I'm using Maven and Eclipse to build my project. I'm letting Maven download all the things I need for running everything, which has worked fine up until now. I need to use the CDK library (https://github.com/egonw/cdk, http://sourceforge.net/projects/cdk/) and once I add the dependencies to my pom.xml Spark starts to complain (this is without calling any function or importing any new library into my code, only by introducing new dependencies to the pom.xml). Trying to set up a SparkContext give me the following errors in the log:
[main] DEBUG org.apache.spark.rdd.HadoopRDD - SplitLocationInfo and other new Hadoop classes are unavailable. Using the older Hadoop location info code. java.lang.ClassNotFoundException: org.apache.hadoop.mapred.InputSplitWithLocationInfo at java.net.URLClassLoader$1.run(URLClassLoader.java:366) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:425) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:358) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:191) at org.apache.spark.rdd.HadoopRDD$SplitInfoReflections.<init>(HadoopRDD.scala:381) at org.apache.spark.rdd.HadoopRDD$.liftedTree1$1(HadoopRDD.scala:391) at org.apache.spark.rdd.HadoopRDD$.<init>(HadoopRDD.scala:390) at org.apache.spark.rdd.HadoopRDD$.<clinit>(HadoopRDD.scala) at org.apache.spark.rdd.HadoopRDD.getJobConf(HadoopRDD.scala:159) at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:194) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:205) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203) at scala.Option.getOrElse(Option.scala:120) at org.apache.spark.rdd.RDD.partitions(RDD.scala:203) at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:28) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:205) at org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203) at scala.Option.getOrElse(Option.scala:120) at org.apache.spark.rdd.RDD.partitions(RDD.scala:203) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1328) at org.apache.spark.rdd.RDD.foreach(RDD.scala:765) later in the log: [Executor task launch worker-0] DEBUG org.apache.spark.deploy.SparkHadoopUtil - Couldn't find method for retrieving thread-level FileSystem input data java.lang.NoSuchMethodException: org.apache.hadoop.fs.FileSystem$Statistics.getThreadStatistics() at java.lang.Class.getDeclaredMethod(Class.java:2009) at org.apache.spark.util.Utils$.invoke(Utils.scala:1733) at org.apache.spark.deploy.SparkHadoopUtil$$anonfun$getFileSystemThreadStatistics$1.apply(SparkHadoopUtil.scala:178) at org.apache.spark.deploy.SparkHadoopUtil$$anonfun$getFileSystemThreadStatistics$1.apply(SparkHadoopUtil.scala:178) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244) at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47) at scala.collection.TraversableLike$class.map(TraversableLike.scala:244) at scala.collection.AbstractTraversable.map(Traversable.scala:105) at org.apache.spark.deploy.SparkHadoopUtil.getFileSystemThreadStatistics(SparkHadoopUtil.scala:178) at org.apache.spark.deploy.SparkHadoopUtil.getFSBytesReadOnThreadCallback(SparkHadoopUtil.scala:138) at org.apache.spark.rdd.HadoopRDD$$anon$1.<init>(HadoopRDD.scala:220) at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:210) at org.apache.spark.rdd.HadoopRDD.compute(HadoopRDD.scala:99) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263) at org.apache.spark.rdd.RDD.iterator(RDD.scala:230) at org.apache.spark.rdd.MappedRDD.compute(MappedRDD.scala:31) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263) at org.apache.spark.rdd.RDD.iterator(RDD.scala:230) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61) at org.apache.spark.scheduler.Task.run(Task.scala:56) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:196) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) There has also been issues related to "HADOOP_HOME" not being set etc., but which seems to be intermittent and only occur sometimes. After testing different versions of both CDK and Spark, I've found out that the Spark version 0.9.1 and earlier DO NOT have this problem, so there is something in the newer versions of Spark that do not play well with others... However, I need the functionality in the later versions of Spark so this do not solve my problem. Anyone willing to try to reproduce the issue can do so by adding the dependencies for CDK: <dependency> <groupId>org.openscience.cdk</groupId> <artifactId>cdk-fingerprint</artifactId> <version>1.5.10</version> </dependency> -- View this message in context: http://apache-spark-user-list.1001560.n3.nabble.com/Issues-when-combining-Spark-and-a-third-party-java-library-tp21367.html Sent from the Apache Spark User List mailing list archive at Nabble.com. --------------------------------------------------------------------- To unsubscribe, e-mail: user-unsubscr...@spark.apache.org For additional commands, e-mail: user-h...@spark.apache.org
