Native libraries with Zeppelin and Spark

["PHELIPOT, REMY" <re...@atos.net>]

Hello,

I’am a new user of Zeppelin and I’m encountering a problem when I want to use native libraries with Spark in cluster mode. The following error message is displayed in the logs:
15/07/21 07:46:12 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker-0,5,main]
java.lang.UnsatisfiedLinkError: no xxxjni in java.library.path
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1865)
        at java.lang.Runtime.loadLibrary0(Runtime.java:870)
        at java.lang.System.loadLibrary(System.java:1119)
        at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
        at org.apache.spark.util.collection.WritablePartitionedIterator$$anon$3.<init>(WritablePartitionedPairCollection.scala:101)
        at org.apache.spark.util.collection.WritablePartitionedIterator$.fromIterator(WritablePartitionedPairCollection.scala:100)
        at org.apache.spark.util.collection.ExternalSorter.insertAll(ExternalSorter.scala:209)
        at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:62)
        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70)
        at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
        at org.apache.spark.scheduler.Task.run(Task.scala:70)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

The environment variables seem to be correctly set in spark-defaults.conf (located in the spark configuration directory):
spark.executor.extraLibraryPath=/usr/lib/:/usr/lib/jni/
spark.driver.extraLibraryPath=/usr/lib/:/usr/lib/jni/
spark.driver.extraClassPath=/usr/share/java
spark.executor.extraClassPath=/usr/share/java

If I copy the libraries in /usr/lib, the error message disappears and the code is executed without errors, but this is an ugly fix.

Do you have any solution to this problem? Is it specific to Zeppelin or Spark?

Kind regards,

Rémy

Ce message et toutes les pièces jointes (ci-après le "message") sont établis à l’intention exclusive des destinataires désignés. Il contient des informations confidentielles et pouvant être protégé par le secret professionnel. Si vous recevez ce message par erreur, merci d'en avertir immédiatement l'expéditeur et de détruire le message. Toute utilisation de ce message non conforme à sa destination, toute diffusion ou toute publication, totale ou partielle, est interdite, sauf autorisation expresse de l’émetteur. L'internet ne garantissant pas l'intégrité de ce message lors de son acheminement, Atos (et ses filiales) décline(nt) toute responsabilité au titre de son contenu. Bien que ce message ait fait l’objet d’un traitement anti-virus lors de son envoi, l’émetteur ne peut garantir l’absence totale de logiciels malveillants dans son contenu et ne pourrait être tenu pour responsable des dommages engendrés par la transmission de l’un d’eux.

This message and any attachments (the "message") are intended solely for the addressee(s). It contains confidential information, that may be privileged. If you receive this message in error, please notify the sender immediately and delete the message. Any use of the message in violation of its purpose, any dissemination or disclosure, either wholly or partially is strictly prohibited, unless it has been explicitly authorized by the sender. As its integrity cannot be secured on the internet, Atos and its subsidiaries decline any liability for the content of this message. Although the sender endeavors to maintain a computer virus-free network, the sender does not warrant that this transmission is virus-free and will not be liable for any damages resulting from any virus transmitted.