CS744 Assignment 1

Due: Oct 1, 2018

Overview

This assignment is designed to support your in-class understanding of how data analytics stacks work and get some hands-on experience in using them. You will need to deploy Apache Hadoop as the underlying file system and Apache Spark as the execution engine. You will then develop several small applications based on them. You will produce a short report detailing your observations and takeaways.

Learning Outcomes

After completing this programming assignment, you should:

Environment Setup

You will complete your assignment in CloudLab. You can refer to Assignment 0 to learn how to use CloudLab. We suggest you create experiments in form of groups and work together. An experiment expires within two days, which is very quick. So, set a time frame that all your group members can sit together and focus on the project.

In this assignment, we provide you a CloudLab profile called “cs744-fa18-assignmentt1-4node” under “UWMadison744-F18” project for you to start your experiment. The profile is a simple 4-node cluster with Ubuntu 16 installed on each machine. You get full control of the machines once the experiment is created, so feel free to download any missing packages you need in the assignment.

As the first step, you should run following commands on every VM:

  1. sudo apt-get update –fix-missing
  2. sudo apt-get install openjdk-8-jdk
  3. enable the SSH service among the nodes in the cluster. To do this, you have to generate a private/public key pair using: ssh-keygen -t rsa on the master node. You should designate a VM to act as a master/slave (say node-0) while the others are assigned as slaves only. Then, manually copy the public key of node-0 to the authorized_keys file in all the nodes(including node-0) under ~/.ssh/. To get the content of the public key, do: 
    cat ~/.ssh/id_rsa.pub

    When you copy the content, make sure you do not append any newlines. Otherwise, it will not work.

Once you have done this you can copy files from the master node (i.e. node-0) to the other nodes using tools like parallel-ssh. To use parallel-ssh you will need to create a file with the hostnames of all the machines. You can test your parallel-ssh with a command like

parallel-ssh -i -h slaves -O StrictHostKeyChecking=no hostname

Part 1: Software Deployment

Apache Hadoop

Apache Hadoop is a collection of open-source software utilities that provides simple distributed programming models for processing of large data sets. It mainly consists of the Hadoop Distribited File System (HDFS), Hadoop MapReduce and Hadoop YARN. In this assignment, we will only use HDFS. HDFS consists of a NameNode process running on the master instance and a set of DataNode processes running on slave instances. The NameNode records metadata and handles requests. The DataNode stores actual data.

You can find the detailed deployment instructions in this link or you can follow our simplified version:

First, let’s download Hadoop on every machine in the cluster. Note that you can do this on the master node and then use parallel-ssh or parallel-scp to run the same command or copy data to all VMs.

wget http://apache.mirrors.hoobly.com/hadoop/common/hadoop-2.7.6/hadoop-2.7.6.tar.gz
tar zvxf hadoop-2.7.6.tar.gz

There are a few configuration files we need to edit. They are originally empty so users have to manually set them. Add the following contents in the <property> field in hadoop-2.7.6/etc/hadoop/core-site.xml:

<configuration>
<property>
<name>fs.default.name</name>
<value>hdfs://namenode_IP:9000</value>
</property>
</configuration>

where namenode_IP refers to the IP address of the master node. This configuration indicates where the NameNode will be listening for connections.

Also you need to add the following in hadoop-2.7.6/etc/hadoop/hdfs-site.xml. Make sure you specify the path by yourself (You should create folders by yourself if needed. For example, create hadoop-2.7.6/data/namenode/ and set it to be the path for namenode dir). These directories indicate where data for the NameNode and DataNode will be stored respectively. Note that the same path needs to exist on all the slave machines which will be running DataNodes.

<configuration>
<property>
<name>dfs.namenode.name.dir</name>
<value>/path/to/namenode/dir/</value>
</property>
<property>
<name>dfs.datanode.data.dir</name>
<value>/path/to/datanode/dir</value>
</property>
</configuration>

You also need to manually specify JAVA_HOME in hadoop-2.7.6/etc/hadoop/hadoop-env.sh. You can get the path with the command: update-alternatives --display java. Take the value of the current link and remove the trailing /bin/java. For example, a possible link can be /usr/lib/jvm/java-8-openjdk-amd64/jre. Then, set the JAVA_HOME by replacing export JAVA_HOME=${JAVA_HOME} with export JAVA_HOME=/actual/path.

Copy the config files with these changes to all the machines.

We also need to edit hadoop-2.7.6/etc/hadoop/slaves to add the IP address of all the datanodes. In our case, we need to add the IP addresses for all the nodes in the cluster, so every node can store data.

Now, we start to format the namenode and start the namymenode daemon. Firstly, add hadoop-2.7.6/bin and hadoop-2.7.6/sbin to $PATH. Then, do:

hdfs namenode -format
start-dfs.sh

This will also start all the datanode daemons:

To check the HDFS status, go to:

<namenode_IP>:50070/dfshealth.html

You can also use command jps to check whether HDFS is up, there should be a NameNode process is running on your master VM, and a DataNode process is running on each of your VMs.

Now, the HDFS is setup. Type the following to see the available commands in HDFS.

hdfs dfs -help

Apache Spark

Apache Spark is a powerful open-source unified analytics engine for big data processing, which is built upon its core idea of Resilient Distributed Datasets (RDDs). Spark standalone consists of a set of daemons: a Master daemon, and a set of Worker daemons. Spark applications are coordinated by a SparkContext object which will connect to the Master, responsible for allocating resources across applications. Once connected, Spark acquires Executors on every Worker node in the cluster, which are processes that run computations and store data for your applications. Finally, the application’s tasks are handled to Executors for execution. We will use Spark in standalone mode, which means it doesn’t need to rely on resource management systems like YARN.

Instructions on building a Spark cluster can be found in Spark’s official document. Or you can follow our instructions:

Firstly, download and decompress the Spark binary on each node in the cluster:

wget https://d3kbcqa49mib13.cloudfront.net/spark-2.2.0-bin-hadoop2.7.tgz
tar zvxf spark-2.2.0-bin-hadoop2.7.tgz

Similar to HDFS you will need to modify spark-2.2.0-bin-hadoop2.7/conf/slaves to include the IP address of all the slave machines.

To start the Spark standalone cluster you can then run the following command on the master node:

spark-2.2.0-bin-hadoop2.7/sbin/start-all.sh

You can go to <master_node_IP>:8080 to check the status of the Spark cluster.

To check that the cluster is up and running you can use jps to check that a Master process is running on your master VM, and a Worker process is running on each of your slave VMs.

To stop all nodes in the cluster, do

spark-2.2.0-bin-hadoop2.7/sbin/stop-all.sh

Next, setup the properties for the memory and CPU used by Spark applications. Set Spark driver memory to 32GB and executor memory to 32GB. Set executor cores to be 10 and number of cpus per task to be 1. Document about setting properties is here.

Part 2: A simple Spark application

In this part, you will implement a simple Spark application. We have provided some sample data collected by IOT devices at http://pages.cs.wisc.edu/~shivaram/cs744-fa18/assets/export.csv. You need to sort the data firstly by the country code alphabetically (the third column) then by the timestamp (the last column). Here is an example:

Input:

… cca2 … device_id … timestamp
… US … 1 … 1
… IN … 2 … 2
… US … 3 … 2
… CN … 4 … 4
… US … 5 … 3
… IN … 6 … 1

Output:

… cca2 … device_id … timestamp
… CN … 4 … 4
… IN … 6 … 1
… IN … 2 … 2
… US … 1 … 1
… US … 3 … 2
… US … 5 … 3

You should first load the data into HDFS. Then, write a Spark program in Java/Python/Scala to sort the data. Finally, output the results into HDFS in form of csv. Your program will take in two arguments, the first a path to the input file and the second the path to the output file. Note that if two data tuples have the same country code and timestamp, the order of them does not matter.

Part 3: PageRank

In this part, you will need to implement the PageRank algorithm, which is an algorithm used by search engines like Google to evaluate the quality of links to a webpage. The algorithm can be summarized as follows:

  1. Set initial rank of each page to be 1.
  2. On each iteration, each page contributes to its neighbors by rank(p)/ # of neighbors.
  3. Update each page’s rank to be 0.15 + 0.85 * (sum of contributions).
  4. Go to next iteration.

In this assignment, we will run the algorithm on two data sets. Berkeley-Stanford web graph is a smaller data set to help you test your algorithm and enwiki-20180601-pages-articles (we have already put it to path /proj/uwmadison744-f18-PG0/test-data/enwiki-pages-articles/) is a larger one to help you better understand the performance of Spark. Each line in the data set consists of a page and one of its neighbors. You need to copy them to HDFS first. In this assignment, always run the algorithm for a total of 10 iterations.

Task 1. Write a Scala/Python/Java Spark application that implements the PageRank algorithm.

Task 2. Add appropriate custom RDD partitioning and see what changes.

Task 3. Persist the appropriate RDD as in-memory objects and see what changes.

Task 4. Kill a Worker process and see the changes. You should trigger the failure to a desired worker VM when the application reaches 50% of its lifetime:

  1. Clear the memory cache using sudo sh -c "sync; echo 3 > /proc/sys/vm/drop_caches".

  2. Kill the Worker process.

With respect to Task 1-4, in your report you should report the application completion time. Present / reason about the difference in performance or your own findings, if any. Take a look at the lineage graphs of applications from Spark UI, or investigate into the log to find the amount of network/storage read/write bandwidth and number of tasks the number of tasks for every execution may help you better understand the performance issues.

Deliverables

You should submit a tar.gz file to your group’s folder in ~cs744-1/handin/groupx, which consists of a brief report(filename: groupx.pdf) and the code of each task. Put the code of each part and each task into separate folders give them meaningful names. Also put a README file for each task and provide the instructions about how to run your code. Also include a run.sh script for each part of the assignment that can re-execute your code on a similar CloudLab cluster assuming that Hadoop and Spark are present in the same location.

Acknowledgements

This assignment uses insights from Professor Aditya Akella’s assignment 1 of CS744 Fall 2017 fall and Professor Mosharaf Chowdhury’s assignment 1 of ECE598 Fall 2017.