org.datanucleus.exceptions.NucleusUserException: Error : Could not find API definition for name "JDO"

Question

I was trying to access hive table in mapreduce through hcatalog and facing below exception : I have googled it and try to find the root cause but could not get success so i am posting my query over here.

2016-12-01 15:48:35,855 INFO  [main] metastore.HiveMetaStore (HiveMetaStore.java:newRawStore(564)) - 0: Opening raw store with implementation class:org.apache.hadoop.hive.metastore.ObjectStore
2016-12-01 15:48:35,857 INFO  [main] metastore.ObjectStore (ObjectStore.java:initialize(325)) - ObjectStore, initialize called
2016-12-01 15:48:35,862 ERROR [main] DataNucleus.Persistence (Log4JLogger.java:error(115)) - Error : Could not find API definition for name "JDO". Perhaps you dont have the requisite datanucleus-api-XXX jar in the CLASSPATH?
Exception in thread "main" java.io.IOException: com.google.common.util.concurrent.UncheckedExecutionException: java.lang.RuntimeException: Unable to instantiate org.apache.hive.hcatalog.common.HiveClientCache$CacheableHiveMetaStoreClient
    at org.apache.hive.hcatalog.mapreduce.HCatInputFormat.setInput(HCatInputFormat.java:97)
    at org.apache.hive.hcatalog.mapreduce.HCatInputFormat.setInput(HCatInputFormat.java:51)
    at hcatalog.DriverClass.run(DriverClass.java:30)
    at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:70)
    at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:84)
    at hcatalog.DriverClass.main(DriverClass.java:48)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.apache.hadoop.util.RunJar.run(RunJar.java:221)
    at org.apache.hadoop.util.RunJar.main(RunJar.java:136)
Caused by: com.google.common.util.concurrent.UncheckedExecutionException: java.lang.RuntimeException: Unable to instantiate org.apache.hive.hcatalog.common.HiveClientCache$CacheableHiveMetaStoreClient
    at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2234)
    at com.google.common.cache.LocalCache.get(LocalCache.java:3965)
    at com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4764)
    at org.apache.hive.hcatalog.common.HiveClientCache.getOrCreate(HiveClientCache.java:227)
    at org.apache.hive.hcatalog.common.HiveClientCache.get(HiveClientCache.java:202)
    at org.apache.hive.hcatalog.common.HCatUtil.getHiveMetastoreClient(HCatUtil.java:558)
    at org.apache.hive.hcatalog.mapreduce.InitializeInput.getInputJobInfo(InitializeInput.java:104)
    at org.apache.hive.hcatalog.mapreduce.InitializeInput.setInput(InitializeInput.java:86)
    at org.apache.hive.hcatalog.mapreduce.HCatInputFormat.setInput(HCatInputFormat.java:95)
    ... 11 more
Caused by: java.lang.RuntimeException: Unable to instantiate org.apache.hive.hcatalog.common.HiveClientCache$CacheableHiveMetaStoreClient
    at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1627)
    at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.<init>(RetryingMetaStoreClient.java:80)
    at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:130)
    at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:115)
    at org.apache.hive.hcatalog.common.HiveClientCache$5.call(HiveClientCache.java:231)
    at org.apache.hive.hcatalog.common.HiveClientCache$5.call(HiveClientCache.java:227)
    at com.google.common.cache.LocalCache$LocalManualCache$1.load(LocalCache.java:4767)
    at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3568)
    at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2350)
    at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2313)
    at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2228)
    ... 19 more
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1625)
    ... 29 more
Caused by: javax.jdo.JDOFatalInternalException: Unexpected exception caught.
NestedThrowables:
java.lang.reflect.InvocationTargetException
    at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1193)
    at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:808)
    at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:701)
    at org.apache.hadoop.hive.metastore.ObjectStore.getPMF(ObjectStore.java:424)
    at org.apache.hadoop.hive.metastore.ObjectStore.getPersistenceManager(ObjectStore.java:453)
    at org.apache.hadoop.hive.metastore.ObjectStore.initialize(ObjectStore.java:327)
    at org.apache.hadoop.hive.metastore.ObjectStore.setConf(ObjectStore.java:294)
    at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:73)
    at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:133)
    at org.apache.hadoop.hive.metastore.RawStoreProxy.<init>(RawStoreProxy.java:58)
    at org.apache.hadoop.hive.metastore.RawStoreProxy.getProxy(RawStoreProxy.java:67)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.newRawStore(HiveMetaStore.java:581)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.getMS(HiveMetaStore.java:546)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.createDefaultDB(HiveMetaStore.java:612)
    at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.init(HiveMetaStore.java:398)
    at org.apache.hadoop.hive.metastore.RetryingHMSHandler.<init>(RetryingHMSHandler.java:78)
    at org.apache.hadoop.hive.metastore.RetryingHMSHandler.getProxy(RetryingHMSHandler.java:84)
    at org.apache.hadoop.hive.metastore.HiveMetaStore.newRetryingHMSHandler(HiveMetaStore.java:6396)
    at org.apache.hadoop.hive.metastore.HiveMetaStoreClient.<init>(HiveMetaStoreClient.java:236)
    at org.apache.hive.hcatalog.common.HiveClientCache$CacheableHiveMetaStoreClient.<init>(HiveClientCache.java:332)
    ... 34 more
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at javax.jdo.JDOHelper$16.run(JDOHelper.java:1965)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.jdo.JDOHelper.invoke(JDOHelper.java:1960)
    at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1166)
    ... 53 more
Caused by: org.datanucleus.exceptions.NucleusUserException: Error : Could not find API definition for name "JDO". Perhaps you dont have the requisite datanucleus-api-XXX jar in the CLASSPATH?
    at org.datanucleus.api.ApiAdapterFactory.getApiAdapter(ApiAdapterFactory.java:94)
    at org.datanucleus.AbstractNucleusContext.<init>(AbstractNucleusContext.java:115)
    at org.datanucleus.PersistenceNucleusContextImpl.<init>(PersistenceNucleusContextImpl.java:165)
    at org.datanucleus.PersistenceNucleusContextImpl.<init>(PersistenceNucleusContextImpl.java:154)
    at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.<init>(JDOPersistenceManagerFactory.java:419)
    at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.createPersistenceManagerFactory(JDOPersistenceManagerFactory.java:308)
    at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.getPersistenceManagerFactory(JDOPersistenceManagerFactory.java:217)

I am using below POM:

<?xml version="1.0"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <modelVersion>4.0.0</modelVersion>
  <groupId>hadoop</groupId>
  <artifactId>hcatlog</artifactId>
  <version>0.1</version>
  <properties>
    <main.class>hcatalog.DriverClass</main.class>
    <datanucleus.version>5.0.1</datanucleus.version>
    <hadoop.version>2.7.3</hadoop.version>
  </properties>
  <dependencies>
    <dependency>
      <groupId>org.apache.hadoop</groupId>
      <artifactId>hadoop-client</artifactId>
      <version>2.7.3</version>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.11</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.apache.mrunit</groupId>
      <artifactId>mrunit</artifactId>
      <version>1.1.0</version>
      <classifier>hadoop2</classifier>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.apache.hadoop</groupId>
      <artifactId>hadoop-minicluster</artifactId>
      <version>2.7.3</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.apache.hive.hcatalog</groupId>
      <artifactId>hive-hcatalog-core</artifactId>
      <version>2.1.0</version>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>mysql</groupId>
      <artifactId>mysql-connector-java</artifactId>
      <version>5.1.5</version>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>javax.jdo</artifactId>
      <version>3.2.0-m1</version>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-core</artifactId>
      <version>(4.1, )</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-api-jdo</artifactId>
      <version>[4.2.0-m1, )</version>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-rdbms</artifactId>
      <version>(4.1, )</version>
      <scope>runtime</scope>
    </dependency>
  </dependencies>
  <repositories>
    <repository>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
      <id>central</id>
      <name>Central Repository</name>
      <url>http://repo.maven.apache.org/maven2</url>
    </repository>
  </repositories>
  <pluginRepositories>
    <pluginRepository>
      <releases>
        <updatePolicy>never</updatePolicy>
      </releases>
      <snapshots>
        <enabled>false</enabled>
      </snapshots>
      <id>central</id>
      <name>Central Repository</name>
      <url>http://repo.maven.apache.org/maven2</url>
    </pluginRepository>
  </pluginRepositories>
  <build>
    <sourceDirectory>/home/impadmin/rampup/projects/hadoop/src</sourceDirectory>
    <scriptSourceDirectory>/home/impadmin/rampup/projects/hadoop/src/main/scripts</scriptSourceDirectory>
    <testSourceDirectory>/home/impadmin/rampup/projects/hadoop/src/test/java</testSourceDirectory>
    <outputDirectory>/home/impadmin/rampup/projects/hadoop/target/classes</outputDirectory>
    <testOutputDirectory>/home/impadmin/rampup/projects/hadoop/target/test-classes</testOutputDirectory>
    <resources>
      <resource>
        <directory>/home/impadmin/rampup/projects/hadoop/src/main/resources</directory>
      </resource>
    </resources>
    <testResources>
      <testResource>
        <directory>/home/impadmin/rampup/projects/hadoop/src/test/resources</directory>
      </testResource>
    </testResources>
    <directory>/home/impadmin/rampup/projects/hadoop/target</directory>
    <finalName>hcatlog-0.1</finalName>
    <pluginManagement>
      <plugins>
        <plugin>
          <artifactId>maven-antrun-plugin</artifactId>
          <version>1.3</version>
        </plugin>
        <plugin>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>2.2-beta-5</version>
        </plugin>
        <plugin>
          <artifactId>maven-dependency-plugin</artifactId>
          <version>2.8</version>
        </plugin>
        <plugin>
          <artifactId>maven-release-plugin</artifactId>
          <version>2.3.2</version>
        </plugin>
      </plugins>
    </pluginManagement>
    <plugins>
      <plugin>
        <artifactId>maven-assembly-plugin</artifactId>
        <version>2.2-beta-5</version>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>single</goal>
            </goals>
            <configuration>
              <archive>
                <manifest>
                  <mainClass>hcatalog.DriverClass</mainClass>
                </manifest>
              </archive>
              <descriptorRefs>
                <descriptorRef>jar-with-dependencies</descriptorRef>
              </descriptorRefs>
              <appendAssemblyId>false</appendAssemblyId>
            </configuration>
          </execution>
        </executions>
        <configuration>
          <archive>
            <manifest>
              <mainClass>hcatalog.DriverClass</mainClass>
            </manifest>
          </archive>
          <descriptorRefs>
            <descriptorRef>jar-with-dependencies</descriptorRef>
          </descriptorRefs>
          <appendAssemblyId>false</appendAssemblyId>
        </configuration>
      </plugin>
      <plugin>
        <artifactId>maven-dependency-plugin</artifactId>
        <version>2.4</version>
        <executions>
          <execution>
            <id>copy-dependencies</id>
            <phase>package</phase>
            <goals>
              <goal>copy-dependencies</goal>
            </goals>
            <configuration>
              <outputDirectory>/home/impadmin/rampup/projects/hadoop/target/jars</outputDirectory>
              <overWriteReleases>false</overWriteReleases>
              <overWriteSnapshots>false</overWriteSnapshots>
              <overWriteIfNewer>true</overWriteIfNewer>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-clean-plugin</artifactId>
        <version>2.5</version>
        <executions>
          <execution>
            <id>default-clean</id>
            <phase>clean</phase>
            <goals>
              <goal>clean</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-resources-plugin</artifactId>
        <version>2.6</version>
        <executions>
          <execution>
            <id>default-testResources</id>
            <phase>process-test-resources</phase>
            <goals>
              <goal>testResources</goal>
            </goals>
          </execution>
          <execution>
            <id>default-resources</id>
            <phase>process-resources</phase>
            <goals>
              <goal>resources</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-jar-plugin</artifactId>
        <version>2.4</version>
        <executions>
          <execution>
            <id>default-jar</id>
            <phase>package</phase>
            <goals>
              <goal>jar</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>2.5.1</version>
        <executions>
          <execution>
            <id>default-compile</id>
            <phase>compile</phase>
            <goals>
              <goal>compile</goal>
            </goals>
          </execution>
          <execution>
            <id>default-testCompile</id>
            <phase>test-compile</phase>
            <goals>
              <goal>testCompile</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>2.12.4</version>
        <executions>
          <execution>
            <id>default-test</id>
            <phase>test</phase>
            <goals>
              <goal>test</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-install-plugin</artifactId>
        <version>2.4</version>
        <executions>
          <execution>
            <id>default-install</id>
            <phase>install</phase>
            <goals>
              <goal>install</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-deploy-plugin</artifactId>
        <version>2.7</version>
        <executions>
          <execution>
            <id>default-deploy</id>
            <phase>deploy</phase>
            <goals>
              <goal>deploy</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-site-plugin</artifactId>
        <version>3.3</version>
        <executions>
          <execution>
            <id>default-site</id>
            <phase>site</phase>
            <goals>
              <goal>site</goal>
            </goals>
            <configuration>
              <outputDirectory>/home/impadmin/rampup/projects/hadoop/target/site</outputDirectory>
              <reportPlugins>
                <reportPlugin>
                  <groupId>org.apache.maven.plugins</groupId>
                  <artifactId>maven-project-info-reports-plugin</artifactId>
                </reportPlugin>
              </reportPlugins>
            </configuration>
          </execution>
          <execution>
            <id>default-deploy</id>
            <phase>site-deploy</phase>
            <goals>
              <goal>deploy</goal>
            </goals>
            <configuration>
              <outputDirectory>/home/impadmin/rampup/projects/hadoop/target/site</outputDirectory>
              <reportPlugins>
                <reportPlugin>
                  <groupId>org.apache.maven.plugins</groupId>
                  <artifactId>maven-project-info-reports-plugin</artifactId>
                </reportPlugin>
              </reportPlugins>
            </configuration>
          </execution>
        </executions>
        <configuration>
          <outputDirectory>/home/impadmin/rampup/projects/hadoop/target/site</outputDirectory>
          <reportPlugins>
            <reportPlugin>
              <groupId>org.apache.maven.plugins</groupId>
              <artifactId>maven-project-info-reports-plugin</artifactId>
            </reportPlugin>
          </reportPlugins>
        </configuration>
      </plugin>
    </plugins>
  </build>
  <reporting>
    <outputDirectory>/home/impadmin/rampup/projects/hadoop/target/site</outputDirectory>
  </reporting>
</project>

Answer 1

try replacing in pom.xml

<dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-core</artifactId>
      <version>(4.1, )</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-api-jdo</artifactId>
      <version>[4.2.0-m1, )</version>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-rdbms</artifactId>
      <version>(4.1, )</version>
      <scope>runtime</scope>
    </dependency>

with

 <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-core</artifactId>
      <version>5.0.1</version>
      <scope>runtime</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-api-jdo</artifactId>
      <version>5.0.1</version>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.datanucleus</groupId>
      <artifactId>datanucleus-rdbms</artifactId>
      <version>5.0.1</version>
      <scope>runtime</scope>
    </dependency>

and do mvn clean install