Clustering Books with LDA, Cloudera Data Science Workbench and Cloudera Altus

This brief example demonstrates clustering text documents using Latent Dirichlet Allocation (LDA). In particular this example uses a large corpus of public-domain texts from Project Gutenberg.

This shows how a data scientist might use the Cloudera Data Science Workbench to interactively explore data and build models on a small cluster, and then leverage a much larger transient cluster provisioned with Cloudera Altus to select and build the best, final model with additional computing power from Amazon Web Services (AWS).

Exploring with the Workbench

A data scientist might first try experimenting in the Workbench, and refine a model building and selection process there, with the help of a small CDH cluster. Once the modeling job is ready, it can be run at larger scale with Altus in the cloud to build a better model.

Get Data

This example requires the complete Project Gutenberg archive. While the public domain text can be copied from the project mirrors, it's very large. A compressed archive of only the text files, with most duplicates and obsolete text files removed, in Parquet format, can be downloaded, decompressed, and uploaded to a directory like /user/ds/gutenberg on HDFS as follows:

curl https://storage.googleapis.com/altus-cdsw-lda-example/gutenberg.tar | tar xv   
hdfs dfs -put gutenberg /user/ds/

The data consists of (path, text) pairs, where "path" is the path from the original Gutenberg archive and "text" is the text of the corresponding file.

If you really want to download all of the files directly, then just the text files can be rsynced with:

rsync --include "*/" --include "*.txt" --exclude "*" -zarv aleph.gutenberg.org::gutenberg gutenberg/

... and then further pared down from there. But this isn't recommended.

Checkout and Run Code in the Workbench

Start by creating a new project in the Workbench project based on the Git repo at https://github.com/nisha/altus-lda-example and open it in the Workbench.

The file spark-defaults.conf contains default resource sizing for a moderately powerful 5-node cluster. This sizing can be increased or reduced to match your cluster. If in doubt, delete this file in your project in order to use cluster defaults.

Run a Scala session with 4 CPUs and 8GB of RAM. (More, or less, depending on your driver resource size.)

AltusLDAExample.scala is set up primarily as code that can be run and manipulated by itself in the Workbench, while still compiling as part of a runnable Spark application. As such it requires running most, but not all, code in the file, as some code here is required for the app packaging but will not work with the Workbench. Select and execute code within the two START/END blocks only.

The code builds and evaluates a few LDA models based on a subset of the data, and prints information about the best model that was found. It also saves the model to the path defined by --outputPath if set.

Scaling Up with Altus

With a working model selection process, it's possible to temporarily leverage much more computing power in the cloud by spinning up a much larger transient cluster with Altus on AWS to try more models on the full data set.

Build the Spark App

Note: You can skip this step and use the pre-built JAR file at s3a://altus-cdsw-lda-example/altus-lda-example-1.0.0-jar-with-dependencies.jar.

The code is already set up to be packaged as a stand-alone JAR file that can be run with spark-submit or Altus. It must first be built. This can be done in the Workbench's Terminal, even.

If Apache Maven is not already available (and it typically is not), install it with a package manager. To install it manually, where this is not possible:

mirror=$(curl -s https://www.apache.org/dyn/closer.lua?preferred=true)
curl "${mirror}/maven/maven-3/3.5.2/binaries/apache-maven-3.5.2-bin.tar.gz" | tar xz
alias mvn=./apache-maven-3.5.2/bin/mvn

To package the application JAR file, just mvn package. This produces a runnable JAR file like altus-lda-example-1.0.0-jar-with-dependencies.jar in target/.

Upload it to S3, like so:

aws s3 cp target/altus-lda-example-1.0.0-jar-with-dependencies.jar s3://[your-bucket-here]/

Get the Data

Note: You can skip this step and use the data already copied to s3a://altus-cdsw-lda-example/.

The data and JAR file both need to first be added to Amazon's S3 storage service. The same data files need to exist in an S3 bucket that you have access to. Given the directory of files that was unpacked above to upload to HDFS, it can be uploaded to an S3 bucket with:

aws s3 cp --recursive gutenberg s3://[your-bucket-here]/gutenberg

Set Up AWS

Using Altus currently means using AWS or Microsoft Azure. We'll use AWS in this example.

You will need an AWS account, one that has billing set up, because the following operations will incur AWS charges. Refer to AWS Account Requirements as well to ensure your AWS account allows the operations Altus needs

You'll also need to know the Access Key and Secret Key for your account. These are available in the AWS Console, in your account menu at the top right, under "My Security Credentials".

Altus will also require an SSH key. Navigate to the EC2 service in AWS, and choose a zone like us-east-2 (US East Ohio) from the region menu at the top right. Under "Network & Security" at the left, see "Key Pairs". Create a new key pair called AltusLDAExampleKey, and make sure to keep and secure the AltusLDAExampleKey.pem private key file that is created.

Set Up Altus

Log in to Altus.

To use Altus, first, you must set up an Environment, if none are already available to you. Choose "Environments" from the left and click "Quickstart". Click "Create" next to "Amazon Web Services".

Set the "Altus Environment Name" to AltusLDAExample and choose the same region in which you created the SSH keys above, such as us-east-2. Leave other options at the default. Supply your AWS Access Key and Secret Key when prompted.

Leave "Archive work loads" suggested, but, the default bucket name is based on the Environment name, and may not be available. Use "Customize Resource Names" at the right to customize the logging bucket if needed.

Deploy to Altus

Return to the main Altus pane and choose "Jobs" from the left, and choose "Submit Jobs". Fill out the details as follows.

Note that --dataDir controls where the input files are read from. An additional option, --outputDir (not shown) causes the final model to be written, as well. This can be another S3 bucket, but must be one you have already set up and have write access to.

• Job Settings
  • Submission: Single job
  • Job Type: Spark
  • Job Name: AltusLDAExample
  • Main Class: altus.AltusLDARunner
  • Jars: s3a://altus-cdsw-lda-example/altus-lda-example-1.0.0-jar-with-dependencies.jar (or your uploaded JAR)
  • Application Arguments:
    • --dataDir=s3a://altus-cdsw-lda-example/gutenberg
    • --sampleRate=1.0
    • --kValues=25,100,200
    • --maxIter=20
  • Spark Arguments:

    --driver-cores 1 --driver-memory 4g 
    --num-executors 8 
    --executor-cores 14 --executor-memory 16g 
    --conf spark.locality.wait=1s
    --conf spark.yarn.executor.memoryOverhead=4g 
    --conf spark.dynamicAllocation.enabled=false 
    --conf fs.s3a.access.key="[AWS Access Key]" 
    --conf fs.s3.awsSecretAccessKey="[AWS Secret Key]"

• Cluster Settings
  • Cluster: Create New
    • Uncheck "Terminate cluster once jobs complete" if you wish to try submitting several jobs, but don't forget to shut it down
  • Cluster Name: AltusLDAExample-cluster
  • Service Type: Spark 2.x
  • CDH Version: CDH 5.13 (Spark 2.2)
  • Environment: AltusLDAExample
• Node Configuration:
  • Worker: 3 x c4.4xlarge
  • Compute Worker: 5 x c4.4xlarge
    • Purchasing Option: Spot, $0.80 / hour
• Credentials:
  • SSH Private Key: (.pem file from SSH key above)
  • Cloudera Manager: (any credentials you like)

You can find application logs on S3 at a path like altus-lda-example-log-archive-bucket/AltusLDAExample-cluster-xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx/hdfs/logs.

Note: Above, AWS credentials are specified on the command line. This means they may be logged, and visible to users who can browse the job's log files. For alternative ways of specifying credentials, see https://www.cloudera.com/documentation/enterprise/latest/topics/spark_s3.html .

Bonus: Altus CLI

If you left the cluster running, or, already have a cluster running in Altus, you can even launch this job from the command line, and from within the Workbench Terminal, too.

First pip install altuscli to get access to the latest Altus CLI tools.

You will also need an Altus Access Key (separate from AWS) in order to invoke Altus commands from the command line. In the Altus console, navigate to "My Account" at the top right. Under "Access Keys", choose "Generate Access Key". You will get an Access Key and Secret Key. Save the secret key! Or keep the window open.

In Terminal, altus configure and enter your Altus Access Key and Secret Key.

At this point, it should be possible to submit a new job with:

altus dataeng submit-jobs \
 --cluster-name AltusLDAExample-cluster \
 --jobs '{ "name": "AltusLDAExample",
           "sparkJob": {
             "jars": [
               "s3a://altus-cdsw-lda-example/altus-lda-example-1.0.0-jar-with-dependencies.jar"
             ],
             "applicationArguments": "...",
             "sparkArguments": "...",
             "mainClass": "altus.AltusLDARunner"
        }}'

The list-jobs and terminate-jobs can be used to manage jobs from the CLI; try altus dataeng help. It's even possible to create clusters from the command line!