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Reference

Production Implementation of Machine Learning models

This is representative of how we implemented and created end to end framework to push machine learning models in production.
Working in large organisations give a challenge to how actually run your code in production to create meaningful business value. Often Machine learning models / Analytics sits in source control  (e.g git) for long long time before actually running and helping customers. This flow can be represented by figure below in which Data Scientists / Analysts make something ( e.g R model ) and now they do not know or have power to actually test it in a line of fire where customers actually are.

We made a machine learning pipeline using Spark  , H2O Sparkling water which gives very nice modular api's to all work from data munging , training , scoring etc. Everything in single code base. 
Spark has fundamentally changed Bigdata world. All the work which we were doing in different sets of tools in past have now unified into one single Swiss knife.
Our new machine learning pipeline looks like as shown below.
  1. Data scientists / Analysts working on specific use case use Spark + Sparkling water to create machine learning models.
  2. Commit there model in git
  3. Code is build in Jenkins to create jar/rpm artifacts which are stored in Nexus
  4. The deployment is automated via the Chef
The whole time to actually running model in production is now short circuit to as small as time taken to train new model + 5 mins.
Data scientists have full power to push any new model to production without going through huge bureaucracy and do A/B testing for the new ideas. All they have to do is just push new code / follow standard peer code review process.

A organisation who can quickly try out new things can fail quickly , learn quickly and innovate quickly. This is kind of culture we are trying to create. Data driven culture of experimentation. 
If you liked reading this , you will also like reading my upcoming book Apache Oozie Essentials , its a use case driven Oozie implementation. This book is sprinkled with the examples and exercises to help you take your big data learning to the next level and you will also get to read my lovely memories in form of Bed Time stories from my awesome Bigdata implementation at Commonwealth Bank Australia. 

Using R and Hadoop Bigdata

Following packages helps working with Bigdata from R.

1. rmr2
2. rhdfs
3. HadoopStreamingR
4. Rhipe
5. h2o
6. SparkR

The links to documentation and tutorials for each of them are below.

All the packages work on the basis of Hadoop Streaming to run the work on cluster instead of single R node. If you are new to Hadoop read the basics of Hadoop Streaming on https://hadoop.apache.org/docs/stable2/hadoop-streaming/HadoopStreaming.html and short tutorial on writing jobs which run using Python. http://www.michael-noll.com/tutorials/writing-an-hadoop-mapreduce-program-in-python/

Package Name

Useful Tutorials / Readings

rmr2

Web links



https://github.com/RevolutionAnalytics/rmr2/blob/master/docs/tutorial.md



Book

R in Nutshell 2nd edition ( Chapter 26 )

http://shop.oreilly.com/product/0636920022008.do




rhdfs

Wiki

https://github.com/RevolutionAnalytics/RHadoop/wiki/user%3Erhdfs%3EHome


HadoopStreamingR


Cran package documentation

https://cran.r-project.org/web/packages/HadoopStreaming/HadoopStreaming.pdf


Rhipe


Web links

http://tessera.io/docs-RHIPE/#install-and-push




h2o

Documentation using h2o from R

http://h2o-release.s3.amazonaws.com/h2o/rel-slater/1/docs-website/h2o-docs/index.html#%E2%80%A6%20From%20R

R h2o package documentation ( ~140 pages )

http://h2o-release.s3.amazonaws.com/h2o/rel-slater/1/docs-website/h2o-r/h2o_package.pdf


SparkR

Api

https://spark.apache.org/docs/latest/api/R/index.html

Documentation

https://spark.apache.org/docs/latest/api/R/index.html

java.lang.NoClassDefFoundError: org/apache/spark/sql/types/AtomicType

15/09/19 12:17:10 INFO DAGScheduler: Job 0 finished: take at CsvRelation.scala:174, took 1.900011 s
Error: application failed with exception
java.lang.NoClassDefFoundError: org/apache/spark/sql/types/AtomicType
at com.databricks.spark.csv.CsvRelation.inferSchema(CsvRelation.scala:155)
at com.databricks.spark.csv.CsvRelation.<init>(CsvRelation.scala:70)
at com.databricks.spark.csv.DefaultSource.createRelation(DefaultSource.scala:138)


If using Spark-csv with Spark 1.3.0 , with spark-csv type inference this error is thrown




Install R package behind the proxy


Sys.setenv(http_proxy="http://username:PASSWORD@proxyurl:8080")

install.packages("RPostgreSQL", dependencies=TRUE)

Initial job has not accepted any resources; check your cluster UI

15/09/19 10:28:44 WARN cluster.YarnScheduler: Initial job has not accepted any resources; check your cluster UI to ensure that workers are registered and have sufficient resources

This message in log means that Hadoop cluster does not have resources which are asked by Job.

I submitted Spark job on my test local cluster , and got this message.

Additional logs also show following , 

15/09/19 10:23:20 INFO yarn.YarnRMClient: Registering the ApplicationMaster  15/09/19 10:23:20 INFO yarn.YarnAllocator: Will request 2 executor containers, each with 1 cores and 1408 MB memory including 384 MB overhead  15/09/19 10:23:20 INFO yarn.YarnAllocator: Container request (host: Any, capability: <memory:1408, vCores:1>)  15/09/19 10:23:20 INFO yarn.YarnAllocator: Container request (host: Any, capability: <memory:1408, vCores:1>)  15/09/19 10:23:20 INFO yarn.ApplicationMaster: Started progress reporter thread with (heartbeat : 5000, initial allocation : 200) intervals
My cluster had only 3 GB RAM so Yarn cannot allocated what Spark was asking

Update R packages

update.packages(ask = FALSE,lib = '/usr/lib64/R/library',repos = "http://local/cran-mirror",dependencies = TRUE)