what were the total sales for India during August? Using streaming computations, we can answer questions like, what are the sales volumes for the United States during this current four-hour marketing promotional period? Or, are sales to North America beginning to slow as the Olympics are aired during prime time?
Data analytics — the process of analyzing raw data to find trends and answer questions. (mastersindatascience.org)
Batch Queries
Before exploring the more advanced topic of streaming computations with Spark Structured Streaming, let’s first use a simple batch query and a batch computation to consume messages from the Kafka topic, perform a basic aggregation, and write the output to both the console and Amazon S3.
PySpark Job 1: Initial Sales Data
Kafka supports Protocol Buffers, JSON Schema, and Avro. However, to keep things simple in this first post, we will use JSON. We will seed a new Kafka topic with an initial batch of 250 JSON-format messages. This first batch of messages represents previous online movie rental sale transaction records. We will use these sales transactions for both batch and streaming queries.
The PySpark script, 01_seed_sales_kafka.py, and the seed data file, sales_seed.csv, are both read from Amazon S3 by Spark, running on Amazon EMR. The location of the Amazon S3 bucket name and the Amazon MSK’s broker list values are pulled from AWS SSM Parameter Store using the parameters created earlier. The Kafka topic that stores the sales data, pagila.sales.spark.streaming, is created automatically by the script the first time it runs.
Update the two environment variables, then submit your first Spark job as an Amazon EMR Step using the AWS CLI and the emr API:
From the Amazon EMR console, we should observe the Spark job has been completed successfully in about 30–90 seconds.
The Kafka Consumer API allows applications to read streams of data from topics in the Kafka cluster. Using the Kafka Consumer API, from within a Kubernetes container running on Amazon EKS or an EC2 instance, we can observe that the new Kafka topic has been successfully created and that messages (initial sales data) have been published to the new Kafka topic.
export BBROKERS="b-1.your-cluster.kafka.us-east-1.amazonaws.com:9098,b-2.your-cluster.kafka.us-east-1.amazonaws.com:9098, ..."
bin/kafka-console-consumer.sh \
--topic pagila.sales.spark.streaming \
--from-beginning \
--property print.key=true \
--property print.value=true \
--property print.offset=true \
--property print.partition=true \
--property print.headers=true \
--property print.timestamp=true \
--bootstrap-server $BBROKERS \
--consumer.config config/client-iam.properties
PySpark Job 2: Batch Query of Amazon MSK Topic
The PySpark script, 02_batch_read_kafka.py, performs a batch query of the initial 250 messages in the Kafka topic. When run, the PySpark script parses the JSON-format messages, then aggregates the data by both total sales and order count, by country, and finally, sorts by total sales.
window = Window.partitionBy("country").orderBy("amount")
window_agg = Window.partitionBy("country")
.withColumn("row", F.row_number().over(window)) \
.withColumn("orders", F.count(F.col("amount")).over(window_agg)) \
.withColumn("sales", F.sum(F.col("amount")).over(window_agg)) \
.where(F.col("row") == 1).drop("row") \
The results are written to both the console as stdout and to Amazon S3 in CSV format.
Again, submit this job as an Amazon EMR Step using the AWS CLI and the emr API:
To view the console output, click on ‘View logs’ in the Amazon EMR console, then click on the stdout logfile, as shown below.
The stdout logfile should contain the top 25 total sales and order counts, by country, based on the initial 250 sales records.
+------------------+------+------+
|country |sales |orders|
+------------------+------+------+
|India |138.80|20 |
|China |133.80|20 |
|Mexico |106.86|14 |
|Japan |100.86|14 |
|Brazil |96.87 |13 |
|Russian Federation|94.87 |13 |
|United States |92.86 |14 |
|Nigeria |58.93 |7 |
|Philippines |58.92 |8 |
|South Africa |46.94 |6 |
|Argentina |42.93 |7 |
|Germany |39.96 |4 |
|Indonesia |38.95 |5 |
|Italy |35.95 |5 |
|Iran |33.95 |5 |
|South Korea |33.94 |6 |
|Poland |30.97 |3 |
|Pakistan |25.97 |3 |
|Taiwan |25.96 |4 |
|Mozambique |23.97 |3 |
|Ukraine |23.96 |4 |
|Vietnam |23.96 |4 |
|Venezuela |22.97 |3 |
|France |20.98 |2 |
|Peru |19.98 |2 |
+------------------+------+------+
only showing top 25 rows
The PySpark script also wrote the same results to Amazon S3 in CSV format.
The total sales and order count for 69 countries were computed, sorted, and coalesced into a single CSV file.
Streaming Queries
To demonstrate streaming queries with Spark Structured Streaming, we will use a combination of two PySpark scripts. The first script, 03_streaming_read_kafka_console.py, will perform a streaming query and computation of messages in the Kafka topic, aggregating the total sales and number of orders. Concurrently, the second PySpark script, 04_incremental_sales_kafka.py, will read additional Pagila sales data from a CSV file located on Amazon S3 and write messages to the Kafka topic at a rate of two messages per second. The first script, 03_streaming_read_kafka_console.py, will stream aggregations in micro-batches of one-minute increments to the console. Spark Structured Streaming queries are processed using a micro-batch processing engine, which processes data streams as a series of small, batch jobs.
Note that this first script performs grouped aggregations as opposed to aggregations over a sliding event-time window. The aggregated results represent the total, all-time sales at a point in time, based on all the messages currently in the topic when the micro-batch was computed.
To follow along with this part of the demonstration, you can run the two Spark jobs as concurrent steps on the existing Amazon EMR cluster, or create a second EMR cluster, identically configured to the existing cluster, to run the second PySpark script, 04_incremental_sales_kafka.py. Using a second cluster, you can use a minimally-sized single master node cluster with no core nodes to save cost.
PySpark Job 3: Streaming Query to Console
The first PySpark scripts, 03_streaming_read_kafka_console.py, performs a streaming query of messages in the Kafka topic. The script then aggregates the data by both total sales and order count, by country, and finally, sorts by total sales.
.groupBy("country") \
.agg(F.count("amount"), F.sum("amount")) \
.orderBy(F.col("sum(amount)").desc()) \
.select("country",
(F.format_number(F.col("sum(amount)"), 2)).alias("sales"),
(F.col("count(amount)")).alias("orders")) \
The results are streamed to the console using the processingTime trigger parameter. A trigger defines how often a streaming query should be executed and emit new data. The processingTime parameter sets a trigger that runs a micro-batch query periodically based on the processing time (e.g. ‘5 minutes’ or ‘1 hour’). The trigger is currently set to a minimal processing time of one minute for ease of demonstration.
.trigger(processingTime="1 minute") \
.outputMode("complete") \
.format("console") \
.option("numRows", 25) \
For demonstration purposes, we will run the Spark job directly from the master node of the EMR Cluster. This method will allow us to easily view the micro-batches and associated logs events as they are output to the console. The console is normally used for testing purposes. Submitting the PySpark script from the cluster’s master node is an alternative to submitting an Amazon EMR Step. Connect to the master node of the Amazon EMR cluster using SSH, as the hadoop user:
export EMR_MASTER=<your-emr-master-dns.compute-1.amazonaws.com>
export EMR_KEY_PATH=path/to/key/<your-ssk-key.pem>
ssh -i ${EMR_KEY_PATH} hadoop@${EMR_MASTER}
Submit the PySpark script, 03_streaming_read_kafka_console.py, to Spark:
export SPARK_BUCKET="<your-bucket-111222333444-us-east-1>"
spark-submit s3a://${SPARK_BUCKET}/spark/03_streaming_read_kafka_console.py
Before running the second PySpark script, 04_incremental_sales_kafka.py, let the first script run long enough to pick up the existing sales data in the Kafka topic. Within about two minutes, you should see the first micro-batch of aggregated sales results, labeled ‘Batch: 0’ output to the console. This initial micro-batch should contain the aggregated results of the existing 250 messages from Kafka. The streaming query’s first micro-batch results should be identical to the previous batch query results.
-------------------------------------------
Batch: 0
-------------------------------------------
+------------------+------+------+
|country |sales |orders|
+------------------+------+------+
|India |138.80|20 |
|China |133.80|20 |
|Mexico |106.86|14 |
|Japan |100.86|14 |
|Brazil |96.87 |13 |
|Russian Federation|94.87 |13 |
|United States |92.86 |14 |
|Nigeria |58.93 |7 |
|Philippines |58.92 |8 |
|South Africa |46.94 |6 |
|Argentina |42.93 |7 |
|Germany |39.96 |4 |
|Indonesia |38.95 |5 |
|Italy |35.95 |5 |
|Iran |33.95 |5 |
|South Korea |33.94 |6 |
|Poland |30.97 |3 |
|Pakistan |25.97 |3 |
|Taiwan |25.96 |4 |
|Mozambique |23.97 |3 |
|Ukraine |23.96 |4 |
|Vietnam |23.96 |4 |
|Venezuela |22.97 |3 |
|France |20.98 |2 |
|Peru |19.98 |2 |
+------------------+------+------+
only showing top 25 rows
Immediately below the batch output, there will be a log entry containing information about the batch. In the log entry snippet below, note the starting and ending offsets of the topic for the Spark job’s Kafka consumer group, 0 (null) to 250, representing the initial sales data.
PySpark Job 4: Incremental Sales Data
As described earlier, the second PySpark script, 04_incremental_sales_kafka.py, reads 1,800 additional sales records from a second CSV file located on Amazon S3, sales_incremental_large.csv. The script then publishes messages to the Kafka topic at a deliberately throttled rate of two messages per second. Concurrently, the first PySpark job, still running and performing a streaming query, will consume the new Kafka messages and stream aggregated total sales and orders in micro-batches of one-minute increments to the console over a period of about 15 minutes.
Submit the second PySpark script as a concurrent Amazon EMR Step to the first EMR cluster, or submit as a step to the second Amazon EMR cluster.
The job sends a total of 1,800 messages to Kafka at a rate of two messages per second for 15 minutes. The total runtime of the job should be approximately 19 minutes, given a few minutes for startup and shutdown. Why run for so long? We want to make sure the job’s runtime will span multiple, overlapping, sliding event-time windows.
After about two minutes, return to the terminal output of the first Spark job, 03_streaming_read_kafka_console.py, running on the master node of the first cluster. As long as new messages are consumed every minute, you should see a new micro-batch of aggregated sales results stream to the console. Below we see an example of Batch 3, which reflects additional sales compared to Batch 0, shown previously. The results reflect the current all-time sales by country in real-time as the sales are published to Kafka.
-------------------------------------------
Batch: 5
-------------------------------------------
+------------------+------+------+
|country |sales |orders|
+------------------+------+------+
|China |473.35|65 |
|India |393.44|56 |
|Japan |292.60|40 |
|Mexico |262.64|36 |
|United States |252.65|35 |
|Russian Federation|243.65|35 |
|Brazil |220.69|31 |
|Philippines |191.75|25 |
|Indonesia |142.81|19 |
|South Africa |110.85|15 |
|Nigeria |108.86|14 |
|Argentina |89.86 |14 |
|Germany |85.89 |11 |
|Israel |68.90 |10 |
|Ukraine |65.92 |8 |
|Turkey |58.91 |9 |
|Iran |58.91 |9 |
|Saudi Arabia |56.93 |7 |
|Poland |50.94 |6 |
|Pakistan |50.93 |7 |
|Italy |48.93 |7 |
|French Polynesia |47.94 |6 |
|Peru |45.95 |5 |
|United Kingdom |45.94 |6 |
|Colombia |44.94 |6 |
+------------------+------+------+
only showing top 25 rows
If we fast forward to a later micro-batch, sometime after the second incremental sales job is completed, we should see the top 25 aggregated sales by country of 2,050 messages — 250 seed plus 1,800 incremental messages.
-------------------------------------------
Batch: 20
-------------------------------------------
+------------------+--------+------+
|country |sales |orders|
+------------------+--------+------+
|China |1,379.05|195 |
|India |1,338.10|190 |
|United States |915.69 |131 |
|Mexico |855.80 |120 |
|Japan |831.88 |112 |
|Russian Federation|723.95 |105 |
|Brazil |613.12 |88 |
|Philippines |528.27 |73 |
|Indonesia |381.46 |54 |
|Turkey |350.52 |48 |
|Argentina |298.57 |43 |
|Nigeria |294.61 |39 |
|South Africa |279.61 |39 |
|Taiwan |221.67 |33 |
|Germany |199.73 |27 |
|United Kingdom |196.75 |25 |
|Poland |182.77 |23 |
|Spain |170.77 |23 |
|Ukraine |160.79 |21 |
|Iran |160.76 |24 |
|Italy |156.79 |21 |
|Pakistan |152.78 |22 |
|Saudi Arabia |146.81 |19 |
|Venezuela |145.79 |21 |
|Colombia |144.78 |22 |
+------------------+--------+------+
only showing top 25 rows
Compare the informational output below for Batch 20 to Batch 0, previously. Note the starting offset of the Kafka consumer group on the topic is 1986, and the ending offset is 2050. This is because all messages have been consumed from the topic and aggregated. If additional messages were streamed to Kafka while the streaming job is still running, additional micro-batches would continue to be streamed to the console every one minute.
PySpark Job 5: Aggregations over Sliding Event-time Window
In the previous example, we analyzed total all-time sales in real-time (e.g., show me the current, total, all-time sales for France compared to the rest of Europe, at regular intervals). This approach is opposed to sales made during a sliding event-time window (e.g., are the total sales for the United States trending better during this current four-hour marketing promotional period than the previous promotional period). In many cases, real-time sales during a distinct period or event window is probably a more commonly tracked KPI than total all-time sales.
If we add a sliding event-time window to the PySpark script, we can easily observe the total sales and order counts made during the sliding event-time window in real-time.
.withWatermark("timestamp", "10 minutes") \
.groupBy("country",
F.window("timestamp", "10 minutes", "5 minutes")) \
.agg(F.count("amount"), F.sum("amount")) \
.orderBy(F.col("window").desc(),
F.col("sum(amount)").desc()) \
Windowed totals would not include sales (messages) present in the Kafka topic before the streaming query beginning, nor in previous sliding windows. Constructing the correct query always starts with a clear understanding of the question you are trying to answer.
Below, in the abridged console output of the micro-batch from the script, 05_streaming_read_kafka_console_window.py, we see the results of three ten-minute sliding event-time windows with a five-minute overlap. The sales and order totals represent the volume sold during that window, with this micro-batch falling within the active current window, 19:30 to 19:40 UTC.
Plotting the total sales over time using sliding event-time windows, we will observe the results do not reflect a running total. Total sales only accumulate within a sliding window.
Compare these results to the results of the previous script, whose total sales reflect a running total.
PySpark Job 6: Streaming Query from/to Amazon MSK
The PySpark script, 06_streaming_read_kafka_kafka.py, performs the same streaming query and grouped aggregation as the previous script, 03_streaming_read_kafka_console.py. However, instead of outputting results to the console, the results of this job will be written to a new Kafka topic on Amazon MSK.
.format("kafka") \
.options(**options_write) \
.option("checkpointLocation", "/checkpoint/kafka/") \
Repeat the same process used with the previous script. Re-run the seed data script, 01_seed_sales_kafka.py, but update the input topic to a new name, such as pagila.sales.spark.streaming.in. Next, run the new script, 06_streaming_read_kafka_kafka.py. Give the script time to start and consume the 250 seed messages from Kafka. Then, update the input topic name and re-run the incremental data PySpark script, 04_incremental_sales_kafka.py, concurrent to the new script on the same cluster or run on the second cluster.
When run, the script, 06_streaming_read_kafka_kafka.py, will continuously consume messages from the new pagila.sales.spark.streaming.in topic and publish grouped aggregation results to a new topic, pagila.sales.spark.streaming.out.
Use the Kafka Consumer API to view new messages as the Spark job publishes them in near real-time to Kafka.
export BBROKERS="b-1.your-cluster.kafka.us-east-1.amazonaws.com:9098,b-2.your-cluster.kafka.us-east-1.amazonaws.com:9098, ..."
bin/kafka-console-consumer.sh \
--topic pagila.sales.spark.streaming.out \
--from-beginning \
--property print.key=true \
--property print.value=true \
--property print.offset=true \
--property print.partition=true \
--property print.headers=true \
--property print.timestamp=true \
--bootstrap-server $BBROKERS \
--consumer.config config/client-iam.properties
PySpark Job 7: Batch Query of Streaming Results from MSK
When run, the previous script produces Kafka messages containing non-windowed sales aggregations to the Kafka topic every minute. Using the next PySpark script, 07_batch_read_kafka.py, we can consume those aggregated messages using a batch query and display the most recent sales totals to the console. Each country’s most recent all-time sales totals and order counts should be identical to the previous script’s results, representing the aggregation of all 2,050 Kafka messages — 250 seed plus 1,800 incremental messages.
To get the latest total sales by country, we will consume all the messages from the output topic, group the results by country, find the maximum (max) value from the sales column for each country, and finally, display the results sorted sales in descending order.
window = Window.partitionBy("country") \
.orderBy(F.col("timestamp").desc())
.withColumn("row", F.row_number().over(window)) \
.where(F.col("row") == 1).drop("row") \
.select("country", "sales", "orders") \
Writing the top 25 results to the console, we should see the same results as we saw in the final micro-batch (Batch 20, shown above) of the PySpark script, 03_streaming_read_kafka_console.py.
+------------------+------+------+
|country |sales |orders|
+------------------+------+------+
|India |948.63|190 |
|China |936.67|195 |
|United States |915.69|131 |
|Mexico |855.80|120 |
|Japan |831.88|112 |
|Russian Federation|723.95|105 |
|Brazil |613.12|88 |
|Philippines |528.27|73 |
|Indonesia |381.46|54 |
|Turkey |350.52|48 |
|Argentina |298.57|43 |
|Nigeria |294.61|39 |
|South Africa |279.61|39 |
|Taiwan |221.67|33 |
|Germany |199.73|27 |
|United Kingdom |196.75|25 |
|Poland |182.77|23 |
|Spain |170.77|23 |
|Ukraine |160.79|21 |
|Iran |160.76|24 |
|Italy |156.79|21 |
|Pakistan |152.78|22 |
|Saudi Arabia |146.81|19 |
|Venezuela |145.79|21 |
|Colombia |144.78|22 |
+------------------+------+------+
only showing top 25 rows
PySpark Job 8: Streaming Query with Static Join and Sliding Window
The PySpark script, 08_streaming_read_kafka_join_window.py, performs the same streaming query and computations over sliding event-time windows as the previous script, 05_streaming_read_kafka_console_window.py. However, instead of totaling sales and orders by country, the script totals by sales and orders sales region. A sales region is composed of multiple countries in the same geographical area. The PySpark script reads in a static list of sales regions and countries from Amazon S3, sales_regions.csv.
The script then performs a join operation between the results of the streaming query and the static list of regions, joining on country. Using the join, the streaming sales data from Kafka is enriched with the sales category. Any sales record whose country does not have an assigned sales region is categorized as ‘Unassigned.’
.join(df_regions, on=["country"], how="leftOuter") \
.na.fill("Unassigned") \
Sales and orders are then aggregated by sales region, and the top 25 are output to the console every minute.
To run the job, repeat the previous process of renaming the topic (e.g., pagila.sales.spark.streaming.region), then running the initial sales data job, this script, and finally, concurrent with this script, the incremental sales data job. Below, we see a later micro-batch output to the console from the Spark job. We see three sets of sales results, by sales region, from three different ten-minute sliding event-time windows with a five-minute overlap.
PySpark Script 9: Static Join with Grouped Aggregations
As a comparison, we can exclude the sliding event-time window operations from the previous streaming query script, 08_streaming_read_kafka_join_window.py, to obtain the current, total, all-time sales by sales region. See the script, 09_streaming_read_kafka_join.py, in the project repository for details.
-------------------------------------------
Batch: 20
-------------------------------------------
+--------------+--------+------+
|sales_region |sales |orders|
+--------------+--------+------+
|Asia & Pacific|5,780.88|812 |
|Europe |3,081.74|426 |
|Latin America |2,545.34|366 |
|Africa |1,029.59|141 |
|North America |997.57 |143 |
|Middle east |541.23 |77 |
|Unassigned |352.47 |53 |
|Arab States |244.68 |32 |
+--------------+--------+------+
Conclusion
In this post, we learned how to get started with Spark Structured Streaming on Amazon EMR. First, we explored how to run jobs written in Python with PySpark on Amazon EMR as Steps and directly from the EMR cluster’s master node. Next, we discovered how to produce and consume messages with Apache Kafka on Amazon MSK, using batch and streaming queries. Finally, we learned about aggregations over a sliding event-time window compared to grouped aggregations and how Structured Streaming queries are processed using a micro-batch.
In a subsequent post, we will learn how to use Apache Avro and the Apicurio Registry with PySpark on Amazon EMR to read and write Apache Avro format messages to Amazon MSK.
This blog represents my own viewpoints and not of my employer, Amazon Web Services (AWS). All product names, logos, and brands are the property of their respective owners.
Running PySpark Applications on Amazon EMR: Methods for Interacting with PySpark on Amazon Elastic MapReduce
Posted by Gary A. Stafford in AWS, Build Automation, Cloud, Python, Software Development on December 2, 2020
Introduction
According to AWS, Amazon Elastic MapReduce (Amazon EMR) is a Cloud-based big data platform for processing vast amounts of data using common open-source tools such as Apache Spark, Hive, HBase, Flink, Hudi, and Zeppelin, Jupyter, and Presto. Using Amazon EMR, data analysts, engineers, and scientists are free to explore, process, and visualize data. EMR takes care of provisioning, configuring, and tuning the underlying compute clusters, allowing you to focus on running analytics.
Users interact with EMR in a variety of ways, depending on their specific requirements. For example, you might create a transient EMR cluster, execute a series of data analytics jobs using Spark, Hive, or Presto, and immediately terminate the cluster upon job completion. You only pay for the time the cluster is up and running. Alternatively, for time-critical workloads or continuously high volumes of jobs, you could choose to create one or more persistent, highly available EMR clusters. These clusters automatically scale compute resources horizontally, including EC2 Spot instances, to meet processing demands, maximizing performance and cost-efficiency.
With EMR, individuals and teams can also use notebooks, including EMR Notebooks, based on JupyterLab, the web-based interactive development environment for Jupyter notebooks for ad-hoc data analytics. Apache Zeppelin is also available to collaborate and interactively explore, process, and visualize data. With EMR notebooks and the EMR API, users can programmatically execute a notebook without the need to interact with the EMR console, referred to as headless execution.
AWS currently offers 5.x and 6.x versions of Amazon EMR. Each major and minor release of Amazon EMR offers incremental versions of nearly 25 different, popular open-source big-data applications to choose from, which Amazon EMR will install and configure when the cluster is created. One major difference between EMR versions relevant to this post is EMR 6.x’s support for the latest Hadoop and Spark 3.x frameworks. The latest Amazon EMR releases are Amazon EMR Release 6.2.0 and Amazon EMR Release 5.32.0.
PySpark on EMR
In the following series of posts, we will focus on the options available to interact with Amazon EMR using the Python API for Apache Spark, known as PySpark. We will divide the methods for accessing PySpark on EMR into two categories: PySpark applications and notebooks. We will explore both interactive and automated patterns for running PySpark applications (Python scripts) and PySpark-based notebooks. In this first post, I will cover the first four PySpark Application Methods listed below. In part two, I will cover Amazon Managed Workflows for Apache Airflow (Amazon MWAA), and in part three, the use of notebooks.
PySpark Application Methods
- Add Job Flow Steps: Remote execution of EMR Steps on an existing EMR cluster using the
add_job_flow_stepsmethod; - EMR Master Node: Remote execution over SSH of PySpark applications using
spark-submiton an existing EMR cluster’s Master node; - Run Job Flow: Remote execution of EMR Steps on a newly created long-lived or auto-terminating EMR cluster using the
run_job_flowmethod; - AWS Step Functions: Remote execution of EMR Steps using AWS Step Functions on an existing or newly created long-lived or auto-terminating EMR cluster;
- Apache Airflow: Remote execution of EMR Steps using the recently released Amazon MWAA on an existing or newly created long-lived or auto-terminating EMR cluster (see part two of this series);
Notebook Methods
- EMR Notebooks for Ad-hoc Analytics: Interactive, ad-hoc analytics and machine learning using Jupyter Notebooks on an existing EMR cluster;
- Headless Execution of EMR Notebooks: Headless execution of notebooks from an existing EMR cluster or newly created auto-terminating cluster;
- Apache Zeppelin for Ad-hoc Analytics: Interactive, ad-hoc analytics and machine learning using Zeppelin notebooks on an existing EMR cluster;
Note that wherever the AWS SDK for Python (boto3) is used in this post, we can substitute the AWS CLI or AWS Tools for PowerShell. Typically, these commands and Python scripts would be run as part of a DevOps or DataOps deployment workflow, using CI/CD platforms like AWS CodePipeline, Jenkins, Harness, CircleCI, Travis CI, or Spinnaker.
Preliminary Tasks
To prepare the AWS EMR environment for this post, we need to perform a few preliminary tasks.
- Download a copy of this post’s GitHub repository;
- Download three Kaggle datasets and organize locally;
- Create an Amazon EC2 key pair;
- Upload the EMR bootstrap script and create the CloudFormation Stack;
- Allow your IP address access to the EMR Master node on port 22;
- Upload CSV data files and PySpark applications to S3;
- Crawl the raw data and create a Data Catalog using AWS Glue;
Step 1: GitHub Repository
Using this git clone command, download a copy of this post’s GitHub repository to your local environment.
git clone --branch main --single-branch --depth 1 --no-tags \
https://github.com/garystafford/emr-demo.git
Step 2: Kaggle Datasets
Kaggle is a well-known data science resource with 50,000 public datasets and 400,000 public notebooks. We will be using three Kaggle datasets in this post. You will need to join Kaggle to access these free datasets. Download the following three Kaggle datasets as CSV files. Since we are working with (moderately) big data, the total size of the datasets will be approximately 1 GB.
- Movie Ratings: https://www.kaggle.com/rounakbanik/the-movies-dataset
- Bakery: https://www.kaggle.com/sulmansarwar/transactions-from-a-bakery
- Stocks: https://www.kaggle.com/timoboz/stock-data-dow-jones
Organize the (38) downloaded CSV files into the raw_data directory of the locally cloned GitHub repository, exactly as shown below. We will upload these files to Amazon S3, in the proceeding step.
> tree raw_data --si -v -A
raw_data
├── [ 128] bakery
│ ├── [711k] BreadBasket_DMS.csv
├── [ 320] movie_ratings
│ ├── [190M] credits.csv
│ ├── [6.2M] keywords.csv
│ ├── [989k] links.csv
│ ├── [183k] links_small.csv
│ ├── [ 34M] movies_metadata.csv
│ ├── [710M] ratings.csv
│ └── [2.4M] ratings_small.csv
└── [1.1k] stocks
├── [151k] AAPL.csv
├── [146k] AXP.csv
├── [150k] BA.csv
├── [147k] CAT.csv
├── [146k] CSCO.csv
├── [149k] CVX.csv
├── [147k] DIS.csv
├── [ 42k] DWDP.csv
├── [150k] GS.csv
└── [...] abrdiged... In this post, we will be using three different datasets. However, if you want to limit the potential costs associated with big data analytics on AWS, you can choose to limit job submissions to only one or two of the datasets. For example, the bakery and stocks datasets are fairly small yet effectively demonstrate most EMR features. In contrast, the movie rating dataset has nearly 27 million rows of ratings data, which starts to demonstrate the power of EMR and PySpark for big data.
Step 3: Amazon EC2 key pair
According to AWS, a key pair, consisting of a private key and a public key, is a set of security credentials that you use to prove your identity when connecting to an [EC2] instance. Amazon EC2 stores the public key, and you store the private key. To SSH into the EMR cluster, you will need an Amazon key pair. If you do not have an existing Amazon EC2 key pair, create one now. The easiest way to create a key pair is from the AWS Management Console.
Your private key is automatically downloaded when you create a key pair in the console. Store your private key somewhere safe. If you use an SSH client on a macOS or Linux computer to connect to EMR, use the following chmod command to set the correct permissions of your private key file so that only you can read it.
chmod 0400 /path/to/my-key-pair.pem
Step 4: Bootstrap Script and CloudFormation Stack
The bulk of the resources that are used as part of this demonstration are created using the CloudFormation stack, emr-dem-dev. The CloudFormation template that creates the stack, cloudformation/emr-demo.yml, is included in the repository. Please review all resources and understand the cost and security implications before continuing.
There is also a JSON-format CloudFormation parameters file, cloudformation/emr-demo-params-dev.json, containing values for all but two of the parameters in the CloudFormation template. The two parameters not in the parameter file are the name of the EC2 key pair you just created and the bootstrap bucket’s name. Both will be passed along with the CloudFormation template using the Python script, create_cfn_stack.py. For each type of environment, such as Development, Test, and Production, you could have a separate CloudFormation parameters file, with different configurations.
The template will create approximately (39) AWS resources, including a new AWS VPC, a public subnet, an internet gateway, route tables, a 3-node EMR v6.2.0 cluster, a series of Amazon S3 buckets, AWS Glue data catalog, AWS Glue crawlers, several Systems Manager Parameter Store parameters, and so forth.
The CloudFormation template includes the location of the EMR bootstrap script located on Amazon S3. Before creating the CloudFormation stack, the Python script creates an S3 bootstrap bucket and copies the bootstrap script, bootstrap_actions.sh, from the local project repository to the S3 bucket. The script will be used to install additional packages on EMR cluster nodes, which are required by our PySpark applications. The script also sets the default AWS Region for boto3.
From the GitHub repository’s local copy, run the following command, which will execute a Python script to create the bootstrap bucket, copy the bootstrap script, and provision the CloudFormation stack. You will need to pass the name of your EC2 key pair to the script as a command-line argument.
python3 ./scripts/create_cfn_stack.py \
--environment dev \
--ec2-key-name <my-key-pair-name>
The CloudFormation template should create a CloudFormation stack, emr-demo-dev, as shown below.
Step 5: SSH Access to EMR
For this demonstration, we will need access to the new EMR cluster’s Master EC2 node, using SSH and your key pair, on port 22. The easiest way to add a new inbound rule to the correct AWS Security Group is to use the AWS Management Console. First, find your EC2 Security Group named ElasticMapReduce-master.
Then, add a new Inbound rule for SSH (port 22) from your IP address, as shown below.
Alternately, you could use the AWS CLI or AWS SDK to create a new security group ingress rule.
export EMR_MASTER_SG_ID=$(aws ec2 describe-security-groups | \
jq -r '.SecurityGroups[] | select(.GroupName=="ElasticMapReduce-master").GroupId')
aws ec2 authorize-security-group-ingress \
--group-id ${EMR_MASTER_SG_ID} \
--protocol tcp \
--port 22 \
--cidr $(curl ipinfo.io/ip)/32
Step 6: Raw Data and PySpark Apps to S3
As part of the emr-demo-dev CloudFormation stack, we now have several new Amazon S3 buckets within our AWS Account. The naming conventions and intended usage of these buckets follow common organizational patterns for data lakes. The data buckets use the common naming convention of raw, processed, and analyzed data in reference to the data stored within them. We also use a widely used, corresponding naming convention of ‘bronze’, ‘silver’, and ‘gold’ when referring to these data buckets as parameters.
> aws s3api list-buckets | \
jq -r '.Buckets[] | select(.Name | startswith("emr-demo-")).Name'
emr-demo-raw-123456789012-us-east-1
emr-demo-processed-123456789012-us-east-1
emr-demo-analyzed-123456789012-us-east-1
emr-demo-work-123456789012-us-east-1
emr-demo-logs-123456789012-us-east-1
emr-demo-glue-db-123456789012-us-east-1
emr-demo-bootstrap-123456789012-us-east-1
There is a raw data bucket (aka bronze) that will contain the original CSV files. There is a processed data bucket (aka silver) that will contain data that might have had any number of actions applied: data cleansing, obfuscation, data transformation, file format changes, file compression, and data partitioning. Finally, there is an analyzed data bucket (aka gold) that has the results of the data analysis. We also have a work bucket that holds the PySpark applications, a logs bucket that holds EMR logs, and a glue-db bucket to hold the Glue Data Catalog metadata.
Whenever we submit PySpark jobs to EMR, the PySpark application files and data will always be accessed from Amazon S3. From the GitHub repository’s local copy, run the following command, which will execute a Python script to upload the approximately (38) Kaggle dataset CSV files to the raw S3 data bucket.
python3 ./scripts/upload_csv_files_to_s3.py
Next, run the following command, which will execute a Python script to upload a series of PySpark application files to the work S3 data bucket.
python3 ./scripts/upload_apps_to_s3.py
Step 7: Crawl Raw Data with Glue
The last preliminary step to prepare the EMR demonstration environment is to catalog the raw CSV data into an AWS Glue data catalog database, using one of the two Glue Crawlers we created. The three kaggle dataset’s data will reside in Amazon S3, while their schema and metadata will reside within tables in the Glue data catalog database, emr_demo. When we eventually query the data from our PySpark applications, we will be querying the Glue data catalog’s database tables, which reference the underlying data in S3.
From the GitHub repository’s local copy, run the following command, which will execute a Python script to run the Glue Crawler and catalog the raw data’s schema and metadata information into the Glue data catalog database, emr_demo.
python3 ./scripts/crawl_raw_data.py --crawler-name emr-demo-raw
Once the crawler is finished, from the AWS Console, we should see a series of nine tables in the Glue data catalog database, emr_demo, all prefixed with raw_. The tables hold metadata and schema information for the three CSV-format Kaggle datasets loaded into S3.
Alternately, we can use the glue get-tables AWS CLI command to review the tables.
> aws glue get-tables --database emr_demo | \
jq -r '.TableList[] | select(.Name | startswith("raw_")).Name'
raw_bakery
raw_credits_csv
raw_keywords_csv
raw_links_csv
raw_links_small_csv
raw_movies_metadata_csv
raw_ratings_csv
raw_ratings_small_csv
raw_stocks
PySpark Applications
Let’s explore four methods to run PySpark applications on EMR.
1. Add Job Flow Steps to an Existing EMR Cluster
We will start by looking at running PySpark applications using EMR Steps. According to AWS, we can use Amazon EMR steps to submit work to the Spark framework installed on an EMR cluster. The EMR step for PySpark uses a spark-submit command. According to Spark’s documentation, the spark-submit script, located in Spark’s bin directory, is used to launch applications on a [EMR] cluster. A typical spark-submit command we will be using resembles the following example. This command runs a PySpark application in S3, bakery_sales_ssm.py.
We will target the existing EMR cluster created by CloudFormation earlier to execute our PySpark applications using EMR Steps. We have two sets of PySpark applications. The first set of three PySpark applications will transform the raw CSV-format datasets into Apache Parquet, a more efficient file format for big data analytics. Alternately, for your workflows, you might prefer AWS Glue ETL Jobs, as opposed to PySpark on EMR, to perform nearly identical data processing tasks. The second set of four PySpark applications perform data analysis tasks on the data.
There are two versions of each PySpark application. Files with suffix _ssm use the AWS Systems Manager (SSM) Parameter Store service to obtain dynamic parameter values at runtime on EMR. Corresponding non-SSM applications require those same parameter values to be passed on the command line when they are submitted to Spark. Therefore, these PySpark applications are not tightly coupled to boto3 or the SSM Parameter Store. We will use _ssm versions of the scripts in this post’s demonstration.
> tree pyspark_apps --si -v -A
pyspark_apps
├── [ 320] analyze
│ ├── [1.4k] bakery_sales.py
│ ├── [1.5k] bakery_sales_ssm.py
│ ├── [2.6k] movie_choices.py
│ ├── [2.7k] movie_choices_ssm.py
│ ├── [2.0k] movies_avg_ratings.py
│ ├── [2.3k] movies_avg_ratings_ssm.py
│ ├── [2.2k] stock_volatility.py
│ └── [2.3k] stock_volatility_ssm.py
└── [ 256] process
├── [1.1k] bakery_csv_to_parquet.py
├── [1.3k] bakery_csv_to_parquet_ssm.py
├── [1.3k] movies_csv_to_parquet.py
├── [1.5k] movies_csv_to_parquet_ssm.py
├── [1.9k] stocks_csv_to_parquet.py
└── [2.0k] stocks_csv_to_parquet_ssm.py We will start by executing the three PySpark processing applications. They will convert the CSV data to Parquet. Below, we see an example of one of the PySpark applications we will run, bakery_csv_to_parquet_ssm.py. The PySpark application will convert the Bakery Sales dataset’s CSV file to Parquet and write it to S3.
The three PySpark data processing application’s spark-submit commands are defined in a separate JSON-format file, job_flow_steps_process.json, a snippet of which is shown below. The same goes for the four analytics applications.
Using this pattern of decoupling the Spark job command and arguments from the execution code, we can define and submit any number of Steps without changing the Python script, add_job_flow_steps_process.py, shown below. Note line 31, where the Steps are injected into the add_job_flow_steps method’s parameters.
The Python script used for this task takes advantage of AWS Systems Manager Parameter Store parameters. The parameters were placed in the Parameter Store, within the /emr_demo path, by CloudFormation. We will reference these parameters in several scripts throughout the post.
> aws ssm get-parameters-by-path --path '/emr_demo' | \
jq -r ".Parameters[] | {Name: .Name, Value: .Value}"
From the GitHub repository’s local copy, run the following command, which will execute a Python script to load the three spark-submit commands from JSON-format file, job_flow_steps_process.json, and run the PySpark processing applications on the existing EMR cluster.
python3 ./scripts/add_job_flow_steps.py --job-type process
While the three Steps are running concurrently, the view from the Amazon EMR Console’s Cluster Steps tab should look similar to the example below.
Once the three Steps have been completed, we should note three sub-directories in the processed data bucket containing Parquet-format files.
Of special note is the Stocks dataset, which has been converted to Parquet and partitioned by stock symbol. According to AWS, by partitioning your data, we can restrict the amount of data scanned by each query by specifying filters based on the partition, thus improving performance and reducing cost.
Lastly, the movie ratings dataset has been divided into sub-directories, based on the schema of each table. Each sub-directory contains Parquet files specific to that unique schema.
Crawl Processed Data with Glue
Similar to the raw data earlier, catalog the newly processed Parquet data into the same AWS Glue data catalog database using one of the two Glue Crawlers we created. Similar to the raw data, earlier, processed data will reside in the Amazon S3 processed data bucket while their schemas and metadata will reside within tables in the Glue data catalog database, emr_demo.
From the GitHub repository’s local copy, run the following command, which will execute a Python script to run the Glue Crawler and catalog the processed data’s schema and metadata information into the Glue data catalog database, emr_demo.
python3 ./scripts/crawl_raw_data.py --crawler-name emr-demo-processed
Once the crawler has finished successfully, using the AWS Console, we should see a series of nine tables in the Glue data catalog database, emr_demo, all prefixed with processed_. The tables represent the three kaggle dataset’s contents converted to Parquet and correspond to the equivalent tables with the raw_ prefix.
Alternately, we can use the glue get-tables AWS CLI command to review the tables.
> aws glue get-tables --database emr_demo | \
jq -r '.TableList[] | select(.Name | startswith("processed_")).Name'
processed_bakery
processed_credits
processed_keywords
processed_links
processed_links_small
processed_movies_metadata
processed_ratings
processed_ratings_small
processed_stocks
2. Run PySpark Jobs from EMR Master Node
Next, we will explore how to execute PySpark applications remotely on the Master node on the EMR cluster using boto3 and SSH. Although this method may be optimal for certain use cases as opposed to using the EMR SDK, remote SSH execution does not scale as well in my opinion due to a lack of automation, and it exposes some potential security risks.
There are four PySpark applications in the GitHub repository. For this part of the demonstration, we will just submit the bakery_sales_ssm.py application. This application will perform a simple analysis of the bakery sales data. While the other three PySpark applications use AWS Glue, the bakery_sales_ssm.py application reads data directly from the processed data S3 bucket.
The application writes its results into the analyzed data S3 bucket, in both Parquet and CSV formats. The CSV file is handy for business analysts and other non-technical stakeholders who might wish to import the results of the analysis into Excel or business applications.
Earlier, we created an inbound rule to allow your IP address to access the Master node on port 22. From the EMR Console’s Cluster Summary tab, note the command necessary to SSH into the Master node of the EMR cluster.
The Python script, submit_spark_ssh.py, shown below, will submit the PySpark job to the EMR Master Node, using paramiko, a Python implementation of SSHv2. The script is replicating the same functionality as the shell-based SSH command above to execute a remote command on the EMR Master Node. The spark-submit command is on lines 36–38, below.
From the GitHub repository’s local copy, run the following command, which will execute a Python script to submit the job. The script requires one input parameter, which is the path to your EC2 key pair (e.g., ~/.ssh/my-key-pair.pem)
python3 ./scripts/submit_spark_ssh.py \
--ec2-key-path </path/to/my-key-pair.pem>
The spark-submit command will be executed remotely on the EMR cluster’s Master node over SSH. All variables in the commands will be replaced by the environment variables, set in advance, which use AWS CLI emr and ssm commands.
Monitoring Spark Jobs
We set spark.yarn.submit.waitAppCompletion to true. According to Spark’s documentation, this property controls whether the client waits to exit in YARN cluster mode until the application is completed. If set to true, the client process will stay alive, reporting the application’s status. Otherwise, the client process will exit after submission. We can watch the job’s progress from the terminal.
We can also use the YARN Timeline Server and the Spark History Server in addition to the terminal. Links to both are shown on both the EMR Console’s Cluster ‘Summary’ and ‘Application user interfaces’ tabs. Unlike other EMR application web interfaces, using port forwarding, also known as creating an SSH tunnel, is not required for the YARN Timeline Server or the Spark History Server.
YARN Timeline Server
Below, we see that the job we submitted running on the YARN Timeline Server also includes useful tools like access to configuration, local logs, server stacks, and server metrics.
YARN Timeline Server allows us to drill down into individual jobs and view logs. Logs are ideal for troubleshooting failed jobs, especially the stdout logs.
Spark History Server
You can also view the PySpark application we submitted from the Master node using the Spark History Server. Below, we see completed Spark applications (aka Spark jobs) in the Spark History Server.
Below, we see more details about our Spark job using the Spark History Server.
We can even see visual representations of each Spark job’s Directed Acyclic Graph (DAG).
3. Run Job Flow on an Auto-Terminating EMR Cluster
The next option to run PySpark applications on EMR is to create a short-lived, auto-terminating EMR cluster using the run_job_flow method. We will create a new EMR cluster, run a series of Steps (PySpark applications), and then auto-terminate the cluster. This is a cost-effective method of running PySpark applications on-demand.
We will create a second 3-node EMR v6.2.0 cluster to demonstrate this method, using Amazon EC2 Spot instances for all the EMR cluster’s Master and Core nodes. Unlike the first, long-lived, more general-purpose EMR cluster, we will only deploy the Spark application to this cluster as that is the only application we will need to run the Steps.
Using the run_job_flow method, we will execute the four PySpark data analysis applications. The PySpark application’s spark-submit commands are defined in a separate JSON-format file, job_flow_steps_analyze.json. Similar to the previous add_job_flow_steps.py script, this pattern of decoupling the Spark job command and arguments from the execution code, we can define and submit any number of Steps without changing the Python execution script. Also similar, this script retrieves parameter values from the SSM Parameter Store.
From the GitHub repository’s local copy, run the following command, which will execute a Python script to create a new cluster, run the two PySpark applications, and then auto-terminate.
python3 ./scripts/run_job_flow.py --job-type analyze
As shown below, we see the short-lived EMR cluster in the process of terminating after successfully running the PySpark applications as EMR Steps.
4. Using AWS Step Functions
According to AWS, AWS Step Functions is a serverless function orchestrator that makes it easy to sequence AWS Lambda functions and multiple AWS services. Step Functions manages sequencing, error handling, retry logic, and state, removing a significant operational burden from your team. Step Functions is based on state machines and tasks. A state machine is a workflow. A task is a state in a workflow that represents a single unit of work that another AWS service performs. Each step in a workflow is a state. Using AWS Step Functions, we define our workflows as state machines, which transform complex code into easy to understand statements and diagrams.
You can use AWS Step Functions to run PySpark applications as EMR Steps on an existing EMR cluster. Using Step Functions, we can also create the cluster, run multiple EMR Steps sequentially or in parallel, and finally, auto-terminate the cluster.
We will create two state machines for this demo, one for the PySpark data processing applications and one for the PySpark data analysis applications. To create state machines, we first need to create JSON-based state machine definition files. The files are written in Amazon States Language. According to AWS, Amazon States Language is a JSON-based, structured language used to define a state machine, a collection of states that can do work (Task states), determine which states to transition to next (Choice states), stop execution with an error (Fail states), and so on.
The definition files contain specific references to AWS resources deployed to your AWS account originally created by CloudFormation. Below is a snippet of the state machine definition file, step_function_emr_analyze.json, showing part of the configuration of the EMR cluster. Note the parameterized key/value pairs (e.g., “Ec2KeyName.$”: “$.InstancesEc2KeyName” on line 5). The values will come from a JSON-formatted inputs file and are dynamically replaced upon the state machine’s execution.
Python Templating
To automate the process of adding dynamic resource references to the state machine’s inputs files, we will use Jinja, the modern and designer-friendly templating language for Python, modeled after Django’s templates. We will render the Jinja template to a JSON-based state machine inputs file, replacing the template’s resource tags (keys) with values from the SSM Parameter Store’s parameters. Below is a snippet from the inputs file Jinja template, step_function_inputs_analyze.j2.
First, install Jinja2, then create two JSON-based state machine inputs files from the Jinja templates using the included Python file.
# install Jinja2 python3 -m pip install Jinja2 python3 ./scripts/create_inputs_files.py
Below we see the same snippet of the final inputs file. Jinja tags have been replaced with values from the SSM Parameter Store.
Using the definition files, create two state machines using the included Python files.
python3 ./scripts/create_state_machine.py \
--definition-file step_function_emr_process.json \
--state-machine EMR-Demo-Process
python3 ./scripts/create_state_machine.py \
--definition-file step_function_emr_analyze.json \
--state-machine EMR-Demo-Analysis
Both state machines should appear in the AWS Step Functions Console’s State Machines tab. Below, we see the ‘EMR-Demo-Analysis’ state machine’s definition both as JSON and rendered visually to a layout.
To execute either of the state machines, use the included Python file, passing in the exact name of the state machine to execute, either ‘EMR-Demo-Process’ or ‘EMR-Demo-Analysis’, and the name of the inputs file. I suggest running the EMR-Demo-Analysis version so as not to re-process all the raw data.
python3 ./scripts/execute_state_machine.py \
--state-machine EMR-Demo-Process \
--inputs-file step_function_inputs_process.json
python3 ./scripts/execute_state_machine.py \
--state-machine EMR-Demo-Analysis \
--inputs-file step_function_inputs_analyze.json
When the PySpark analysis application’s Step Function state machine is executed, a new EMR cluster is created, the PySpark applications are run, and finally, the cluster is auto-terminated. Below, we see a successfully executed state machine, which successfully ran the four PySpark analysis applications in parallel, on a new auto-terminating EMR cluster.
Conclusion
This post explored four methods for running PySpark applications on Amazon Elastic MapReduce (Amazon EMR). The key to scaling data analytics with PySpark on EMR is the use of automation. Therefore, we looked at ways to automate the deployment of EMR resources, create and submit PySpark jobs, and terminate EMR resources when the jobs are complete. Furthermore, we were able to decouple references to dynamic AWS resources within our PySpark applications using parameterization. This allows us to deploy and run PySpark resources across multiple AWS Accounts and AWS Regions without code changes.
In part two of the series, we will explore the use of the recently announced service, Amazon Managed Workflows for Apache Airflow (MWAA), and in part three, the use of Juypter and Zeppelin notebooks for data science, scientific computing, and machine learning on EMR.
This blog represents my own viewpoints and not of my employer, Amazon Web Services. All product names, logos, and brands are the property of their respective owners.
Getting Started with Data Analytics using Jupyter Notebooks, PySpark, and Docker
Posted by Gary A. Stafford in Bash Scripting, Big Data, Build Automation, DevOps, Python, Software Development on December 6, 2019
There is little question, big data analytics, data science, artificial intelligence (AI), and machine learning (ML), a subcategory of AI, have all experienced a tremendous surge in popularity over the last few years. Behind the marketing hype, these technologies are having a significant influence on many aspects of our modern lives. Due to their popularity and potential benefits, commercial enterprises, academic institutions, and the public sector are rushing to develop hardware and software solutions to lower the barriers to entry and increase the velocity of ML and Data Scientists and Engineers.
(courtesy Google Trends and Plotly)
Many open-source software projects are also lowering the barriers to entry into these technologies. An excellent example of one such open-source project working on this challenge is Project Jupyter. Similar to Apache Zeppelin and the newly open-sourced Netflix’s Polynote, Jupyter Notebooks enables data-driven, interactive, and collaborative data analytics.
This post will demonstrate the creation of a containerized data analytics environment using Jupyter Docker Stacks. The particular environment will be suited for learning and developing applications for Apache Spark using the Python, Scala, and R programming languages. We will focus on Python and Spark, using PySpark.
Featured Technologies
The following technologies are featured prominently in this post.
Jupyter Notebooks
According to Project Jupyter, the Jupyter Notebook, formerly known as the IPython Notebook, is an open-source web application that allows users to create and share documents that contain live code, equations, visualizations, and narrative text. Uses include data cleansing and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. The word, Jupyter, is a loose acronym for Julia, Python, and R, but today, Jupyter supports many programming languages.
Interest in Jupyter Notebooks has grown dramatically over the last 3–5 years, fueled in part by the major Cloud providers, AWS, Google Cloud, and Azure. Amazon Sagemaker, Amazon EMR (Elastic MapReduce), Google Cloud Dataproc, Google Colab (Collaboratory), and Microsoft Azure Notebooks all have direct integrations with Jupyter notebooks for big data analytics and machine learning.
(courtesy Google Trends and Plotly)
Jupyter Docker Stacks
To enable quick and easy access to Jupyter Notebooks, Project Jupyter has created Jupyter Docker Stacks. The stacks are ready-to-run Docker images containing Jupyter applications, along with accompanying technologies. Currently, the Jupyter Docker Stacks focus on a variety of specializations, including the r-notebook, scipy-notebook, tensorflow-notebook, datascience-notebook, pyspark-notebook, and the subject of this post, the all-spark-notebook. The stacks include a wide variety of well-known packages to extend their functionality, such as scikit-learn, pandas, Matplotlib, Bokeh, NumPy, and Facets.
Apache Spark
According to Apache, Spark is a unified analytics engine for large-scale data processing. Starting as a research project at the UC Berkeley AMPLab in 2009, Spark was open-sourced in early 2010 and moved to the Apache Software Foundation in 2013. Reviewing the postings on any major career site will confirm that Spark is widely used by well-known modern enterprises, such as Netflix, Adobe, Capital One, Lockheed Martin, JetBlue Airways, Visa, and Databricks. At the time of this post, LinkedIn, alone, had approximately 3,500 listings for jobs that reference the use of Apache Spark, just in the United States.
With speeds up to 100 times faster than Hadoop, Apache Spark achieves high performance for static, batch, and streaming data, using a state-of-the-art DAG (Directed Acyclic Graph) scheduler, a query optimizer, and a physical execution engine. Spark’s polyglot programming model allows users to write applications quickly in Scala, Java, Python, R, and SQL. Spark includes libraries for Spark SQL (DataFrames and Datasets), MLlib (Machine Learning), GraphX (Graph Processing), and DStreams (Spark Streaming). You can run Spark using its standalone cluster mode, Apache Hadoop YARN, Mesos, or Kubernetes.
PySpark
The Spark Python API, PySpark, exposes the Spark programming model to Python. PySpark is built on top of Spark’s Java API and uses Py4J. According to Apache, Py4J, a bridge between Python and Java, enables Python programs running in a Python interpreter to dynamically access Java objects in a Java Virtual Machine (JVM). Data is processed in Python and cached and shuffled in the JVM.
Docker
According to Docker, their technology gives developers and IT the freedom to build, manage, and secure business-critical applications without the fear of technology or infrastructure lock-in. For this post, I am using the current stable version of Docker Desktop Community version for macOS, as of March 2020.
Docker Swarm
Current versions of Docker include both a Kubernetes and Swarm orchestrator for deploying and managing containers. We will choose Swarm for this demonstration. According to Docker, the cluster management and orchestration features embedded in the Docker Engine are built using swarmkit. Swarmkit is a separate project that implements Docker’s orchestration layer and is used directly within Docker.
PostgreSQL
PostgreSQL is a powerful, open-source, object-relational database system. According to their website, PostgreSQL comes with many features aimed to help developers build applications, administrators to protect data integrity and build fault-tolerant environments, and help manage data no matter how big or small the dataset.
Demonstration
In this demonstration, we will explore the capabilities of the Spark Jupyter Docker Stack to provide an effective data analytics development environment. We will explore a few everyday uses, including executing Python scripts, submitting PySpark jobs, and working with Jupyter Notebooks, and reading and writing data to and from different file formats and a database. We will be using the latest jupyter/all-spark-notebook Docker Image. This image includes Python, R, and Scala support for Apache Spark, using Apache Toree.
Architecture
As shown below, we will deploy a Docker stack to a single-node Docker swarm. The stack consists of a Jupyter All-Spark-Notebook, PostgreSQL (Alpine Linux version 12), and Adminer container. The Docker stack will have two local directories bind-mounted into the containers. Files from our GitHub project will be shared with the Jupyter application container through a bind-mounted directory. Our PostgreSQL data will also be persisted through a bind-mounted directory. This allows us to persist data external to the ephemeral containers. If the containers are restarted or recreated, the data is preserved locally.
Source Code
All source code for this post can be found on GitHub. Use the following command to clone the project. Note this post uses the v2 branch.
git clone \ --branch v2 --single-branch --depth 1 --no-tags \ https://github.com/garystafford/pyspark-setup-demo.git
Source code samples are displayed as GitHub Gists, which may not display correctly on some mobile and social media browsers.
Deploy Docker Stack
To start, create the $HOME/data/postgres directory to store PostgreSQL data files.
mkdir -p ~/data/postgres
This directory will be bind-mounted into the PostgreSQL container on line 41 of the stack.yml file, $HOME/data/postgres:/var/lib/postgresql/data. The HOME environment variable assumes you are working on Linux or macOS and is equivalent to HOMEPATH on Windows.
The Jupyter container’s working directory is set on line 15 of the stack.yml file, working_dir: /home/$USER/work. The local bind-mounted working directory is $PWD/work. This path is bind-mounted to the working directory in the Jupyter container, on line 29 of the Docker stack file, $PWD/work:/home/$USER/work. The PWD environment variable assumes you are working on Linux or macOS (CD on Windows).
By default, the user within the Jupyter container is jovyan. We will override that user with our own local host’s user account, as shown on line 21 of the Docker stack file, NB_USER: $USER. We will use the host’s USER environment variable value (equivalent to USERNAME on Windows). There are additional options for configuring the Jupyter container. Several of those options are used on lines 17–22 of the Docker stack file (gist).
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| # docker stack deploy -c stack.yml jupyter | |
| # optional pgadmin container | |
| version: "3.7" | |
| networks: | |
| demo-net: | |
| services: | |
| spark: | |
| image: jupyter/all-spark-notebook:latest | |
| ports: | |
| – "8888:8888/tcp" | |
| – "4040:4040/tcp" | |
| networks: | |
| – demo-net | |
| working_dir: /home/$USER/work | |
| environment: | |
| CHOWN_HOME: "yes" | |
| GRANT_SUDO: "yes" | |
| NB_UID: 1000 | |
| NB_GID: 100 | |
| NB_USER: $USER | |
| NB_GROUP: staff | |
| user: root | |
| deploy: | |
| replicas: 1 | |
| restart_policy: | |
| condition: on-failure | |
| volumes: | |
| – $PWD/work:/home/$USER/work | |
| postgres: | |
| image: postgres:12-alpine | |
| environment: | |
| POSTGRES_USERNAME: postgres | |
| POSTGRES_PASSWORD: postgres1234 | |
| POSTGRES_DB: bakery | |
| ports: | |
| – "5432:5432/tcp" | |
| networks: | |
| – demo-net | |
| volumes: | |
| – $HOME/data/postgres:/var/lib/postgresql/data | |
| deploy: | |
| restart_policy: | |
| condition: on-failure | |
| adminer: | |
| image: adminer:latest | |
| ports: | |
| – "8080:8080/tcp" | |
| networks: | |
| – demo-net | |
| deploy: | |
| restart_policy: | |
| condition: on-failure | |
| # pgadmin: | |
| # image: dpage/pgadmin4:latest | |
| # environment: | |
| # PGADMIN_DEFAULT_EMAIL: user@domain.com | |
| # PGADMIN_DEFAULT_PASSWORD: 5up3rS3cr3t! | |
| # ports: | |
| # – "8180:80/tcp" | |
| # networks: | |
| # – demo-net | |
| # deploy: | |
| # restart_policy: | |
| # condition: on-failure |
The jupyter/all-spark-notebook Docker image is large, approximately 5 GB. Depending on your Internet connection, if this is the first time you have pulled this image, the stack may take several minutes to enter a running state. Although not required, I usually pull new Docker images in advance.
docker pull jupyter/all-spark-notebook:latest docker pull postgres:12-alpine docker pull adminer:latest
Assuming you have a recent version of Docker installed on your local development machine and running in swarm mode, standing up the stack is as easy as running the following docker command from the root directory of the project.
docker stack deploy -c stack.yml jupyter
The Docker stack consists of a new overlay network, jupyter_demo-net, and three containers. To confirm the stack deployed successfully, run the following docker command.
docker stack ps jupyter --no-trunc
To access the Jupyter Notebook application, you need to obtain the Jupyter URL and access token. The Jupyter URL and the access token are output to the Jupyter container log, which can be accessed with the following command.
docker logs $(docker ps | grep jupyter_spark | awk '{print $NF}')
You should observe log output similar to the following. Retrieve the complete URL, for example, http://127.0.0.1:8888/?token=f78cbe..., to access the Jupyter web-based user interface.
From the Jupyter dashboard landing page, you should see all the files in the project’s work/ directory. Note the types of files you can create from the dashboard, including Python 3, R, and Scala (using Apache Toree or spylon-kernal) notebooks, and text. You can also open a Jupyter terminal or create a new Folder from the drop-down menu. At the time of this post (March 2020), the latest jupyter/all-spark-notebook Docker Image runs Spark 2.4.5, Scala 2.11.12, Python 3.7.6, and OpenJDK 64-Bit Server VM, Java 1.8.0 Update 242.
Bootstrap Environment
Included in the project is a bootstrap script, bootstrap_jupyter.sh. The script will install the required Python packages using pip, the Python package installer, and a requirement.txt file. The bootstrap script also installs the latest PostgreSQL driver JAR, configures Apache Log4j to reduce log verbosity when submitting Spark jobs, and installs htop. Although these tasks could also be done from a Jupyter terminal or from within a Jupyter notebook, using a bootstrap script ensures you will have a consistent work environment every time you spin up the Jupyter Docker stack. Add or remove items from the bootstrap script as necessary.
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| #!/bin/bash | |
| set -ex | |
| # update/upgrade and install htop | |
| sudo apt-get update -y && sudo apt-get upgrade -y | |
| sudo apt-get install htop | |
| # install required python packages | |
| python3 -m pip install –user –upgrade pip | |
| python3 -m pip install -r requirements.txt –upgrade | |
| # download latest postgres driver jar | |
| POSTGRES_JAR="postgresql-42.2.17.jar" | |
| if [ -f "$POSTGRES_JAR" ]; then | |
| echo "$POSTGRES_JAR exist" | |
| else | |
| wget -nv "https://jdbc.postgresql.org/download/${POSTGRES_JAR}" | |
| fi | |
| # spark-submit logging level from INFO to WARN | |
| sudo cp log4j.properties /usr/local/spark/conf/log4j.properties |
That’s it, our new Jupyter environment is ready to start exploring.
Running Python Scripts
One of the simplest tasks we could perform in our new Jupyter environment is running Python scripts. Instead of worrying about installing and maintaining the correct versions of Python and multiple Python packages on your own development machine, we can run Python scripts from within the Jupyter container. At the time of this post update, the latest jupyter/all-spark-notebook Docker image runs Python 3.7.3 and Conda 4.7.12. Let’s start with a simple Python script, 01_simple_script.py.
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| #!/usr/bin/python3 | |
| import random | |
| technologies = [ | |
| 'PySpark', 'Python', 'Spark', 'Scala', 'Java', 'Project Jupyter', 'R' | |
| ] | |
| print("Technologies: %s\n" % technologies) | |
| technologies.sort() | |
| print("Sorted: %s\n" % technologies) | |
| print("I'm interested in learning about %s." % random.choice(technologies)) |
From a Jupyter terminal window, use the following command to run the script.
python3 01_simple_script.py
You should observe the following output.
Kaggle Datasets
To explore more features of the Jupyter and PySpark, we will use a publicly available dataset from Kaggle. Kaggle is an excellent open-source resource for datasets used for big-data and ML projects. Their tagline is ‘Kaggle is the place to do data science projects’. For this demonstration, we will use the Transactions from a bakery dataset from Kaggle. The dataset is available as a single CSV-format file. A copy is also included in the project.
The ‘Transactions from a bakery’ dataset contains 21,294 rows with 4 columns of data. Although certainly not big data, the dataset is large enough to test out the Spark Jupyter Docker Stack functionality. The data consists of 9,531 customer transactions for 21,294 bakery items between 2016-10-30 and 2017-04-09 (gist).
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| Date | Time | Transaction | Item | |
|---|---|---|---|---|
| 2016-10-30 | 09:58:11 | 1 | Bread | |
| 2016-10-30 | 10:05:34 | 2 | Scandinavian | |
| 2016-10-30 | 10:05:34 | 2 | Scandinavian | |
| 2016-10-30 | 10:07:57 | 3 | Hot chocolate | |
| 2016-10-30 | 10:07:57 | 3 | Jam | |
| 2016-10-30 | 10:07:57 | 3 | Cookies | |
| 2016-10-30 | 10:08:41 | 4 | Muffin | |
| 2016-10-30 | 10:13:03 | 5 | Coffee | |
| 2016-10-30 | 10:13:03 | 5 | Pastry | |
| 2016-10-30 | 10:13:03 | 5 | Bread |
Submitting Spark Jobs
We are not limited to Jupyter notebooks to interact with Spark. We can also submit scripts directly to Spark from the Jupyter terminal. This is typically how Spark is used in a Production for performing analysis on large datasets, often on a regular schedule, using tools such as Apache Airflow. With Spark, you are load data from one or more data sources. After performing operations and transformations on the data, the data is persisted to a datastore, such as a file or a database, or conveyed to another system for further processing.
The project includes a simple Python PySpark ETL script, 02_pyspark_job.py. The ETL script loads the original Kaggle Bakery dataset from the CSV file into memory, into a Spark DataFrame. The script then performs a simple Spark SQL query, calculating the total quantity of each type of bakery item sold, sorted in descending order. Finally, the script writes the results of the query to a new CSV file, output/items-sold.csv.
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| #!/usr/bin/python3 | |
| from pyspark.sql import SparkSession | |
| spark = SparkSession \ | |
| .builder \ | |
| .appName('spark-demo') \ | |
| .getOrCreate() | |
| df_bakery = spark.read \ | |
| .format('csv') \ | |
| .option('header', 'true') \ | |
| .option('delimiter', ',') \ | |
| .option('inferSchema', 'true') \ | |
| .load('BreadBasket_DMS.csv') | |
| df_sorted = df_bakery.cube('item').count() \ | |
| .filter('item NOT LIKE \'NONE\'') \ | |
| .filter('item NOT LIKE \'Adjustment\'') \ | |
| .orderBy(['count', 'item'], ascending=[False, True]) | |
| df_sorted.show(10, False) | |
| df_sorted.coalesce(1) \ | |
| .write.format('csv') \ | |
| .option('header', 'true') \ | |
| .save('output/items-sold.csv', mode='overwrite') |
Run the script directly from a Jupyter terminal using the following command.
python3 02_pyspark_job.py
An example of the output of the Spark job is shown below.
Typically, you would submit the Spark job using the spark-submit command. Use a Jupyter terminal to run the following command.
$SPARK_HOME/bin/spark-submit 02_pyspark_job.py
Below, we see the output from the spark-submit command. Printing the results in the output is merely for the purposes of the demo. Typically, Spark jobs are submitted non-interactively, and the results are persisted directly to a datastore or conveyed to another system.
Using the following commands, we can view the resulting CVS file, created by the spark job.
ls -alh output/items-sold.csv/ head -5 output/items-sold.csv/*.csv
An example of the files created by the spark job is shown below. We should have discovered that coffee is the most commonly sold bakery item with 5,471 sales, followed by bread with 3,325 sales.
Interacting with Databases
To demonstrate the flexibility of Jupyter to work with databases, PostgreSQL is part of the Docker Stack. We can read and write data from the Jupyter container to the PostgreSQL instance, running in a separate container. To begin, we will run a SQL script, written in Python, to create our database schema and some test data in a new database table. To do so, we will use the psycopg2, the PostgreSQL database adapter package for the Python, we previously installed into our Jupyter container using the bootstrap script. The below Python script, 03_load_sql.py, will execute a set of SQL statements contained in a SQL file, bakery.sql, against the PostgreSQL container instance.
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| #!/usr/bin/python3 | |
| import psycopg2 | |
| # connect to database | |
| connect_str = 'host=postgres port=5432 dbname=bakery user=postgres password=postgres1234' | |
| conn = psycopg2.connect(connect_str) | |
| conn.autocommit = True | |
| cursor = conn.cursor() | |
| # execute sql script | |
| sql_file = open('bakery.sql', 'r') | |
| sqlFile = sql_file.read() | |
| sql_file.close() | |
| sqlCommands = sqlFile.split(';') | |
| for command in sqlCommands: | |
| print(command) | |
| if command.strip() != '': | |
| cursor.execute(command) | |
| # import data from csv file | |
| with open('BreadBasket_DMS.csv', 'r') as f: | |
| next(f) # Skip the header row. | |
| cursor.copy_from( | |
| f, | |
| 'transactions', | |
| sep=',', | |
| columns=('date', 'time', 'transaction', 'item') | |
| ) | |
| conn.commit() | |
| # confirm by selecting record | |
| command = 'SELECT COUNT(*) FROM public.transactions;' | |
| cursor.execute(command) | |
| recs = cursor.fetchall() | |
| print('Row count: %d' % recs[0]) |
The SQL file, bakery.sql.
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| DROP TABLE IF EXISTS "transactions"; | |
| DROP SEQUENCE IF EXISTS transactions_id_seq; | |
| CREATE SEQUENCE transactions_id_seq INCREMENT 1 MINVALUE 1 MAXVALUE 2147483647 START 1 CACHE 1; | |
| CREATE TABLE "public"."transactions" | |
| ( | |
| "id" integer DEFAULT nextval('transactions_id_seq') NOT NULL, | |
| "date" character varying(10) NOT NULL, | |
| "time" character varying(8) NOT NULL, | |
| "transaction" integer NOT NULL, | |
| "item" character varying(50) NOT NULL | |
| ) WITH (oids = false); |
To execute the script, run the following command.
python3 03_load_sql.py
This should result in the following output, if successful.
Adminer
To confirm the SQL script’s success, use Adminer. Adminer (formerly phpMinAdmin) is a full-featured database management tool written in PHP. Adminer natively recognizes PostgreSQL, MySQL, SQLite, and MongoDB, among other database engines. The current version is 4.7.6 (March 2020).
Adminer should be available on localhost port 8080. The password credentials, shown below, are located in the stack.yml file. The server name, postgres, is the name of the PostgreSQL Docker container. This is the domain name the Jupyter container will use to communicate with the PostgreSQL container.
Connecting to the new bakery database with Adminer, we should see the transactions table.
The table should contain 21,293 rows, each with 5 columns of data.
pgAdmin
Another excellent choice for interacting with PostgreSQL, in particular, is pgAdmin 4. It is my favorite tool for the administration of PostgreSQL. Although limited to PostgreSQL, the user interface and administrative capabilities of pgAdmin is superior to Adminer, in my opinion. For brevity, I chose not to include pgAdmin in this post. The Docker stack also contains a pgAdmin container, which has been commented out. To use pgAdmin, just uncomment the container and re-run the Docker stack deploy command. pgAdmin should then be available on localhost port 81. The pgAdmin login credentials are in the Docker stack file.
Developing Jupyter Notebooks
The real power of the Jupyter Docker Stacks containers is Jupyter Notebooks. According to the Jupyter Project, the notebook extends the console-based approach to interactive computing in a qualitatively new direction, providing a web-based application suitable for capturing the whole computation process, including developing, documenting, and executing code, as well as communicating the results. Notebook documents contain the inputs and outputs of an interactive session as well as additional text that accompanies the code but is not meant for execution.
To explore the capabilities of Jupyter notebooks, the project includes two simple Jupyter notebooks. The first notebooks, 04_notebook.ipynb, demonstrates typical PySpark functions, such as loading data from a CSV file and from the PostgreSQL database, performing basic data analysis with Spark SQL including the use of PySpark user-defined functions (UDF), graphing the data using BokehJS, and finally, saving data back to the database, as well as to the fast and efficient Apache Parquet file format. Below we see several notebook cells demonstrating these features.
IDE Integration
Recall, the working directory, containing the GitHub source code for the project, is bind-mounted to the Jupyter container. Therefore, you can also edit any of the files, including notebooks, in your favorite IDE, such as JetBrains PyCharm and Microsoft Visual Studio Code. PyCharm has built-in language support for Jupyter Notebooks, as shown below.
As does Visual Studio Code using the Python extension.
Using Additional Packages
As mentioned in the Introduction, the Jupyter Docker Stacks come ready-to-run, with a wide variety of Python packages to extend their functionality. To demonstrate the use of these packages, the project contains a second Jupyter notebook document, 05_notebook.ipynb. This notebook uses SciPy, the well-known Python package for mathematics, science, and engineering, NumPy, the well-known Python package for scientific computing, and the Plotly Python Graphing Library. While NumPy and SciPy are included on the Jupyter Docker Image, the bootstrap script uses pip to install the required Plotly packages. Similar to Bokeh, shown in the previous notebook, we can use these libraries to create richly interactive data visualizations.
Plotly
To use Plotly from within the notebook, you will first need to sign up for a free account and obtain a username and API key. To ensure we do not accidentally save sensitive Plotly credentials in the notebook, we are using python-dotenv. This Python package reads key/value pairs from a .env file, making them available as environment variables to our notebook. Modify and run the following two commands from a Jupyter terminal to create the .env file and set you Plotly username and API key credentials. Note that the .env file is part of the .gitignore file and will not be committed to back to git, potentially compromising the credentials.
echo "PLOTLY_USERNAME=your-username" >> .env echo "PLOTLY_API_KEY=your-api-key" >> .env
The notebook expects to find the two environment variables, which it uses to authenticate with Plotly.
Shown below, we use Plotly to construct a bar chart of daily bakery items sold. The chart uses SciPy and NumPy to construct a linear fit (regression) and plot a line of best fit for the bakery data and overlaying the vertical bars. The chart also uses SciPy’s Savitzky-Golay Filter to plot the second line, illustrating a smoothing of our bakery data.
Plotly also provides Chart Studio Online Chart Maker. Plotly describes Chart Studio as the world’s most modern enterprise data visualization solutions. We can enhance, stylize, and share our data visualizations using the free version of Chart Studio Cloud.
Jupyter Notebook Viewer
Notebooks can also be viewed using nbviewer, an open-source project under Project Jupyter. Thanks to Rackspace hosting, the nbviewer instance is a free service.
Using nbviewer, below, we see the output of a cell within the 04_notebook.ipynb notebook. View this notebook, here, using nbviewer.
