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Posted to issues@spark.apache.org by "Dmitry Goldenberg (JIRA)" <ji...@apache.org> on 2015/04/26 21:37:39 UTC
[jira] [Comment Edited] (SPARK-7154) Spark distro appears to be
pulling in incorrect protobuf classes
[ https://issues.apache.org/jira/browse/SPARK-7154?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14513217#comment-14513217 ]
Dmitry Goldenberg edited comment on SPARK-7154 at 4/26/15 7:37 PM:
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The attached output for building Spark 1.3.1 includes
[INFO] Including com.google.protobuf:protobuf-java:jar:2.5.0 in the shaded jar.
for building the assembly. Yet the classes in protobuf are different.
was (Author: dgoldenberg):
This maven output includes
[INFO] Including com.google.protobuf:protobuf-java:jar:2.5.0 in the shaded jar.
for building the assembly. Yet the classes in protobuf are different.
> Spark distro appears to be pulling in incorrect protobuf classes
> ----------------------------------------------------------------
>
> Key: SPARK-7154
> URL: https://issues.apache.org/jira/browse/SPARK-7154
> Project: Spark
> Issue Type: Bug
> Components: Build
> Affects Versions: 1.3.0
> Reporter: Dmitry Goldenberg
> Attachments: in-google-protobuf-2.5.0.zip, in-spark-1.3.1-local-build.zip, spark-1.3.1-local-build.txt
>
>
> If you download Spark via the site:
> https://spark.apache.org/downloads.html,
> for example I chose:
> http://www.apache.org/dyn/closer.cgi/spark/spark-1.3.1/spark-1.3.1-bin-hadoop2.4.tgz
> then you may see incompatibility with other libraries due to incorrect protobuf classes.
> I'm seeing such a case in my Spark Streaming job which attempts to use Apache Phoenix to update records in HBase. The job is built with with protobuf 2.5.0 dependency. However, at runtime Spark's classes take precedence in class loading and that is causing exceptions such as the following:
> java.util.concurrent.ExecutionException: java.lang.IllegalAccessError: com/google/protobuf/HBaseZeroCopyByteString
> at java.util.concurrent.FutureTask.report(FutureTask.java:122)
> at java.util.concurrent.FutureTask.get(FutureTask.java:192)
> at org.apache.hadoop.hbase.client.HTable.coprocessorService(HTable.java:1620)
> at org.apache.hadoop.hbase.client.HTable.coprocessorService(HTable.java:1577)
> at org.apache.phoenix.query.ConnectionQueryServicesImpl.metaDataCoprocessorExec(ConnectionQueryServicesImpl.java:1007)
> at org.apache.phoenix.query.ConnectionQueryServicesImpl.getTable(ConnectionQueryServicesImpl.java:1257)
> at org.apache.phoenix.schema.MetaDataClient.updateCache(MetaDataClient.java:350)
> at org.apache.phoenix.schema.MetaDataClient.updateCache(MetaDataClient.java:311)
> at org.apache.phoenix.schema.MetaDataClient.updateCache(MetaDataClient.java:307)
> at org.apache.phoenix.compile.FromCompiler$BaseColumnResolver.createTableRef(FromCompiler.java:333)
> at org.apache.phoenix.compile.FromCompiler$SingleTableColumnResolver.<init>(FromCompiler.java:237)
> at org.apache.phoenix.compile.FromCompiler$SingleTableColumnResolver.<init>(FromCompiler.java:231)
> at org.apache.phoenix.compile.FromCompiler.getResolverForMutation(FromCompiler.java:207)
> at org.apache.phoenix.compile.UpsertCompiler.compile(UpsertCompiler.java:248)
> at org.apache.phoenix.jdbc.PhoenixStatement$ExecutableUpsertStatement.compilePlan(PhoenixStatement.java:503)
> at org.apache.phoenix.jdbc.PhoenixStatement$ExecutableUpsertStatement.compilePlan(PhoenixStatement.java:494)
> at org.apache.phoenix.jdbc.PhoenixStatement$2.call(PhoenixStatement.java:295)
> at org.apache.phoenix.jdbc.PhoenixStatement$2.call(PhoenixStatement.java:288)
> at org.apache.phoenix.call.CallRunner.run(CallRunner.java:53)
> at org.apache.phoenix.jdbc.PhoenixStatement.executeMutation(PhoenixStatement.java:287)
> at org.apache.phoenix.jdbc.PhoenixStatement.execute(PhoenixStatement.java:219)
> at org.apache.phoenix.jdbc.PhoenixPreparedStatement.execute(PhoenixPreparedStatement.java:174)
> at org.apache.phoenix.jdbc.PhoenixPreparedStatement.execute(PhoenixPreparedStatement.java:179)
> at com.kona.core.upload.persistence.hdfshbase.HUploadWorkqueueHelper.updateUploadWorkqueueEntry(HUploadWorkqueueHelper.java:139)
> at com.kona.core.upload.persistence.hdfshbase.HdfsHbaseUploadPersistenceProvider.updateUploadWorkqueueEntry(HdfsHbaseUploadPersistenceProvider.java:144)
> at com.kona.pipeline.sparkplug.error.UploadEntryErrorHandlerImpl.onError(UploadEntryErrorHandlerImpl.java:62)
> at com.kona.pipeline.sparkplug.pipeline.KonaPipelineImpl.processError(KonaPipelineImpl.java:305)
> at com.kona.pipeline.sparkplug.pipeline.KonaPipelineImpl.processPipelineDocument(KonaPipelineImpl.java:208)
> at com.kona.pipeline.sparkplug.runner.KonaPipelineRunnerImpl.notifyItemReceived(KonaPipelineRunnerImpl.java:79)
> at com.kona.pipeline.streaming.spark.ProcessPartitionFunction.call(ProcessPartitionFunction.java:83)
> at com.kona.pipeline.streaming.spark.ProcessPartitionFunction.call(ProcessPartitionFunction.java:25)
> at org.apache.spark.api.java.JavaRDDLike$$anonfun$foreachPartition$1.apply(JavaRDDLike.scala:198)
> at org.apache.spark.api.java.JavaRDDLike$$anonfun$foreachPartition$1.apply(JavaRDDLike.scala:198)
> at org.apache.spark.rdd.RDD$$anonfun$foreachPartition$1.apply(RDD.scala:806)
> at org.apache.spark.rdd.RDD$$anonfun$foreachPartition$1.apply(RDD.scala:806)
> at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1497)
> at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1497)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
> at org.apache.spark.scheduler.Task.run(Task.scala:64)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:203)
> 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)
> Caused by: java.lang.IllegalAccessError: com/google/protobuf/HBaseZeroCopyByteString
> at org.apache.phoenix.query.ConnectionQueryServicesImpl$7.call(ConnectionQueryServicesImpl.java:1265)
> at org.apache.phoenix.query.ConnectionQueryServicesImpl$7.call(ConnectionQueryServicesImpl.java:1258)
> at org.apache.hadoop.hbase.client.HTable$17.call(HTable.java:1608)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> If you look at the protobuf classes inside the Spark assembly jar, they do not match (use the cmp command) the classes in the stock protobuf 2.5.0 jar:
> BoundedByteString$1.class
> BoundedByteString$BoundedByteIterator.class
> BoundedByteString.class
> ByteString$1.class
> ByteString$ByteIterator.class
> ByteString$CodedBuilder.class
> ByteString$Output.class
> ByteString.class
> CodedInputStream.class
> CodedOutputStream$OutOfSpaceException.class
> CodedOutputStream.class
> LiteralByteString$1.class
> LiteralByteString$LiteralByteIterator.class
> LiteralByteString.class
> All of these are dependency classes for HBaseZeroCopyByteString and they're incompatible which explains the java.lang.IllegalAccessError.
> What's not yet clear to me is how they can be wrong if the Spark pom specifies 2.5.0:
> <profile>
> <id>hadoop-2.4</id>
> <properties>
> <hadoop.version>2.4.0</hadoop.version>
> <protobuf.version>2.5.0</protobuf.version>
> <jets3t.version>0.9.3</jets3t.version>
> <hbase.version>0.98.7-hadoop2</hbase.version>
> <commons.math3.version>3.1.1</commons.math3.version>
> <avro.mapred.classifier>hadoop2</avro.mapred.classifier>
> <codehaus.jackson.version>1.9.13</codehaus.jackson.version>
> </properties>
> </profile>
> This looks correct and in theory should override the <protobuf.version>2.4.1</protobuf.version> specified higher up in the parent pom (https://github.com/apache/spark/blob/master/pom.xml).
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