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moj-analytical-services / splink_demos

Interactive notebooks containing demonstration code of the splink library
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Pyspark issue #97

Open MarnusStoltz opened 8 months ago

MarnusStoltz commented 8 months ago

Hi there,

I am experiencing some issue with a simple Pyspark record linkage procedure. It worked in DuckDB, but I tried to scale it up but had to switch to Pyspark. So using the exact same simple case

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An error was encountered: An error occurred while calling o545.parquet. : org.apache.spark.SparkException: Job aborted. at org.apache.spark.sql.errors.QueryExecutionErrors$.jobAbortedError(QueryExecutionErrors.scala:651) at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:279) at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:193) at org.apache.spark.sql.execution.command.DataWritingCommandExec.sideEffectResult$lzycompute(commands.scala:113) at org.apache.spark.sql.execution.command.DataWritingCommandExec.sideEffectResult(commands.scala:111) at org.apache.spark.sql.execution.command.DataWritingCommandExec.executeCollect(commands.scala:125) at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.$anonfun$applyOrElse$1(QueryExecution.scala:104) at org.apache.spark.sql.catalyst.QueryPlanningTracker$.withTracker(QueryPlanningTracker.scala:107) at org.apache.spark.sql.execution.SQLExecution$.withTracker(SQLExecution.scala:224) at org.apache.spark.sql.execution.SQLExecution$.executeQuery$1(SQLExecution.scala:114) at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$7(SQLExecution.scala:139) at org.apache.spark.sql.catalyst.QueryPlanningTracker$.withTracker(QueryPlanningTracker.scala:107) at org.apache.spark.sql.execution.SQLExecution$.withTracker(SQLExecution.scala:224) at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$6(SQLExecution.scala:139) at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:245) at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$1(SQLExecution.scala:138) at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:68) at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:101) at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:97) at org.apache.spark.sql.catalyst.trees.TreeNode.$anonfun$transformDownWithPruning$1(TreeNode.scala:626) at org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(TreeNode.scala:179) at org.apache.spark.sql.catalyst.trees.TreeNode.transformDownWithPruning(TreeNode.scala:626) at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.org$apache$spark$sql$catalyst$plans$logical$AnalysisHelper$$super$transformDownWithPruning(LogicalPlan.scala:31) at org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning(AnalysisHelper.scala:267) at org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning$(AnalysisHelper.scala:263) at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:31) at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:31) at org.apache.spark.sql.catalyst.trees.TreeNode.transformDown(TreeNode.scala:602) at org.apache.spark.sql.execution.QueryExecution.eagerlyExecuteCommands(QueryExecution.scala:97) at org.apache.spark.sql.execution.QueryExecution.commandExecuted$lzycompute(QueryExecution.scala:84) at org.apache.spark.sql.execution.QueryExecution.commandExecuted(QueryExecution.scala:82) at org.apache.spark.sql.execution.QueryExecution.assertCommandExecuted(QueryExecution.scala:125) at org.apache.spark.sql.DataFrameWriter.runCommand(DataFrameWriter.scala:860) at org.apache.spark.sql.DataFrameWriter.saveToV1Source(DataFrameWriter.scala:390) at org.apache.spark.sql.DataFrameWriter.saveInternal(DataFrameWriter.scala:363) at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:239) at org.apache.spark.sql.DataFrameWriter.parquet(DataFrameWriter.scala:793) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:282) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:238) at java.lang.Thread.run(Thread.java:750) Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 1 in stage 10.0 failed 4 times, most recent failure: Lost task 1.3 in stage 10.0 (TID 48) (ip-10-19-13-49.eu-central-1.compute.internal executor 6): java.lang.RuntimeException: Failed to run command: virtualenv_application_1708424875696_0004_0/bin/python -m pip install splink at org.apache.spark.api.python.VirtualEnvFactory.execCommand(VirtualEnvFactory.scala:125) at org.apache.spark.api.python.VirtualEnvFactory.$anonfun$setupVirtualEnv$6(VirtualEnvFactory.scala:103) at org.apache.spark.api.python.VirtualEnvFactory.$anonfun$setupVirtualEnv$6$adapted(VirtualEnvFactory.scala:91) at scala.collection.immutable.List.foreach(List.scala:431) at org.apache.spark.api.python.VirtualEnvFactory.setupVirtualEnv(VirtualEnvFactory.scala:91) at org.apache.spark.api.python.PythonWorkerFactory.(PythonWorkerFactory.scala:95) at org.apache.spark.SparkEnv.$anonfun$createPythonWorker$1(SparkEnv.scala:128) at scala.collection.mutable.HashMap.getOrElseUpdate(HashMap.scala:86) at org.apache.spark.SparkEnv.createPythonWorker(SparkEnv.scala:128) at org.apache.spark.api.python.BasePythonRunner.compute(PythonRunner.scala:164) at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:65) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.UnionRDD.compute(UnionRDD.scala:106) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:52) at org.apache.spark.scheduler.Task.run(Task.scala:138) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:548) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1516) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:551) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:750)

Driver stacktrace: at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2863) at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2799) at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2798) at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62) at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2798) at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1239) at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1239) at scala.Option.foreach(Option.scala:407) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1239) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:3051) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2993) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2982) at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49) at org.apache.spark.sql.execution.adaptive.AdaptiveExecutor.checkNoFailures(AdaptiveExecutor.scala:154) at org.apache.spark.sql.execution.adaptive.AdaptiveExecutor.doRun(AdaptiveExecutor.scala:88) at org.apache.spark.sql.execution.adaptive.AdaptiveExecutor.tryRunningAndGetFuture(AdaptiveExecutor.scala:66) at org.apache.spark.sql.execution.adaptive.AdaptiveExecutor.execute(AdaptiveExecutor.scala:57) at org.apache.spark.sql.execution.adaptive.AdaptiveSparkPlanExec.$anonfun$getFinalPhysicalPlan$1(AdaptiveSparkPlanExec.scala:249) at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:779) at org.apache.spark.sql.execution.adaptive.AdaptiveSparkPlanExec.getFinalPhysicalPlan(AdaptiveSparkPlanExec.scala:248) at org.apache.spark.sql.execution.adaptive.AdaptiveSparkPlanExec.withFinalPlanUpdate(AdaptiveSparkPlanExec.scala:521) at org.apache.spark.sql.execution.adaptive.AdaptiveSparkPlanExec.doExecute(AdaptiveSparkPlanExec.scala:507) at org.apache.spark.sql.execution.SparkPlan.$anonfun$execute$1(SparkPlan.scala:213) at org.apache.spark.sql.execution.SparkPlan.$anonfun$executeQuery$1(SparkPlan.scala:251) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:248) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:209) at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:213) ... 47 more Caused by: java.lang.RuntimeException: Failed to run command: virtualenv_application_1708424875696_0004_0/bin/python -m pip install splink at org.apache.spark.api.python.VirtualEnvFactory.execCommand(VirtualEnvFactory.scala:125) at org.apache.spark.api.python.VirtualEnvFactory.$anonfun$setupVirtualEnv$6(VirtualEnvFactory.scala:103) at org.apache.spark.api.python.VirtualEnvFactory.$anonfun$setupVirtualEnv$6$adapted(VirtualEnvFactory.scala:91) at scala.collection.immutable.List.foreach(List.scala:431) at org.apache.spark.api.python.VirtualEnvFactory.setupVirtualEnv(VirtualEnvFactory.scala:91) at org.apache.spark.api.python.PythonWorkerFactory.(PythonWorkerFactory.scala:95) at org.apache.spark.SparkEnv.$anonfun$createPythonWorker$1(SparkEnv.scala:128) at scala.collection.mutable.HashMap.getOrElseUpdate(HashMap.scala:86) at org.apache.spark.SparkEnv.createPythonWorker(SparkEnv.scala:128) at org.apache.spark.api.python.BasePythonRunner.compute(PythonRunner.scala:164) at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:65) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.UnionRDD.compute(UnionRDD.scala:106) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:365) at org.apache.spark.rdd.RDD.iterator(RDD.scala:329) at org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:52) at org.apache.spark.scheduler.Task.run(Task.scala:138) at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:548) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1516) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:551) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more