EMR – Random IT Utensils https://blog.adamfurmanek.pl IT, operating systems, maths, and more. Thu, 19 Mar 2020 00:51:49 +0000 en-US hourly 1 https://wordpress.org/?v=6.5.2 Data encryption in s3 in Spark in EMR with multiple encryption schemes https://blog.adamfurmanek.pl/2020/04/04/data-encryption-in-s3-in-spark-in-emr-with-multiple-encryption-schemes/ https://blog.adamfurmanek.pl/2020/04/04/data-encryption-in-s3-in-spark-in-emr-with-multiple-encryption-schemes/#respond Sat, 04 Apr 2020 08:00:59 +0000 https://blog.adamfurmanek.pl/?p=3269 Continue reading Data encryption in s3 in Spark in EMR with multiple encryption schemes]]> Spark supports multiple encryption schemes. You can use client side encryption, server side encryption, etc. What wasn’t working for me for a long time is reading encrypted data and writing as a plain text. Before reading I was configuring encryption and this was working fine. However, writing as plain text didn’t work (data was encrypted), even though I was disabling encryption.

I was told that this is because encryption settings are cached and my changes are not honored. However, what works for me now is using different access protocols to read and write s3 files.

So, for configuration do this:

// Enable CSE for s3:// prefix  
spark.conf.set("fs.s3.enableServerSideEncryption", "false")
spark.conf.set("fs.s3.cse.enabled", "true")
spark.conf.set("fs.s3.cse.encryptionMaterialsProvider", "com.amazon.ws.emr.hadoop.fs.cse.KMSEncryptionMaterialsProvider")
spark.conf.set("fs.s3.cse.kms.keyId", "KMS ID") // KMS key to encrypt the data with
spark.conf.set("fs.s3.cse.kms.region", "us-east-1") // the region for the KMS key

// Disable CSE for s3a:// prefix to not encrypt 
spark.conf.set("fs.s3a.enableServerSideEncryption", "false")
spark.conf.set("fs.s3a.cse.enabled", "false")
spark.conf.set("fs.s3a.canned.acl","BucketOwnerFullControl")
spark.conf.set("fs.s3a.acl.default","BucketOwnerFullControl")
spark.conf.set("fs.s3a.acl","bucket-owner-full-control")

or in Python do this:

# Enable CSE for s3:// prefix 
spark._jsc.hadoopConfiguration().set("fs.s3.enableServerSideEncryption", "false")
spark._jsc.hadoopConfiguration().set("fs.s3.cse.enabled", "true")
spark._jsc.hadoopConfiguration().set("fs.s3.cse.encryptionMaterialsProvider", "com.amazon.ws.emr.hadoop.fs.cse.KMSEncryptionMaterialsProvider")
spark._jsc.hadoopConfiguration().set("fs.s3.cse.kms.keyId", "KMS ID") # KMS key to encrypt the data with
spark._jsc.hadoopConfiguration().set("fs.s3.cse.kms.region", "us-east-1") # the region for the KMS key

# Disable CSE for s3a:// prefix to not encrypt 
spark._jsc.hadoopConfiguration().set("fs.s3a.enableServerSideEncryption", "false")
spark._jsc.hadoopConfiguration().set("fs.s3a.cse.enabled", "false")
spark._jsc.hadoopConfiguration().set("fs.s3a.canned.acl","BucketOwnerFullControl")
spark._jsc.hadoopConfiguration().set("fs.s3a.acl.default","BucketOwnerFullControl")
spark._jsc.hadoopConfiguration().set("fs.s3a.acl","bucket-owner-full-control")

Now, when you read or write file using s3 prefix, it uses encryption with KMS key. However, if you read or write using s3a, it doesn’t encrypt. You can use s3n prefix to configure yet another encryption scheme. If you want to do more, you need to dig into protocol handlers.

]]> https://blog.adamfurmanek.pl/2020/04/04/data-encryption-in-s3-in-spark-in-emr-with-multiple-encryption-schemes/feed/ 0 Running Anaconda with DGL and mxnet on CUDA GPU in Spark running in EMR https://blog.adamfurmanek.pl/2020/03/28/running-anaconda-with-dgl-and-mxnet-on-cuda-gpu-in-spark-running-in-emr/ https://blog.adamfurmanek.pl/2020/03/28/running-anaconda-with-dgl-and-mxnet-on-cuda-gpu-in-spark-running-in-emr/#respond Sat, 28 Mar 2020 09:00:14 +0000 https://blog.adamfurmanek.pl/?p=3266 Continue reading Running Anaconda with DGL and mxnet on CUDA GPU in Spark running in EMR]]> Today I’m going to share my configuration for running custom Anaconda Python with DGL (Deep Graph Library) and mxnet library, with GPU support via CUDA, running in Spark hosted in EMR. Actually, I have Redshift configuration as well, with support for gensim, tensorflow, keras, theano, pygpu, and cloudpickle. You can also install more libraries if needed. All this for Google to index keywords. Let’s begin.

My configuration uses EMR 5.17.2 and CUDA 9.2. When I’m writing it, there is EMR 5.27 available but it comes with the same CUDA version so I presume it should work as well. I’m also using Python 3.7.

First, create a cluster. Do not select mxnet as a provided library in EMR, we will install it later. As a master node use p3.8xlarge instance type — this instance must have GPU and this is where we will run DGL and mxnet. For slaves you can use anything, I’m going with 19 r3.4xlarge nodes (they don’t have GPU).

We need to install some custom libraries. I am using bootstrap script for that but you can just SSH into the host manually and run this code:

sudo mkdir /mnt/usr-moved
sudo mv /usr/local /mnt/usr-moved/
sudo ln -s /mnt/usr-moved/local /usr/
sudo mv /usr/share /mnt/usr-moved/
sudo ln -s /mnt/usr-moved/share /usr/

sudo mkdir /mnt/home
sudo chown hadoop.hadoop /mnt/home

wget https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh -O ~/anaconda.sh
bash ~/anaconda.sh -b -p /mnt/home/hadoop/anaconda
echo -e '\nexport PATH=/mnt/home/hadoop/anaconda/bin:$PATH' >> $HOME/.bashrc && source $HOME/.bashrc
echo -e '\nexport PYSPARK_PYTHON=/mnt/home/hadoop/anaconda/bin/python' >> $HOME/.bashrc && source $HOME/.bashrc

/mnt/home/hadoop/anaconda/bin/conda install -y gensim
/mnt/home/hadoop/anaconda/bin/conda install -y tensorflow
/mnt/home/hadoop/anaconda/bin/conda install -y keras
/mnt/home/hadoop/anaconda/bin/conda install -y theano
/mnt/home/hadoop/anaconda/bin/conda install -y pygpu
/mnt/home/hadoop/anaconda/bin/conda upgrade -y cloudpickle
yes | sudo /mnt/home/hadoop/anaconda/bin/pip install --pre mxnet-cu92mkl
/mnt/home/hadoop/anaconda/bin/conda install -y -c dglteam dgl-cuda9.2
/mnt/home/hadoop/anaconda/bin/conda install -y s3fs

First, I’m making a symlink to not fill the disk while installing packages. Then in line 10 I download Anaconda. Finally, lines 15-23 install some additional libraries. Notice that in line 21 I install mxnet compiled for CUDA 9.2, and in line 22 the same for DGL. Also, s3fs is required for nice reading from s3.

When this is done and cluster is created, I replace Python for Zeppelin interpreter to point to /mnt/home/hadoop/anaconda/bin/python and add Redshift configuration. I do this with the following command line (this you need to run manually after the cluster is created):

sudo /usr/lib/zeppelin/bin/install-interpreter.sh --name jdbc
cd /usr/lib/zeppelin/interpreter/jdbc/
sudo wget https://s3.amazonaws.com/redshift-downloads/drivers/jdbc/1.2.20.1043/RedshiftJDBC42-no-awssdk-1.2.20.1043.jar

sudo cat | sudo tee /etc/zeppelin/conf/interpreter.json <<'endmsg'
{
  "interpreterSettings": {
    "2ANGGHHMQ": {
      "id": "2ANGGHHMQ",
      "name": "spark",
      "group": "spark",
      "properties": {
        "zeppelin.spark.printREPLOutput": "true",
        "spark.yarn.jar": "",
        "master": "yarn-client",
        "zeppelin.spark.maxResult": "1000",
        "zeppelin.dep.localrepo": "/usr/lib/zeppelin/local-repo",
        "spark.app.name": "Zeppelin",
        "zeppelin.spark.importImplicit": "true",
        "zeppelin.spark.useHiveContext": "true",
        "args": "",
        "spark.home": "/usr/lib/spark",
        "zeppelin.spark.concurrentSQL": "false",
        "zeppelin.pyspark.python": "/mnt/home/hadoop/anaconda/bin/python"
      },
      "status": "READY",
      "interpreterGroup": [
        {
          "name": "spark",
          "class": "org.apache.zeppelin.spark.SparkInterpreter",
          "defaultInterpreter": false,
          "editor": {
            "language": "scala",
            "editOnDblClick": false
          }
        },
        {
          "name": "pyspark",
          "class": "org.apache.zeppelin.spark.PySparkInterpreter",
          "defaultInterpreter": false,
          "editor": {
            "language": "python",
            "editOnDblClick": false
          }
        },
        {
          "name": "sql",
          "class": "org.apache.zeppelin.spark.SparkSqlInterpreter",
          "defaultInterpreter": false,
          "editor": {
            "language": "sql",
            "editOnDblClick": false
          }
        }
      ],
      "dependencies": [
        {
          "groupArtifactVersion": "/usr/lib/zeppelin/interpreter/jdbc/RedshiftJDBC42-no-awssdk-1.2.20.1043.jar",
          "local": false
        }
      ],
      "option": {
        "remote": true,
        "port": -1,
        "perNote": "shared",
        "perUser": "shared",
        "isExistingProcess": false,
                "setPermission": false,
        "users": [],
        "isUserImpersonate": false
      }
    },
    "2AM1YV5CU": {
      "id": "2AM1YV5CU",
      "name": "angular",
      "group": "angular",
      "properties": {},
      "status": "READY",
      "interpreterGroup": [
        {
          "name": "angular",
          "class": "org.apache.zeppelin.angular.AngularInterpreter",
          "defaultInterpreter": false,
          "editor": {
            "editOnDblClick": true
          }
        }
      ],
      "dependencies": [],
      "option": {
        "remote": true,
        "port": -1,
        "perNote": "shared",
        "perUser": "shared",
        "isExistingProcess": false,
        "setPermission": false,
        "isUserImpersonate": false
      }
    },
    "2BRWU4WXC": {
      "id": "2BRWU4WXC",
      "name": "python",
      "group": "python",
      "properties": {
        "zeppelin.python": "/mnt/home/hadoop/anaconda/bin/python",
        "zeppelin.python.maxResult": "1000"
      },
      "status": "READY",
      "interpreterGroup": [
        {
          "name": "python",
          "class": "org.apache.zeppelin.python.PythonInterpreter",
          "defaultInterpreter": false,
          "editor": {
            "language": "python",
            "editOnDblClick": false
          }
        }
      ],
      "dependencies": [],
      "option": {
        "remote": true,
        "port": -1,
        "perNote": "shared",
        "perUser": "shared",
        "isExistingProcess": false,
        "setPermission": false,
        "users": [],
        "isUserImpersonate": false
              }
    },
    "2AJXGMUUJ": {
      "id": "2AJXGMUUJ",
      "name": "md",
      "group": "md",
      "properties": {},
      "status": "READY",
      "interpreterGroup": [
        {
          "name": "md",
          "class": "org.apache.zeppelin.markdown.Markdown",
          "defaultInterpreter": false,
          "editor": {
            "language": "markdown",
            "editOnDblClick": true
          }
        }
      ],
      "dependencies": [],
      "option": {
        "remote": true,
        "port": -1,
        "perNote": "shared",
        "perUser": "shared",
        "isExistingProcess": false,
        "setPermission": false,
        "isUserImpersonate": false
      }
    },
    "2AKK3QQXU": {
      "id": "2AKK3QQXU",
      "name": "sh",
      "group": "sh",
      "properties": {
        "shell.command.timeout.millisecs": "60000"
      },
      "status": "READY",
      "interpreterGroup": [
        {
          "name": "sh",
          "class": "org.apache.zeppelin.shell.ShellInterpreter",
          "defaultInterpreter": false,
          "editor": {
            "language": "sh",
            "editOnDblClick": false
          }
        }
      ],
      "dependencies": [],
      "option": {
        "remote": true,
        "port": -1,
        "perNote": "shared",
        "perUser": "shared",
        "isExistingProcess": false,
        "setPermission": false,
        "isUserImpersonate": false
      }
    }
  },
  "interpreterBindings": {
    "2EMW16J14": [
      "2ANGGHHMQ",
      "2AJXGMUUJ",
      "2AM1YV5CU",
      "2AKK3QQXU",
      "2BRWU4WXC"
    ],
    "2A94M5J1Z": [
      "2ANGGHHMQ",
      "2AJXGMUUJ",
      "2AM1YV5CU",
      "2AKK3QQXU",
      "2BRWU4WXC"
    ]
  },
  "interpreterRepositories": [
    {
      "id": "central",
      "type": "default",
      "url": "http://repo1.maven.org/maven2/",
      "releasePolicy": {
      "enabled": true,
        "updatePolicy": "daily",
        "checksumPolicy": "warn"
      },
      "snapshotPolicy": {
        "enabled": true,
        "updatePolicy": "daily",
        "checksumPolicy": "warn"
      },
      "mirroredRepositories": [],
      "repositoryManager": false
    },
    {
      "id": "local",
      "type": "default",
      "url": "file:///var/lib/zeppelin/.m2/repository",
      "releasePolicy": {
        "enabled": true,
        "updatePolicy": "daily",
        "checksumPolicy": "warn"
      },
      "snapshotPolicy": {
        "enabled": true,
        "updatePolicy": "daily",
        "checksumPolicy": "warn"
      },
      "mirroredRepositories": [],
      "repositoryManager": false
    }
  ]
}
endmsg

Now, I need to tune default spark submit options:

sudo cat | sudo tee /etc/zeppelin/conf.dist/zeppelin-env.sh <<'endmsg'
export ZEPPELIN_PORT=8890
export ZEPPELIN_CONF_DIR=/etc/zeppelin/conf
export ZEPPELIN_LOG_DIR=/var/log/zeppelin
export ZEPPELIN_PID_DIR=/var/run/zeppelin
export ZEPPELIN_PID=$ZEPPELIN_PID_DIR/zeppelin.pid
export ZEPPELIN_WAR_TEMPDIR=/var/run/zeppelin/webapps
export ZEPPELIN_NOTEBOOK_DIR=/var/lib/zeppelin/notebook
export MASTER=yarn-client
export SPARK_HOME=/usr/lib/spark
export HADOOP_CONF_DIR=/etc/hadoop/conf
export LD_LIBRARY_PATH=/usr/local/cuda/lib64/
export CLASSPATH=":/usr/lib/hadoop-lzo/lib/*:/usr/lib/hadoop/hadoop-aws.jar:/usr/share/aws/aws-java-sdk/*:/usr/share/aws/emr/emrfs/conf:/usr/share/aws/emr/emrfs/lib/*:/usr/share/aws/emr/emrfs/auxlib/*:/usr/share/aws/hmclient/lib/aws-glue-datacatalog-spark-client.jar:/usr/share/aws/sagemaker-spark-sdk/lib/sagemaker-spark-sdk.jar"


export SPARK_SUBMIT_OPTIONS="--jars=YOUR_JARS_HERE --conf spark.executor.extraClassPath=/usr/lib/hadoop-lzo/lib/*:/usr/lib/hadoop/hadoop-aws.jar:/usr/share/aws/aws-java-sdk/*:/usr/share/aws/emr/emrfs/conf:/usr/share/aws/emr/emrfs/lib/*:/usr/share/aws/emr/emrfs/auxlib/*:/usr/share/aws/emr/security/conf:/usr/share/aws/emr/security/lib/* --conf spark.driver.extraClassPath=/usr/lib/hadoop-lzo/lib/*:/usr/lib/hadoop/hadoop-aws.jar:/usr/share/aws/aws-java-sdk/*:/usr/share/aws/emr/emrfs/conf:/usr/share/aws/emr/emrfs/lib/*:/usr/share/aws/emr/emrfs/auxlib/*:/usr/share/aws/emr/security/conf:/usr/share/aws/emr/security/lib/* --conf 'spark.executorEnv.PYTHONPATH=/usr/lib/spark/python/lib/py4j-src.zip:/usr/lib/spark/python/:<CPS>{{PWD}}/pyspark.zip<CPS>{{PWD}}/py4j-src.zip' --conf spark.yarn.isPython=true --conf spark.driver.maxResultSize=80G --num-executors 56 --executor-cores 5 --executor-memory 38G --driver-memory 90G --conf 'spark.dynamicAllocation.enabled=false' --conf 'spark.hadoop.fs.s3.canned.acl=BucketOwnerFullControl' --conf 'spark.hadoop.fs.s3.acl.default=BucketOwnerFullControl' --conf 'spark.hadoop.fs.s3.acl=bucket-owner-full-control' --conf 'spark.hadoop.fs.s3n.acl=bucket-owner-full-control' --conf 'spark.hadoop.fs.s3.cse.enabled=false'"
export ZEPPELIN_NOTEBOOK_STORAGE=org.apache.zeppelin.notebook.repo.S3NotebookRepo
endmsg

This is not the full content! I omit some of my internal settings so generally don’t copy it blindly, just extend the zeppelin-env.sh file as needed. Important things are:
export LD_LIBRARY_PATH=/usr/local/cuda/lib64/ — this points to CUDA libraries
--conf spark.driver.maxResultSize=80G --num-executors 56 --executor-cores 5 --executor-memory 38G --driver-memory 90G --conf 'spark.dynamicAllocation.enabled=false' — this configures executors and memory. You need to tune it for your cluster size.

Now, restart Zeppelin. You should now be able to run:

%spark.pyspark
print(mx.__version__)
print(np.__version__)

1.6.0
1.14.6

Now you can create GPU context:

ctx = mx.gpu(0)

and it should work as a charm.

So now you have power of Spark — you can easily distribute job and use all slaves. And also, you have GPU at your hand, so whenever you use ndarray from mxnet, it can use the GPU power.

If you don’t want to use GPU, then just install these libraries instead:

yes | sudo /mnt/home/hadoop/anaconda/bin/pip install --pre mxnet
/mnt/home/hadoop/anaconda/bin/conda install -y -c dglteam dgl

and use mx.cpu() context. This works as well, obviously, much slower. For my use case GPU calculations were 80 times faster than when running on CPU.

]]> https://blog.adamfurmanek.pl/2020/03/28/running-anaconda-with-dgl-and-mxnet-on-cuda-gpu-in-spark-running-in-emr/feed/ 0 Running any query in Redshift or JDBC from Spark in EMR https://blog.adamfurmanek.pl/2020/03/21/running-any-query-in-redshift-or-jdbc-from-spark-in-emr/ https://blog.adamfurmanek.pl/2020/03/21/running-any-query-in-redshift-or-jdbc-from-spark-in-emr/#respond Sat, 21 Mar 2020 09:00:20 +0000 https://blog.adamfurmanek.pl/?p=3264 Continue reading Running any query in Redshift or JDBC from Spark in EMR]]> Last time we saw how to connect to Redshift from Spark running in EMR. Provided solution was nice but allowed for reading data only. Sometimes we might want to run any DDL or DML query, not only simple read statements.

To do that, we need to connect to Redshift directly over JDBC. I assume you configured your cluster the same way as in the previous part. Now use this code:

def executeNonQuery(query: String) = {
    import java.sql._
    import java.util._
    
    var connectionProps = new Properties();

    var connection = DriverManager.getConnection(getConnectionString(), connectionProps);
    var statement = connection.createStatement(query);
    statement.executeUpdate();
}

We first import packages for JDBC. Next, we create new properties for the connection which can be empty. Then, we open the connection using JDBC infrastructure, prepare the query and execute it. Please remember that this query must return row count so it shouldn’t be SELECT query.

We can use it like this:

%spark
executeNonQuery(s"""DROP TABLE IF EXISTS table""")

Query is pretty much anything you can run in SQL Workbench. It works with temporary tables as well (unlike prepareStatement).

]]> https://blog.adamfurmanek.pl/2020/03/21/running-any-query-in-redshift-or-jdbc-from-spark-in-emr/feed/ 0 Connecting to Redshift from Spark running in EMR https://blog.adamfurmanek.pl/2020/03/14/connecting-to-redshift-from-spark-running-in-emr/ https://blog.adamfurmanek.pl/2020/03/14/connecting-to-redshift-from-spark-running-in-emr/#respond Sat, 14 Mar 2020 09:00:22 +0000 https://blog.adamfurmanek.pl/?p=3261 Continue reading Connecting to Redshift from Spark running in EMR]]> Today I’ll share my configuration for Spark running in EMR to connect to Redshift cluster. First, I assume the cluster is accessible (so configure virtual subnet, allowed IPs and all network stuff before running this).

I’m using Zeppelin so I’ll show two interpreters configured for the connection, but the same thing should work with standalone job (as long as it has the same libraries configured). I tested things with EMR 5.17.2 but it should work with other versions as well.

Redshift interpreter

First, let’s configure separate interpreter to use in Zeppelin. SSH into the master node of the cluster and install JDBC interpreter:

sudo /usr/lib/zeppelin/bin/install-interpreter.sh --name jdbc

Next, download the driver:

cd /usr/lib/zeppelin/interpreter/jdbc/
sudo wget https://s3.amazonaws.com/redshift-downloads/drivers/jdbc/1.2.20.1043/RedshiftJDBC42-no-awssdk-1.2.20.1043.jar

Restart zeppelin:

sudo stop zeppelin
sudo start zeppelin

Go to interpreters configuration in Zeppelin and add new JDBC named redshift. Use the following settings:

default.driver	com.amazon.redshift.jdbc42.Driver
default.url	jdbc:redshift://your-redshift-instance-address.redshift.amazonaws.com:5439/your-database
default.user	redshift_user
default.password	redshift_password

Now create new paragraph like below:

%redshift
SELECT * FROM table

And it should work.

Spark interpreter

Download driver the same way as before. Now, go to interpreter settings and add dependency to Spark interpreter:

/usr/lib/zeppelin/interpreter/jdbc/RedshiftJDBC42-no-awssdk-1.2.20.1043.jar

Now you can start reading data like this:

%spark
import org.apache.spark.sql._

def getConnectionString() = {
    val url = "cluster url"
    val port = 8192
    val database = "database name"
    val user = "user"
    val password = "password"
    
    s"jdbc:redshift://${url}:$port/$database?user=$user&password=$password"
}

def runQuery(query: String) = {
    val df: DataFrame = sqlContext.read
      .format("jdbc")
      .option("driver", "com.amazon.redshift.jdbc42.Driver")
      .option("url", getConnectionString())
      .option("dbtable", s"($query) tmp")
      .load()
    
    df
}

var table = runQuery(s"""
SELECT * FROM Table AS t
""")

This is even nicer because you can use string interpolation to provide parameters for queries.

]]> https://blog.adamfurmanek.pl/2020/03/14/connecting-to-redshift-from-spark-running-in-emr/feed/ 0 Updating Tomcat in an EMR cluster https://blog.adamfurmanek.pl/2020/02/08/updating-tomcat-in-an-emr-cluster/ https://blog.adamfurmanek.pl/2020/02/08/updating-tomcat-in-an-emr-cluster/#respond Sat, 08 Feb 2020 09:00:22 +0000 https://blog.adamfurmanek.pl/?p=3234 Continue reading Updating Tomcat in an EMR cluster]]> This is a short story of fixing Tomcat in an EMR cluster. There is a CVE about Tomcat 8 hole. I’m using EMR 5.12.2. Let’s try installing CVE patch as a bootstrap action with

sudo yum update -y --releasever=latest --cve CVE-2019-0232

sudo shutdown -r now

It should fix the mentioned hole but after bringing up the new cluster and running

[hadoop@ip-10-0-1-84 ~]$ yum info tomcat8
Loaded plugins: priorities, update-motd, upgrade-helper
6 packages excluded due to repository priority protections
Installed Packages
Name        : tomcat8
Arch        : noarch
Version     : 8.5.29
Release     : 1.77.amzn1
Size        : 324 k
Repo        : installed
From repo   : amzn-updates
Summary     : Apache Servlet/JSP Engine, RI for Servlet 3.1/JSP 2.3 API
URL         : http://tomcat.apache.org/ 
License     : ASL 2.0
Description : Tomcat is the servlet container that is used in the official Reference
            : Implementation for the Java Servlet and JavaServer Pages technologies.
            : The Java Servlet and JavaServer Pages specifications are developed by
            : Sun under the Java Community Process.
            :
            : Tomcat is developed in an open and participatory environment and
            : released under the Apache Software License version 2.0. Tomcat is intended
            : to be a collaboration of the best-of-breed developers from around the world.

we can see that it installs version 8.5.29 of tomcat (instead of 8.5.42 or something newer). Why? Let’s SSH into the EMR and check:

[hadoop@ip-10-0-1-84 ~]$ yum --showduplicates list tomcat8
Loaded plugins: priorities, update-motd, upgrade-helper
6 packages excluded due to repository priority protections
Installed Packages
tomcat8.noarch                                                                                                8.5.29-1.77.amzn1                                                                                                 @amzn-updates
Available Packages
tomcat8.noarch                                                                                                8.5.16-1.74.amzn1                                                                                                 amzn-main
tomcat8.noarch                                                                                                8.5.23-1.75.amzn1                                                                                                 amzn-updates
tomcat8.noarch                                                                                                8.5.28-1.76.amzn1                                                                                                 amzn-updates
tomcat8.noarch                                                                                                8.5.29-1.77.amzn1                                                                                                 amzn-updates

So there is no newer version. But if we try applying the CVE patch again we get:

[hadoop@ip-10-0-1-84 /]$ sudo yum update -y --releasever=latest --cve CVE-2019-0232
Loaded plugins: priorities, update-motd, upgrade-helper
amzn-main                                                                                                                                                                                                             | 2.1 kB  00:00:00
amzn-updates                                                                                                                                                                                                          | 2.5 kB  00:00:00
emr-applications                                                                                                                                                                                                      | 2.9 kB  00:00:00
8 packages excluded due to repository priority protections
6 package(s) needed (+0 related) for security, out of 130 available
Resolving Dependencies
--> Running transaction check
---> Package tomcat8.noarch 0:8.5.29-1.77.amzn1 will be updated
---> Package tomcat8.noarch 0:8.5.42-1.80.amzn1 will be an update
---> Package tomcat8-el-3.0-api.noarch 0:8.5.29-1.77.amzn1 will be updated
---> Package tomcat8-el-3.0-api.noarch 0:8.5.42-1.80.amzn1 will be an update
---> Package tomcat8-jsp-2.3-api.noarch 0:8.5.29-1.77.amzn1 will be updated
---> Package tomcat8-jsp-2.3-api.noarch 0:8.5.42-1.80.amzn1 will be an update
---> Package tomcat8-lib.noarch 0:8.5.29-1.77.amzn1 will be updated
---> Package tomcat8-lib.noarch 0:8.5.42-1.80.amzn1 will be an update
---> Package tomcat8-servlet-3.1-api.noarch 0:8.5.29-1.77.amzn1 will be updated
---> Package tomcat8-servlet-3.1-api.noarch 0:8.5.42-1.80.amzn1 will be an update
---> Package tomcat8-webapps.noarch 0:8.5.29-1.77.amzn1 will be updated
---> Package tomcat8-webapps.noarch 0:8.5.42-1.80.amzn1 will be an update
--> Finished Dependency Resolution

Dependencies Resolved

=============================================================================================================================================================================================================================================
 Package                                                           Arch                                             Version                                                     Repository                                              Size
=============================================================================================================================================================================================================================================
Updating:
 tomcat8                                                           noarch                                           8.5.42-1.80.amzn1                                           amzn-updates                                           102 k
 tomcat8-el-3.0-api                                                noarch                                           8.5.42-1.80.amzn1                                           amzn-updates                                           110 k
 tomcat8-jsp-2.3-api                                               noarch                                           8.5.42-1.80.amzn1                                           amzn-updates                                            68 k
 tomcat8-lib                                                       noarch                                           8.5.42-1.80.amzn1                                           amzn-updates                                           4.3 M
 tomcat8-servlet-3.1-api                                           noarch                                           8.5.42-1.80.amzn1                                           amzn-updates                                           255 k
 tomcat8-webapps                                                   noarch                                           8.5.42-1.80.amzn1                                           amzn-updates                                           358 k

Transaction Summary
=============================================================================================================================================================================================================================================
Upgrade  6 Packages

Total download size: 5.2 M
Downloading packages:
(1/6): tomcat8-el-3.0-api-8.5.42-1.80.amzn1.noarch.rpm                                                                                                                                                                | 110 kB  00:00:00
(2/6): tomcat8-8.5.42-1.80.amzn1.noarch.rpm                                                                                                                                                                           | 102 kB  00:00:00
(3/6): tomcat8-jsp-2.3-api-8.5.42-1.80.amzn1.noarch.rpm                                                                                                                                                               |  68 kB  00:00:00
(4/6): tomcat8-webapps-8.5.42-1.80.amzn1.noarch.rpm                                                                                                                                                                   | 358 kB  00:00:00
(5/6): tomcat8-lib-8.5.42-1.80.amzn1.noarch.rpm                                                                                                                                                                       | 4.3 MB  00:00:00
(6/6): tomcat8-servlet-3.1-api-8.5.42-1.80.amzn1.noarch.rpm                                                                                                                                                           | 255 kB  00:00:00
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                                                                                                                        6.0 MB/s | 5.2 MB  00:00:00
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
  Updating   : tomcat8-servlet-3.1-api-8.5.42-1.80.amzn1.noarch                                                                                                                                                                         1/12
  Updating   : tomcat8-el-3.0-api-8.5.42-1.80.amzn1.noarch                                                                                                                                                                              2/12
  Updating   : tomcat8-jsp-2.3-api-8.5.42-1.80.amzn1.noarch                                                                                                                                                                             3/12
  Updating   : tomcat8-lib-8.5.42-1.80.amzn1.noarch                                                                                                                                                                                     4/12
  Updating   : tomcat8-8.5.42-1.80.amzn1.noarch                                                                                                                                                                                         5/12
  Updating   : tomcat8-webapps-8.5.42-1.80.amzn1.noarch                                                                                                                                                                                 6/12
  Cleanup    : tomcat8-webapps-8.5.29-1.77.amzn1.noarch                                                                                                                                                                                 7/12
  Cleanup    : tomcat8-8.5.29-1.77.amzn1.noarch                                                                                                                                                                                         8/12
  Cleanup    : tomcat8-lib-8.5.29-1.77.amzn1.noarch                                                                                                                                                                                     9/12
  Cleanup    : tomcat8-jsp-2.3-api-8.5.29-1.77.amzn1.noarch                                                                                                                                                                            10/12
  Cleanup    : tomcat8-el-3.0-api-8.5.29-1.77.amzn1.noarch                                                                                                                                                                             11/12
  Cleanup    : tomcat8-servlet-3.1-api-8.5.29-1.77.amzn1.noarch                                                                                                                                                                        12/12
  Verifying  : tomcat8-webapps-8.5.42-1.80.amzn1.noarch                                                                                                                                                                                 1/12
  Verifying  : tomcat8-jsp-2.3-api-8.5.42-1.80.amzn1.noarch                                                                                                                                                                             2/12
  Verifying  : tomcat8-lib-8.5.42-1.80.amzn1.noarch                                                                                                                                                                                     3/12
  Verifying  : tomcat8-el-3.0-api-8.5.42-1.80.amzn1.noarch                                                                                                                                                                              4/12
  Verifying  : tomcat8-servlet-3.1-api-8.5.42-1.80.amzn1.noarch                                                                                                                                                                         5/12
  Verifying  : tomcat8-8.5.42-1.80.amzn1.noarch                                                                                                                                                                                         6/12
  Verifying  : tomcat8-webapps-8.5.29-1.77.amzn1.noarch                                                                                                                                                                                 7/12
  Verifying  : tomcat8-lib-8.5.29-1.77.amzn1.noarch                                                                                                                                                                                     8/12
  Verifying  : tomcat8-jsp-2.3-api-8.5.29-1.77.amzn1.noarch                                                                                                                                                                             9/12
  Verifying  : tomcat8-8.5.29-1.77.amzn1.noarch                                                                                                                                                                                        10/12
  Verifying  : tomcat8-servlet-3.1-api-8.5.29-1.77.amzn1.noarch                                                                                                                                                                        11/12
  Verifying  : tomcat8-el-3.0-api-8.5.29-1.77.amzn1.noarch                                                                                                                                                                             12/12

Updated:
  tomcat8.noarch 0:8.5.42-1.80.amzn1           tomcat8-el-3.0-api.noarch 0:8.5.42-1.80.amzn1   tomcat8-jsp-2.3-api.noarch 0:8.5.42-1.80.amzn1   tomcat8-lib.noarch 0:8.5.42-1.80.amzn1   tomcat8-servlet-3.1-api.noarch 0:8.5.42-1.80.amzn1
  tomcat8-webapps.noarch 0:8.5.42-1.80.amzn1

Complete!
[hadoop@ip-10-0-1-84 /]$ yum info tomcat8
Loaded plugins: priorities, update-motd, upgrade-helper
6 packages excluded due to repository priority protections
Installed Packages
Name        : tomcat8
Arch        : noarch
Version     : 8.5.42
Release     : 1.80.amzn1
Size        : 326 k
Repo        : installed
From repo   : amzn-updates
Summary     : Apache Servlet/JSP Engine, RI for Servlet 3.1/JSP 2.3 API
URL         : http://tomcat.apache.org/
License     : ASL 2.0
Description : Tomcat is the servlet container that is used in the official Reference
            : Implementation for the Java Servlet and JavaServer Pages technologies.
            : The Java Servlet and JavaServer Pages specifications are developed by
            : Sun under the Java Community Process.
            :
            : Tomcat is developed in an open and participatory environment and
            : released under the Apache Software License version 2.0. Tomcat is intended
            : to be a collaboration of the best-of-breed developers from around the world.

So it was able to update the Tomcat even though the same command run through bootstrap didn’t do it. What’s happening?

Let’s try installing it manually. Add another boostrap action before the AWS script:

#!/bin/sh

set -ex

{
	yum info tomcat8
	yum --showduplicates --releasever=latest list tomcat8
	sudo yum update --releasever=latest --cve CVE-2019-0232
	sudo yum update -y --releasever=latest tomcat8
	sudo yum update -y --releasever=latest tomcat8-8.5.42-1.80.amzn1
} >> /home/hadoop/cves.out 2>> /home/hadoop/cves.err

Logs show this:

Loaded plugins: priorities, update-motd, upgrade-helper
6 packages excluded due to repository priority protections
Available Packages
Name        : tomcat8
Arch        : noarch
Version     : 8.5.29
Release     : 1.77.amzn1
Size        : 102 k
Repo        : amzn-updates/2017.09
Summary     : Apache Servlet/JSP Engine, RI for Servlet 3.1/JSP 2.3 API
URL         : http://tomcat.apache.org/ 
License     : ASL 2.0
Description : Tomcat is the servlet container that is used in the official
            : Reference Implementation for the Java Servlet and JavaServer Pages
            : technologies. The Java Servlet and JavaServer Pages specifications
            : are developed by Sun under the Java Community Process.
            :
            : Tomcat is developed in an open and participatory environment and
            : released under the Apache Software License version 2.0. Tomcat is
            : intended to be a collaboration of the best-of-breed developers
            : from around the world.

Loaded plugins: priorities, update-motd, upgrade-helper
8 packages excluded due to repository priority protections
Available Packages
tomcat8.noarch                  8.5.29-1.77.amzn1                   amzn-main
tomcat8.noarch                  8.5.32-1.78.amzn1                   amzn-updates
tomcat8.noarch                  8.5.40-1.79.amzn1                   amzn-updates
tomcat8.noarch                  8.5.42-1.80.amzn1                   amzn-updates
Loaded plugins: priorities, update-motd, upgrade-helper
8 packages excluded due to repository priority protections
No packages needed for security; 126 packages available
Resolving Dependencies
Loaded plugins: priorities, update-motd, upgrade-helper
8 packages excluded due to repository priority protections
Package(s) tomcat8 available, but not installed.
No packages marked for update
Loaded plugins: priorities, update-motd, upgrade-helper
8 packages excluded due to repository priority protections
Package(s) tomcat8-8.5.42-1.80.amzn1 available, but not installed.
No packages marked for update

So it could find version 8.5.42 but refused to update it. How to fix that? The solution is to install instead of update. Let’s try this:

#!/bin/sh

set -ex

{
	sudo yum install -y --releasever=latest tomcat8-servlet-3.1-api-8.5.42
	sudo yum install -y --releasever=latest tomcat8-el-3.0-api-8.5.42
	sudo yum install -y --releasever=latest tomcat8-jsp-2.3-api-8.5.42
	sudo yum install -y --releasever=latest tomcat8-lib-8.5.42
	sudo yum install -y --releasever=latest tomcat8-8.5.42
	sudo yum install -y --releasever=latest tomcat8-webapps-8.5.42
	exit 0
} >> /home/hadoop/cves.out 2>> /home/hadoop/cves.err

And now it works as expected. Unfortunately, installing specific Tomcat version (instead of latest one) is not the best idea but at least this solves the issue.

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