Writing to DSE graph from EMR

Question

We are trying to write to write to a DSE graph (cassandra) from EMR and keep getting these errors. My JAR is a shaded jar with the byos dependencies. Any help would be appreciated.

java.lang.UnsatisfiedLinkError: org.apache.cassandra.utils.NativeLibraryLinux.getpid()J
    at org.apache.cassandra.utils.NativeLibraryLinux.getpid(Native Method)
    at org.apache.cassandra.utils.NativeLibraryLinux.callGetpid(NativeLibraryLinux.java:124)
    at org.apache.cassandra.utils.NativeLibrary.getProcessID(NativeLibrary.java:429)
    at org.apache.cassandra.utils.UUIDGen.hash(UUIDGen.java:386)
    at org.apache.cassandra.utils.UUIDGen.makeNode(UUIDGen.java:367)
    at org.apache.cassandra.utils.UUIDGen.makeClockSeqAndNode(UUIDGen.java:300)
    at org.apache.cassandra.utils.UUIDGen.<clinit>(UUIDGen.java:41)
    at com.datastax.bdp.graph.spark.sql.vertex.SimpleVertexIdAssigner$.simpleEdgeId(SimpleVertexIdAssigner.scala:19)
    at com.datastax.bdp.graph.spark.graphframe.DseGraphFrame$$anonfun$3.apply(DseGraphFrame.scala:417)
    at com.datastax.bdp.graph.spark.graphframe.DseGraphFrame$$anonfun$3.apply(DseGraphFrame.scala:416)
    at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
    at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
    at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$11$$anon$1.hasNext(WholeStageCodegenExec.scala:619)
    at org.apache.spark.sql.execution.columnar.CachedRDDBuilder$$anonfun$1$$anon$1.hasNext(InMemoryRelation.scala:131)
    at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:220)
    at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:298)
    at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
    at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
    at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
    at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
    at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
    at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:121)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

19/04/26 12:55:49 WARN TaskSetManager: Lost task 0.0 in stage 5.0 (TID 18, ip-10-69-16-79.vpc.internal, executor 1): java.lang.NoClassDefFoundError: Could not initialize class org.apache.cassandra.utils.UUIDGen
    at com.datastax.bdp.graph.spark.sql.vertex.SimpleVertexIdAssigner$.simpleEdgeId(SimpleVertexIdAssigner.scala:19)
    at com.datastax.bdp.graph.spark.graphframe.DseGraphFrame$$anonfun$3.apply(DseGraphFrame.scala:417)
    at com.datastax.bdp.graph.spark.graphframe.DseGraphFrame$$anonfun$3.apply(DseGraphFrame.scala:416)
    at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
    at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)

score 0 · Answer 1 · answered Apr 26 '19 at 14:40

0

Usually such errors happen when temporary directory is mounted with noexec attribute that prevents loading of the native library that is used by java driver. Usual workaround to point Java to another location for temporary files with -Djava.io.tmpdir=... flag - this location shouldn't be mounted with noexec flag.

P.S. Unfortunately I don't know much about EMR

answered Apr 26 '19 at 14:40

Alex Ott

80,552
8
87
132

thanks Alex, unfortunately that didn't work for us. – mat77 Apr 26 '19 at 17:06
Can you try to select another OS version for EMR? What is used right now? – Alex Ott Apr 26 '19 at 17:54

score 0 · Answer 2 · answered Apr 27 '19 at 19:41

0

Turned out to be a JNA issue. Added the JNA dependency as a part of the shaded jar and it worked.

<dependency>
        <groupId>net.java.dev.jna</groupId>
        <artifactId>jna</artifactId>
        <version>4.2.2</version>
</dependency>

answered Apr 27 '19 at 19:41

mat77

436
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7

Writing to DSE graph from EMR

2 Answers2