com.microsoft.sqlserver.jdbc.SQLServerException: Operation timed out after processing 50k records

[dvellanki]

Caused by: org.apache.flink.runtime.operators.chaining.ExceptionInChainedStubException: Exception in chained task 'FlatMap (FlatMap at Step-Read from OHDSI OMOP CDM NOTE Table via JDBC/JDBC Break Fusion/ParDo(Anonymous)2/ParMultiDo(Anonymous).output)'
at org.apache.flink.runtime.operators.chaining.ChainedFlatMapDriver.collect(ChainedFlatMapDriver.java:81) ~[flink-dist-1.18.0.jar:1.18.0]
at org.apache.flink.runtime.operators.util.metrics.CountingCollector.collect(CountingCollector.java:35) ~[flink-dist-1.18.0.jar:1.18.0]
at org.apache.beam.runners.flink.translation.functions.FlinkDoFnFunction$DoFnOutputManager.output(FlinkDoFnFunction.java:221) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner.outputWindowedValue(SimpleDoFnRunner.java:275) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner.access$900(SimpleDoFnRunner.java:85) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:423) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:411) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.ohnlp.backbone.io.Repartition$2.process(Repartition.java:35) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
Caused by: org.apache.beam.sdk.util.UserCodeException: com.microsoft.sqlserver.jdbc.SQLServerException: Operation timed out
at org.apache.beam.sdk.util.UserCodeException.wrap(UserCodeException.java:39) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.sdk.io.jdbc.JdbcIO$ReadFn$DoFnInvoker.invokeProcessElement(Unknown Source) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:211) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner.processElement(SimpleDoFnRunner.java:188) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.flink.metrics.DoFnRunnerWithMetricsUpdate.processElement(DoFnRunnerWithMetricsUpdate.java:62) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.flink.translation.functions.FlinkDoFnFunction.flatMap(FlinkDoFnFunction.java:122) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.flink.translation.functions.FlinkDoFnFunction.flatMap(FlinkDoFnFunction.java:59) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.flink.runtime.operators.chaining.ChainedFlatMapDriver.collect(ChainedFlatMapDriver.java:79) ~[flink-dist-1.18.0.jar:1.18.0]
at org.apache.flink.runtime.operators.util.metrics.CountingCollector.collect(CountingCollector.java:35) ~[flink-dist-1.18.0.jar:1.18.0]
at org.apache.beam.runners.flink.translation.functions.FlinkMultiOutputPruningFunction.flatMap(FlinkMultiOutputPruningFunction.java:60) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.flink.translation.functions.FlinkMultiOutputPruningFunction.flatMap(FlinkMultiOutputPruningFunction.java:35) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.flink.runtime.operators.chaining.ChainedFlatMapDriver.collect(ChainedFlatMapDriver.java:79) ~[flink-dist-1.18.0.jar:1.18.0]
at org.apache.flink.runtime.operators.util.metrics.CountingCollector.collect(CountingCollector.java:35) ~[flink-dist-1.18.0.jar:1.18.0]
at org.apache.beam.runners.flink.translation.functions.FlinkDoFnFunction$DoFnOutputManager.output(FlinkDoFnFunction.java:221) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner.outputWindowedValue(SimpleDoFnRunner.java:275) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner.access$900(SimpleDoFnRunner.java:85) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:423) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:411) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
at org.ohnlp.backbone.io.Repartition$2.process(Repartition.java:35) ~[blob_p-d4181180679729d5d91f014d15121541223f762e-299a7510626f2ff4190dcd6013bcab32:?]
... 18 more
Caused by: com.microsoft.sqlserver.jdbc.SQLServerException: Operation timed out