Apache Zeppelin cannot deserialize dataset: "NoSuchMethodError"

Question

I am trying to use Apache Zeppelin (0.7.2, net install running locally on a Mac) to explore data loaded from an s3 bucket. The data seems to load just fine, as the command:

val p = spark.read.textFile("s3a://sparkcookbook/person")

gives the result:

p: org.apache.spark.sql.Dataset[String] = [value: string]

However, when I try to call methods on the object p, I get an error. For example:

p.take(1)

results in:

java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
  at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:132)
  at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:113)
  at org.apache.spark.sql.execution.SparkPlan.getByteArrayRdd(SparkPlan.scala:225)
  at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:308)
  at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
  at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$execute$1$1.apply(Dataset.scala:2371)
  at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
  at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2765)
  at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$execute$1(Dataset.scala:2370)
  at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collect(Dataset.scala:2377)
  at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2113)
  at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2112)
  at org.apache.spark.sql.Dataset.withTypedCallback(Dataset.scala:2795)
  at org.apache.spark.sql.Dataset.head(Dataset.scala:2112)
  at org.apache.spark.sql.Dataset.take(Dataset.scala:2327)

My conf/zeppelin-env.sh is the same as the default, except that I have amazon access key and secret key environment variables defined there. In the Spark interpreter in the Zeppelin notebook, I have added the following artifacts:

org.apache.hadoop:hadoop-aws:2.7.3  
com.amazonaws:aws-java-sdk:1.7.9    
com.fasterxml.jackson.core:jackson-core:2.9.0   
com.fasterxml.jackson.core:jackson-databind:2.9.0   
com.fasterxml.jackson.core:jackson-annotations:2.9.0

(I think only the first two are necessary). The two commands above work fine in the Spark shell, just not in the Zeppelin notebook (see How to use s3 with Apache spark 2.2 in the Spark shell for how that was set up).

So it seems that there is a problem with one of the Jackson libraries. Maybe I'm using the wrong artifacts above for the Zeppelin interpreter?

UPDATE: Following the advice in the proposed answer below, I removed the jackson jars that came with Zeppelin, and replaced them with the following:

jackson-annotations-2.6.0.jar
jackson-core-2.6.7.jar
jackson-databind-2.6.7.jar

And replaced the artifacts with these, so my artifacts are now:

org.apache.hadoop:hadoop-aws:2.7.3  
com.amazonaws:aws-java-sdk:1.7.9    
com.fasterxml.jackson.core:jackson-core:2.6.7   
com.fasterxml.jackson.core:jackson-databind:2.6.7   
com.fasterxml.jackson.core:jackson-annotations:2.6.0

The error I get, however, from running the above commands is the same.

UDPATE2: As per I removed the jackson libraries from the list of artifacts, since they are already now in the jars/ folder - the only added artifacts are now the aws artifacts above. I then cleaned the classpath by entering the following in the notebook (as per the instructions):

%spark.dep
z.reset()

I get a different error now:

val p = spark.read.textFile("s3a://sparkcookbook/person")
p.take(1)

p: org.apache.spark.sql.Dataset[String] = [value: string]
java.lang.NoSuchMethodError: com.fasterxml.jackson.module.scala.deser.BigDecimalDeserializer$.handledType()Ljava/lang/Class;
  at com.fasterxml.jackson.module.scala.deser.NumberDeserializers$.<init>(ScalaNumberDeserializersModule.scala:49)
  at com.fasterxml.jackson.module.scala.deser.NumberDeserializers$.<clinit>(ScalaNumberDeserializersModule.scala)
  at com.fasterxml.jackson.module.scala.deser.ScalaNumberDeserializersModule$class.$init$(ScalaNumberDeserializersModule.scala:61)
  at com.fasterxml.jackson.module.scala.DefaultScalaModule.<init>(DefaultScalaModule.scala:20)
  at com.fasterxml.jackson.module.scala.DefaultScalaModule$.<init>(DefaultScalaModule.scala:37)
  at com.fasterxml.jackson.module.scala.DefaultScalaModule$.<clinit>(DefaultScalaModule.scala)
  at org.apache.spark.rdd.RDDOperationScope$.<init>(RDDOperationScope.scala:82)
  at org.apache.spark.rdd.RDDOperationScope$.<clinit>(RDDOperationScope.scala)
  at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:132)
  at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:113)
  at org.apache.spark.sql.execution.SparkPlan.getByteArrayRdd(SparkPlan.scala:225)
  at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:308)
  at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
  at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$execute$1$1.apply(Dataset.scala:2371)
  at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
  at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2765)

UPDATE3: As per the suggestion in a comment to the proposed answer below, I cleaned the class path by deleting all the files in the local repo:

rm -rf local-repo/*

I then restarted the Zeppelin server. To check the class path, I executed the following in the notebook:

val cl = ClassLoader.getSystemClassLoader
cl.asInstanceOf[java.net.URLClassLoader].getURLs.foreach(println)

This gave the following output (I include only the jackson libraries from the output here, otherwise the output is too long to paste):

...
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-annotations-2.1.1.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-annotations-2.2.3.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-core-2.1.1.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-core-2.2.3.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-core-asl-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-databind-2.1.1.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-databind-2.2.3.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-jaxrs-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-mapper-asl-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/local-repo/2CT9CPAA9/jackson-xc-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/lib/jackson-annotations-2.6.0.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/lib/jackson-core-2.6.7.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/lib/jackson-databind-2.6.7.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/jackson-annotations-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/jackson-core-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/jackson-core-asl-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/jackson-databind-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/zeppelin-0.7.2-bin-netinst/jackson-mapper-asl-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-annotations-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-core-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-core-asl-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-databind-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-jaxrs-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-mapper-asl-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-module-paranamer-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-module-scala_2.11-2.6.5.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/jackson-xc-1.9.13.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/json4s-jackson_2.11-3.2.11.jar
file:/Users/shafiquejamal/allfiles/scala/spark/spark-2.1.0-bin-hadoop2.7/jars/parquet-jackson-1.8.1.jar
...

It seems that multiple versions are fetched from the repo. Should I exclude the older versions? If so, how do I do that?

Answer 1

Use this jar versions;

aws-java-sdk-1.7.4.jar

hadoop-aws-2.6.0.jar

like in this script : https://github.com/2dmitrypavlov/sparkDocker/blob/master/zeppelin.sh do not use package but download the jars and put them in a path, let's say in "/root/jars/" then edit your zeppelin-env.sh; then run this command from zeppelin/conf dir;

echo 'export SPARK_SUBMIT_OPTIONS="--jars /root/jars/mysql-connector-java-5.1.39.jar,/root/jars/aws-java-sdk-1.7.4.jar,/root/jars/hadoop-aws-2.6.0.jar"'>>zeppelin-env.sh

after that restart zeppelin.

The code at the link above is pasted below (just in case the link becomes stale):

#!/bin/bash
# Download jars
cd /root/jars
wget http://central.maven.org/maven2/mysql/mysql-connector-java/5.1.39/mysql-connector-java-5.1.39.jar

cd /usr/share/
wget http://archive.apache.org/dist/zeppelin/zeppelin-0.7.1/zeppelin-0.7.1-bin-all.tgz
tar -zxvf zeppelin-0.7.1-bin-all.tgz
cd zeppelin-0.7.1-bin-all/conf
cp zeppelin-env.sh.template zeppelin-env.sh
echo 'export MASTER=spark://'$MASTERZ':7077'>>zeppelin-env.sh
echo 'export SPARK_SUBMIT_OPTIONS="--jars /root/jars/mysql-connector-java-5.1.39.jar,/root/jars/aws-java-sdk-1.7.4.jar,/root/jars/hadoop-aws-2.6.0.jar"'>>zeppelin-env.sh
echo 'export ZEPPELIN_NOTEBOOK_STORAGE="org.apache.zeppelin.notebook.repo.VFSNotebookRepo, org.apache.zeppelin.notebook.repo.zeppelinhub.ZeppelinHubRepo"'>>zeppelin-env.sh
echo 'export ZEPPELINHUB_API_ADDRESS="https://www.zeppelinhub.com"'>>zeppelin-env.sh
echo 'export ZEPPELIN_PORT=9999'>>zeppelin-env.sh
echo 'export SPARK_HOME=/usr/share/spark'>>zeppelin-env.sh

cd ../bin/
./zeppelin.sh

Answer 2

You are probably using a too recent Jackson version. Even spark 2.3 is still on `2.6.7. Downgrade, and make sure that all your jackson JARs are consistent.