Error parsing conf core-default.xml While running shadow jar of geotool with Spark

1
votes

I have created a spark application that process lat/long and identifies the zone defined in custom shape files provided by client. Given this requirement, i have created a shadow jar file using maven. But when i run application via spark-submit it throws following error

WARNING: User-defined SPARK_HOME (/opt/cloudera/parcels/CDH-5.13.2-1.cdh5.13.2.p0.3/lib/spark) overrides detected (/app/cloudera/parcels/CDH-5.13.2-1.cdh5.13.2.p0.3/lib/spark). WARNING: Running spark-class from user-defined location. 18/10/19 17:41:58 INFO SparkContext: Running Spark version 1.6.0 18/10/19 17:41:59 ERROR Configuration: error parsing conf core-default.xml javax.xml.parsers.ParserConfigurationException: Feature 'http://apache.org/xml/features/xinclude' is not recognized. at org.apache.xerces.jaxp.DocumentBuilderFactoryImpl.newDocumentBuilder(Unknown Source) at org.apache.hadoop.conf.Configuration.loadResource(Configuration.java:2694) at org.apache.hadoop.conf.Configuration.loadResources(Configuration.java:2653) at org.apache.hadoop.conf.Configuration.getProps(Configuration.java:2559) at org.apache.hadoop.conf.Configuration.get(Configuration.java:1078) at org.apache.hadoop.conf.Configuration.getTrimmed(Configuration.java:1132) at org.apache.hadoop.conf.Configuration.getBoolean(Configuration.java:1540) at org.apache.hadoop.security.SecurityUtil.setConfigurationInternal(SecurityUtil.java:85) at org.apache.hadoop.security.SecurityUtil.(SecurityUtil.java:74) at org.apache.hadoop.security.UserGroupInformation.initialize(UserGroupInformation.java:316) at org.apache.hadoop.security.UserGroupInformation.ensureInitialized(UserGroupInformation.java:304) at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:891) at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:857) at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:724) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2214) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2214) at scala.Option.getOrElse(Option.scala:120) at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2214) at org.apache.spark.SparkContext.(SparkContext.scala:324) at org.apache.spark.api.java.JavaSparkContext.(JavaSparkContext.scala:59) at com.abc.xyz.ShapeFileDataProcessor.main(ShapeFileDataProcessor.java:36) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:730) at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181) at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) Exception in thread "main" java.lang.ExceptionInInitializerError at org.apache.hadoop.security.UserGroupInformation.initialize(UserGroupInformation.java:316) at org.apache.hadoop.security.UserGroupInformation.ensureInitialized(UserGroupInformation.java:304) at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:891) at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:857) at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:724) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2214) at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2214) at scala.Option.getOrElse(Option.scala:120) at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2214) at org.apache.spark.SparkContext.(SparkContext.scala:324) at org.apache.spark.api.java.JavaSparkContext.(JavaSparkContext.scala:59) at com.abc.xyz.ShapeFileDataProcessor.main(ShapeFileDataProcessor.java:36) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:730) at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181) at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) Caused by: java.lang.RuntimeException: javax.xml.parsers.ParserConfigurationException: Feature 'http://apache.org/xml/features/xinclude' is not recognized. at org.apache.hadoop.conf.Configuration.loadResource(Configuration.java:2820) at org.apache.hadoop.conf.Configuration.loadResources(Configuration.java:2653) at org.apache.hadoop.conf.Configuration.getProps(Configuration.java:2559) at org.apache.hadoop.conf.Configuration.get(Configuration.java:1078) at org.apache.hadoop.conf.Configuration.getTrimmed(Configuration.java:1132) at org.apache.hadoop.conf.Configuration.getBoolean(Configuration.java:1540) at org.apache.hadoop.security.SecurityUtil.setConfigurationInternal(SecurityUtil.java:85) at org.apache.hadoop.security.SecurityUtil.(SecurityUtil.java:74) ... 21 more Caused by: javax.xml.parsers.ParserConfigurationException: Feature 'http://apache.org/xml/features/xinclude' is not recognized. at org.apache.xerces.jaxp.DocumentBuilderFactoryImpl.newDocumentBuilder(Unknown Source) at org.apache.hadoop.conf.Configuration.loadResource(Configuration.java:2694) ... 28 more

Here is the spark-submit command

spark-submit --name ShapeFileProcessor --master yarn-client --files application.properties --conf "spark.driver.extraJavaOptions=-XX:+UseConcMarkSweepGC -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/tmp/adp-spark-stream/ " --conf "spark.eventLog.enabled=true" --conf "spark.executor.extraJavaOptions=-XX:+UseConcMarkSweepGC -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/tmp/adp-spark-stream/ " --class com.abc.xyz.ShapeFileDataProcessor CustomShapeFileAggregator-0.0.1.jar

here is code snippet from gradle for repository and dependency

    repositories {
            mavenLocal()
            maven { url 'http://maven.geo-solutions.it' }
            maven { url 'http://download.java.net/maven/2' }
            maven { url 'http://download.osgeo.org/webdav/geotools/' }
    }


   task shadowJar(type: Jar) {
     manifest {
        attributes 'Implementation-Title': 'My Application',
                   'Implementation-Version': version
     }
    baseName = project.name
    from { 
           configurations.compile.collect { 
              it.isDirectory() ? it : zipTree(it) 
           } 
         }
    with jar
  }  

dependencies {
        compile    group: 'org.geotools',    name: 'gt-shapefile',    version: '14.5'
        compile    group: 'org.geotools',    name: 'gt-swing',    version: '14.5'

        provided    group: 'org.apache.spark',  name: 'spark-core_2.10',   version: '1.6.0'
        provided    group: 'org.apache.spark',  name: 'spark-sql_2.10',    version: '1.6.0'
        provided    group: 'org.apache.spark',  name: 'spark-hive_2.10',   version: '1.6.0'
}
1
javaapache-sparkcloudera-cdhgeotools
I'm not seeing any GeoTools code in there? did you miss tag the question? – Ian Turton
Does your shadow jar include any XML parsing libraries? Perhaps there's a conflicting XML library which is conflicting with Hadoop's XML parsing libraries... – GeoMesaJim
@GeoMesaJim geotool reads the sahpe file that is in xml format. May be it has something to do with it when all code combined into shadow jar – Faisal Ahmed Siddiqui
@IanTurton I have geotool code that i integrated with spark application. When i build shadow jar without geotool dependency then this error does not occur. Hence it has certainly something todo with geotool when it combined all dependencies into shadow jar – Faisal Ahmed Siddiqui
which geotools dependencies do you have in your pom file? how did you build the shadow jar? – Ian Turton

1 Answers

0
votes

For me it was a dependency issue. There were jars of "xerces" imported from some other dependencies. Excluding these dependencies of "xerces" from my pom.xml, solved the issue.

<exclusions>
            <exclusion>
                <artifactId>xercesImpl</artifactId>
                <groupId>xerces</groupId>
            </exclusion>
            <exclusion>
                <artifactId>xmlParserAPIs</artifactId>
                <groupId>xerces</groupId>
            </exclusion>
        </exclusions>