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Posted to issues@iceberg.apache.org by "W-Ely (via GitHub)" <gi...@apache.org> on 2024/02/01 21:11:57 UTC
[I] Iceberg Glue - Timeouts (maybe others) can result in missing metadata_location [iceberg]
W-Ely opened a new issue, #9618:
URL: https://github.com/apache/iceberg/issues/9618
### Apache Iceberg version
1.4.2
### Query engine
Spark
### Please describe the bug 🐞
We are running on AWS EMR so the version is technically 1.4.2-amaz-0.
We found that approximately 10 seconds after the S3 file(s) were written and the Glue metadata entry updated, the S3 files were deleted but the metadata location in Glue was not reset so the current pointed at the S3 file that was removed.
We had to manually update the Glue entry correcting the current to point to the previous and update the previous to the correct previous.
Due to the current still pointing to the metadata that we deleted from S3, this stack trace was raised:
```
Exception in thread 'main'; org.apache.iceberg.exceptions.NotFoundException: Location does not exist: s3://lakehouse--managed-us-west-2--prod/main/uel_raw/push_notification/metadata/01788-f6d8e6b6-644e-4cf9-8129-65e9e03aa20e.metadata.json
at org.apache.iceberg.aws.s3.S3InputStream.openStream(S3InputStream.java:251)
at org.apache.iceberg.aws.s3.S3InputStream.positionStream(S3InputStream.java:234)
at org.apache.iceberg.aws.s3.S3InputStream.lambda$read$1(S3InputStream.java:127)
at org.apache.iceberg.util.Tasks$Builder.runTaskWithRetry(Tasks.java:413)
at org.apache.iceberg.util.Tasks$Builder.runSingleThreaded(Tasks.java:219)
at org.apache.iceberg.util.Tasks$Builder.run(Tasks.java:203)
at org.apache.iceberg.util.Tasks$Builder.run(Tasks.java:196)
at org.apache.iceberg.aws.s3.S3InputStream.retryAndThrow(S3InputStream.java:266)
at org.apache.iceberg.aws.s3.S3InputStream.read(S3InputStream.java:123)
at org.apache.iceberg.shaded.com.fasterxml.jackson.core.json.ByteSourceJsonBootstrapper.ensureLoaded(ByteSourceJsonBootstrapper.java:539)
at org.apache.iceberg.shaded.com.fasterxml.jackson.core.json.ByteSourceJsonBootstrapper.detectEncoding(ByteSourceJsonBootstrapper.java:133)
at org.apache.iceberg.shaded.com.fasterxml.jackson.core.json.ByteSourceJsonBootstrapper.constructParser(ByteSourceJsonBootstrapper.java:256)
at org.apache.iceberg.shaded.com.fasterxml.jackson.core.JsonFactory._createParser(JsonFactory.java:1744)
at org.apache.iceberg.shaded.com.fasterxml.jackson.core.JsonFactory.createParser(JsonFactory.java:1143)
at org.apache.iceberg.shaded.com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3809)
at org.apache.iceberg.TableMetadataParser.read(TableMetadataParser.java:273)
at org.apache.iceberg.TableMetadataParser.read(TableMetadataParser.java:266)
at org.apache.iceberg.BaseMetastoreTableOperations.lambda$refreshFromMetadataLocation$0(BaseMetastoreTableOperations.java:189)
at org.apache.iceberg.BaseMetastoreTableOperations.lambda$refreshFromMetadataLocation$1(BaseMetastoreTableOperations.java:208)
at org.apache.iceberg.util.Tasks$Builder.runTaskWithRetry(Tasks.java:413)
at org.apache.iceberg.util.Tasks$Builder.runSingleThreaded(Tasks.java:219)
at org.apache.iceberg.util.Tasks$Builder.run(Tasks.java:203)
at org.apache.iceberg.util.Tasks$Builder.run(Tasks.java:196)
at org.apache.iceberg.BaseMetastoreTableOperations.refreshFromMetadataLocation(BaseMetastoreTableOperations.java:208)
at org.apache.iceberg.BaseMetastoreTableOperations.refreshFromMetadataLocation(BaseMetastoreTableOperations.java:185)
at org.apache.iceberg.BaseMetastoreTableOperations.refreshFromMetadataLocation(BaseMetastoreTableOperations.java:176)
at org.apache.iceberg.aws.glue.GlueTableOperations.doRefresh(GlueTableOperations.java:141)
at org.apache.iceberg.BaseMetastoreTableOperations.refresh(BaseMetastoreTableOperations.java:97)
at org.apache.iceberg.SnapshotProducer.refresh(SnapshotProducer.java:354)
at org.apache.iceberg.SnapshotProducer.apply(SnapshotProducer.java:219)
at org.apache.iceberg.SnapshotProducer.lambda$commit$2(SnapshotProducer.java:376)
at org.apache.iceberg.util.Tasks$Builder.runTaskWithRetry(Tasks.java:413)
at org.apache.iceberg.util.Tasks$Builder.runSingleThreaded(Tasks.java:219)
at org.apache.iceberg.util.Tasks$Builder.run(Tasks.java:203)
at org.apache.iceberg.util.Tasks$Builder.run(Tasks.java:196)
at org.apache.iceberg.SnapshotProducer.commit(SnapshotProducer.java:374)
at org.apache.iceberg.spark.source.SparkWrite.commitOperation(SparkWrite.java:233)
at org.apache.iceberg.spark.source.SparkWrite.access$1300(SparkWrite.java:84)
at org.apache.iceberg.spark.source.SparkWrite$BatchAppend.commit(SparkWrite.java:296)
at org.apache.spark.sql.execution.datasources.v2.V2TableWriteExec.writeWithV2(WriteToDataSourceV2Exec.scala:399)
at org.apache.spark.sql.execution.datasources.v2.V2TableWriteExec.writeWithV2$(WriteToDataSourceV2Exec.scala:359)
at org.apache.spark.sql.execution.datasources.v2.AppendDataExec.writeWithV2(WriteToDataSourceV2Exec.scala:225)
at org.apache.spark.sql.execution.datasources.v2.V2ExistingTableWriteExec.run(WriteToDataSourceV2Exec.scala:337)
at org.apache.spark.sql.execution.datasources.v2.V2ExistingTableWriteExec.run$(WriteToDataSourceV2Exec.scala:336)
at org.apache.spark.sql.execution.datasources.v2.AppendDataExec.run(WriteToDataSourceV2Exec.scala:225)
at org.apache.spark.sql.execution.datasources.v2.V2CommandExec.result$lzycompute(V2CommandExec.scala:43)
at org.apache.spark.sql.execution.datasources.v2.V2CommandExec.result(V2CommandExec.scala:43)
at org.apache.spark.sql.execution.datasources.v2.V2CommandExec.executeCollect(V2CommandExec.scala:49)
at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.$anonfun$applyOrElse$1(QueryExecution.scala:113)
at org.apache.spark.sql.catalyst.QueryPlanningTracker$.withTracker(QueryPlanningTracker.scala:108)
at org.apache.spark.sql.execution.SQLExecution$.withTracker(SQLExecution.scala:255)
at org.apache.spark.sql.execution.SQLExecution$.executeQuery$1(SQLExecution.scala:129)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$9(SQLExecution.scala:165)
at org.apache.spark.sql.catalyst.QueryPlanningTracker$.withTracker(QueryPlanningTracker.scala:108)
at org.apache.spark.sql.execution.SQLExecution$.withTracker(SQLExecution.scala:255)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$8(SQLExecution.scala:165)
at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:276)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId$1(SQLExecution.scala:164)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:900)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:70)
at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:110)
at org.apache.spark.sql.execution.QueryExecution$$anonfun$eagerlyExecuteCommands$1.applyOrElse(QueryExecution.scala:101)
at org.apache.spark.sql.catalyst.trees.TreeNode.$anonfun$transformDownWithPruning$1(TreeNode.scala:503)
at org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(origin.scala:76)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformDownWithPruning(TreeNode.scala:503)
at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.org$apache$spark$sql$catalyst$plans$logical$AnalysisHelper$$super$transformDownWithPruning(LogicalPlan.scala:33)
at org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning(AnalysisHelper.scala:267)
at org.apache.spark.sql.catalyst.plans.logical.AnalysisHelper.transformDownWithPruning$(AnalysisHelper.scala:263)
at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:33)
at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.transformDownWithPruning(LogicalPlan.scala:33)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformDown(TreeNode.scala:479)
at org.apache.spark.sql.execution.QueryExecution.eagerlyExecuteCommands(QueryExecution.scala:101)
at org.apache.spark.sql.execution.QueryExecution.commandExecuted$lzycompute(QueryExecution.scala:88)
at org.apache.spark.sql.execution.QueryExecution.commandExecuted(QueryExecution.scala:86)
at org.apache.spark.sql.Dataset.<init>(Dataset.scala:222)
at org.apache.spark.sql.Dataset$.$anonfun$ofRows$2(Dataset.scala:102)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:900)
at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:99)
at org.apache.spark.sql.SparkSession.$anonfun$sql$4(SparkSession.scala:691)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:900)
at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:682)
at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:713)
at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:744)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.lakehouseTableUpdate(UELS3ToLakehouseWorker.scala:184)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.lakehouseWrite(UELS3ToLakehouseWorker.scala:178)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.writeData(UELS3ToLakehouseWorker.scala:137)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.$anonfun$processTable$1(UELS3ToLakehouseWorker.scala:78)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.$anonfun$processTable$1$adapted(UELS3ToLakehouseWorker.scala:73)
at scala.collection.immutable.List.foreach(List.scala:431)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.processTable(UELS3ToLakehouseWorker.scala:73)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.$anonfun$run$1(UELS3ToLakehouseWorker.scala:48)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at scala.util.Try$.apply(Try.scala:213)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.retry(UELS3ToLakehouseWorker.scala:241)
at com.remitly.lakehouse.raw.UELS3ToLakehouseWorker.run(UELS3ToLakehouseWorker.scala:48)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
Caused by: software.amazon.awssdk.services.s3.model.NoSuchKeyException: The specified key does not exist. (Service: S3, Status Code: 404, Request ID: XSE4WS8T9Z5B2T07, Extended Request ID: uEngnDPadZItGQIUd5jNzee1cAgESyUVIwmRfvFt2YgUHnE7UeGscO5fDjPrRm2m2aAu8u/vIbw=)
at software.amazon.awssdk.core.internal.http.CombinedResponseHandler.handleErrorResponse(CombinedResponseHandler.java:125)
at software.amazon.awssdk.core.internal.http.CombinedResponseHandler.handleResponse(CombinedResponseHandler.java:82)
at software.amazon.awssdk.core.internal.http.CombinedResponseHandler.handle(CombinedResponseHandler.java:60)
at software.amazon.awssdk.core.internal.http.CombinedResponseHandler.handle(CombinedResponseHandler.java:41)
at software.amazon.awssdk.core.internal.http.pipeline.stages.HandleResponseStage.execute(HandleResponseStage.java:50)
at software.amazon.awssdk.core.internal.http.pipeline.stages.HandleResponseStage.execute(HandleResponseStage.java:38)
at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptTimeoutTrackingStage.execute(ApiCallAttemptTimeoutTrackingStage.java:72)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptTimeoutTrackingStage.execute(ApiCallAttemptTimeoutTrackingStage.java:42)
at software.amazon.awssdk.core.internal.http.pipeline.stages.TimeoutExceptionHandlingStage.execute(TimeoutExceptionHandlingStage.java:78)
at software.amazon.awssdk.core.internal.http.pipeline.stages.TimeoutExceptionHandlingStage.execute(TimeoutExceptionHandlingStage.java:40)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptMetricCollectionStage.execute(ApiCallAttemptMetricCollectionStage.java:55)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptMetricCollectionStage.execute(ApiCallAttemptMetricCollectionStage.java:39)
at software.amazon.awssdk.core.internal.http.pipeline.stages.RetryableStage.execute(RetryableStage.java:81)
at software.amazon.awssdk.core.internal.http.pipeline.stages.RetryableStage.execute(RetryableStage.java:36)
at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206)
at software.amazon.awssdk.core.internal.http.StreamManagingStage.execute(StreamManagingStage.java:56)
at software.amazon.awssdk.core.internal.http.StreamManagingStage.execute(StreamManagingStage.java:36)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallTimeoutTrackingStage.executeWithTimer(ApiCallTimeoutTrackingStage.java:80)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallTimeoutTrackingStage.execute(ApiCallTimeoutTrackingStage.java:60)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallTimeoutTrackingStage.execute(ApiCallTimeoutTrackingStage.java:42)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallMetricCollectionStage.execute(ApiCallMetricCollectionStage.java:50)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallMetricCollectionStage.execute(ApiCallMetricCollectionStage.java:32)
at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206)
at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ExecutionFailureExceptionReportingStage.execute(ExecutionFailureExceptionReportingStage.java:37)
at software.amazon.awssdk.core.internal.http.pipeline.stages.ExecutionFailureExceptionReportingStage.execute(ExecutionFailureExceptionReportingStage.java:26)
at software.amazon.awssdk.core.internal.http.AmazonSyncHttpClient$RequestExecutionBuilderImpl.execute(AmazonSyncHttpClient.java:198)
at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.invoke(BaseSyncClientHandler.java:103)
at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.doExecute(BaseSyncClientHandler.java:171)
at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.lambda$execute$0(BaseSyncClientHandler.java:68)
at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.measureApiCallSuccess(BaseSyncClientHandler.java:179)
at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.execute(BaseSyncClientHandler.java:62)
at software.amazon.awssdk.core.client.handler.SdkSyncClientHandler.execute(SdkSyncClientHandler.java:52)
at software.amazon.awssdk.awscore.client.handler.AwsSyncClientHandler.execute(AwsSyncClientHandler.java:63)
at software.amazon.awssdk.services.s3.DefaultS3Client.getObject(DefaultS3Client.java:4533)
at org.apache.iceberg.aws.s3.S3InputStream.openStream(S3InputStream.java:249)
... 97 more
```
We suspect that when a Glue operation succeeds but the success isn't communicated something in this bit:
https://github.com/apache/iceberg/blob/9de693f1e7f46024f47cdc971d8603fd76d87705/core/src/main/java/org/apache/iceberg/SnapshotProducer.java#L383
doesn't work quite right.
Similar but not the same issues https://github.com/apache/iceberg/issues/9411l , https://github.com/apache/iceberg/issues/8927
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Re: [I] Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location [iceberg]
Posted by "kmurra (via GitHub)" <gi...@apache.org>.
kmurra commented on issue #9618:
URL: https://github.com/apache/iceberg/issues/9618#issuecomment-1922294340
We suspect that the check for [unknown commit status](https://github.com/apache/iceberg/blob/main/aws/src/main/java/org/apache/iceberg/aws/glue/GlueTableOperations.java#L169) in the GlueTableOperations does not account for all situations where commit status may be unknown. For example, an OperationTimeoutException without retries would assume the commit failed but should instead be unknown.
We would recommend that the commit status defaults to unknown instead of failure, and then only flip it to failure for known failures or failing the commit check.
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Re: [I] Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location [iceberg]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on issue #9618:
URL: https://github.com/apache/iceberg/issues/9618#issuecomment-2409443905
This issue has been automatically marked as stale because it has been open for 180 days with no activity. It will be closed in next 14 days if no further activity occurs. To permanently prevent this issue from being considered stale, add the label 'not-stale', but commenting on the issue is preferred when possible.
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Re: [I] Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location [iceberg]
Posted by "W-Ely (via GitHub)" <gi...@apache.org>.
W-Ely commented on issue #9618:
URL: https://github.com/apache/iceberg/issues/9618#issuecomment-3423554804
We haven't hit this case since reporting it. It would require an Iceberg change to fully fix.
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Re: [I] Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location [iceberg]
Posted by "vikas-n (via GitHub)" <gi...@apache.org>.
vikas-n commented on issue #9618:
URL: https://github.com/apache/iceberg/issues/9618#issuecomment-3419544964
Hi, was anyone able to resolve this one? I also saw this happen in our env where the data and metadata file in S3 shows as deleted but glue still pointing to the deleted metadata file. We had to do a manual rollback to previous metadata to restore the table
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Re: [I] Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location [iceberg]
Posted by "kmurra (via GitHub)" <gi...@apache.org>.
kmurra commented on issue #9618:
URL: https://github.com/apache/iceberg/issues/9618#issuecomment-1946863112
Adding a bit more results of investigation, server side timeouts are not retried. They are assigned a 4xx class error code by the SDK. However, a server side timeout may still result in a successful commit (all business logic is run and the connection times out when trying to transmit the result).
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Re: [I] Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location [iceberg]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on issue #9618:
URL: https://github.com/apache/iceberg/issues/9618#issuecomment-2440238550
This issue has been closed because it has not received any activity in the last 14 days since being marked as 'stale'
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Re: [I] Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location [iceberg]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] closed issue #9618: Iceberg Glue - Timeouts (maybe others client side error cases) can result in missing metadata_location
URL: https://github.com/apache/iceberg/issues/9618
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