Created
February 22, 2023 17:55
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Show first occurrence Output of !grep -a -m 1 -B 5 -A 200 OutOfMemoryError {CROMWELL_SERVER_LOG}
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| [INFO] [02/22/2023 08:52:28.908] [cromwell-system-akka.dispatchers.backend-dispatcher-4207] [akka://cromwell-system/user/cromwell-service/WorkflowManagerActor/WorkflowActor-b35166e1-eb7f-4d64-b58d-37636db405c3/WorkflowExecutionActor-b35166e1-eb7f-4d64-b58d-37636db405c3/b35166e1-eb7f-4d64-b58d-37636db405c3-SubWorkflowExecutionActor-SubWorkflow-GvsUnified:-1:1/6b303fbe-2d58-493d-a4e5-34a86b8e3366-SubWorkflowActor-SubWorkflow-GvsUnified:-1:1/6b303fbe-2d58-493d-a4e5-34a86b8e3366-SubWorkflowExecutionActor-SubWorkflow-GvsImportGenomes:-1:1/e5f30ea8-a4c9-4690-aa22-e575cdcb5996-SubWorkflowActor-SubWorkflow-GvsImportGenomes:-1:1/e5f30ea8-a4c9-4690-aa22-e575cdcb5996-EngineJobExecutionActor-GvsImportGenomes.LoadData:209:1/e5f30ea8-a4c9-4690-aa22-e575cdcb5996-BackendJobExecutionActor-GvsImportGenomes.LoadData:209:1/PipelinesApiAsyncBackendJobExecutionActor] PipelinesApiAsyncBackendJobExecutionActor [UUID(e5f30ea8)GvsImportGenomes.LoadData:209:1]: Status change from Running to Success | |
| [WARN] [02/22/2023 08:52:34.215] [cromwell-system-akka.dispatchers.service-dispatcher-53] [akka://cromwell-system/user/cromwell-service/ServiceRegistryActor/MetadataService/WriteMetadataActor] Metadata event writes have failed for the following workflows. They will be retried: e5f30ea8-a4c9-4690-aa22-e575cdcb5996: 196 | |
| [ERROR] [02/22/2023 08:52:34.215] [cromwell-system-akka.dispatchers.service-dispatcher-12] [akka://cromwell-system/user/cromwell-service/ServiceRegistryActor/MetadataService/WriteMetadataActor] WriteMetadataActor Failed to properly process data | |
| java.sql.SQLException: java.lang.OutOfMemoryError: Java heap space | |
| at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.addBatch(Unknown Source) | |
| at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.addBatch(HikariProxyPreparedStatement.java) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19(JdbcActionComponent.scala:540) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19$adapted(JdbcActionComponent.scala:538) | |
| at scala.collection.immutable.VectorStatics$.foreachRec(Vector.scala:1856) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1862) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$18(JdbcActionComponent.scala:538) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement(JdbcBackend.scala:427) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement$(JdbcBackend.scala:422) | |
| at slick.jdbc.JdbcBackend$BaseSession.withPreparedStatement(JdbcBackend.scala:491) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl.preparedInsert(JdbcActionComponent.scala:511) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.run(JdbcActionComponent.scala:536) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:28) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:25) | |
| at slick.dbio.DBIOAction$$anon$1.$anonfun$run$1(DBIOAction.scala:186) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1856) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:186) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:183) | |
| at slick.dbio.SynchronousDatabaseAction$$anon$7.run(DBIOAction.scala:486) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.liftedTree1$1(BasicBackend.scala:276) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.run(BasicBackend.scala:276) | |
| at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) | |
| at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) | |
| at java.base/java.lang.Thread.run(Thread.java:833) | |
| Caused by: org.hsqldb.HsqlException: java.lang.OutOfMemoryError: Java heap space | |
| at org.hsqldb.error.Error.error(Unknown Source) | |
| at org.hsqldb.SessionData.allocateLobForResult(Unknown Source) | |
| at org.hsqldb.Session.allocateResultLob(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.performPreExecute(Unknown Source) | |
| ... 24 more | |
| Caused by: java.lang.OutOfMemoryError: Java heap space | |
| at org.hsqldb.persist.LobStoreMem.setBlockBytes(Unknown Source) | |
| at org.hsqldb.persist.LobManager.setBytesISNormal(Unknown Source) | |
| at org.hsqldb.persist.LobManager.setBytesIS(Unknown Source) | |
| at org.hsqldb.persist.LobManager.setCharsForNewClob(Unknown Source) | |
| at org.hsqldb.SessionData.allocateLobForResult(Unknown Source) | |
| at org.hsqldb.Session.allocateResultLob(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.performPreExecute(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.addBatch(Unknown Source) | |
| at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.addBatch(HikariProxyPreparedStatement.java) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19(JdbcActionComponent.scala:540) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19$adapted(JdbcActionComponent.scala:538) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$Lambda$2699/0x000000080171c9b8.apply(Unknown Source) | |
| at scala.collection.immutable.VectorStatics$.foreachRec(Vector.scala:1856) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1862) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$18(JdbcActionComponent.scala:538) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$Lambda$2698/0x000000080171c5e8.apply(Unknown Source) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement(JdbcBackend.scala:427) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement$(JdbcBackend.scala:422) | |
| at slick.jdbc.JdbcBackend$BaseSession.withPreparedStatement(JdbcBackend.scala:491) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl.preparedInsert(JdbcActionComponent.scala:511) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.run(JdbcActionComponent.scala:536) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:28) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:25) | |
| at slick.dbio.DBIOAction$$anon$1.$anonfun$run$1(DBIOAction.scala:186) | |
| at slick.dbio.DBIOAction$$anon$1$$Lambda$2704/0x000000080171ed68.apply(Unknown Source) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1856) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:186) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:183) | |
| at slick.dbio.SynchronousDatabaseAction$$anon$7.run(DBIOAction.scala:486) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.liftedTree1$1(BasicBackend.scala:276) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.run(BasicBackend.scala:276) | |
| at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) | |
| [INFO] [02/22/2023 08:52:38.974] [cromwell-system-akka.dispatchers.engine-dispatcher-41] [akka://cromwell-system/user/cromwell-service/JobExecutionTokenDispenser] Assigned new job execution tokens to the following groups: b35166e1: 1 | |
| [ERROR] [02/22/2023 08:52:39.361] [cromwell-system-akka.dispatchers.service-dispatcher-10] [akka://cromwell-system/user/cromwell-service/ServiceRegistryActor/MetadataService/WriteMetadataActor] WriteMetadataActor Failed to properly process data | |
| java.sql.SQLException: java.lang.OutOfMemoryError: Java heap space | |
| at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.addBatch(Unknown Source) | |
| at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.addBatch(HikariProxyPreparedStatement.java) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19(JdbcActionComponent.scala:540) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19$adapted(JdbcActionComponent.scala:538) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1856) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$18(JdbcActionComponent.scala:538) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement(JdbcBackend.scala:427) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement$(JdbcBackend.scala:422) | |
| at slick.jdbc.JdbcBackend$BaseSession.withPreparedStatement(JdbcBackend.scala:491) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl.preparedInsert(JdbcActionComponent.scala:511) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.run(JdbcActionComponent.scala:536) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:28) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:25) | |
| at slick.dbio.DBIOAction$$anon$1.$anonfun$run$1(DBIOAction.scala:186) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1856) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:186) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:183) | |
| at slick.dbio.SynchronousDatabaseAction$$anon$7.run(DBIOAction.scala:486) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.liftedTree1$1(BasicBackend.scala:276) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.run(BasicBackend.scala:276) | |
| at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) | |
| at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) | |
| at java.base/java.lang.Thread.run(Thread.java:833) | |
| Caused by: org.hsqldb.HsqlException: java.lang.OutOfMemoryError: Java heap space | |
| at org.hsqldb.error.Error.error(Unknown Source) | |
| at org.hsqldb.SessionData.allocateLobForResult(Unknown Source) | |
| at org.hsqldb.Session.allocateResultLob(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.performPreExecute(Unknown Source) | |
| ... 23 more | |
| Caused by: java.lang.OutOfMemoryError: Java heap space | |
| at org.hsqldb.persist.LobStoreMem.setBlockBytes(Unknown Source) | |
| at org.hsqldb.persist.LobManager.setBytesISNormal(Unknown Source) | |
| at org.hsqldb.persist.LobManager.setBytesIS(Unknown Source) | |
| at org.hsqldb.persist.LobManager.setCharsForNewClob(Unknown Source) | |
| at org.hsqldb.SessionData.allocateLobForResult(Unknown Source) | |
| at org.hsqldb.Session.allocateResultLob(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.performPreExecute(Unknown Source) | |
| at org.hsqldb.jdbc.JDBCPreparedStatement.addBatch(Unknown Source) | |
| at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.addBatch(HikariProxyPreparedStatement.java) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19(JdbcActionComponent.scala:540) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$19$adapted(JdbcActionComponent.scala:538) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$Lambda$2699/0x000000080171c9b8.apply(Unknown Source) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1856) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.$anonfun$run$18(JdbcActionComponent.scala:538) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction$$Lambda$2698/0x000000080171c5e8.apply(Unknown Source) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement(JdbcBackend.scala:427) | |
| at slick.jdbc.JdbcBackend$SessionDef.withPreparedStatement$(JdbcBackend.scala:422) | |
| at slick.jdbc.JdbcBackend$BaseSession.withPreparedStatement(JdbcBackend.scala:491) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl.preparedInsert(JdbcActionComponent.scala:511) | |
| at slick.jdbc.JdbcActionComponent$InsertActionComposerImpl$MultiInsertAction.run(JdbcActionComponent.scala:536) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:28) | |
| at slick.jdbc.JdbcActionComponent$SimpleJdbcProfileAction.run(JdbcActionComponent.scala:25) | |
| at slick.dbio.DBIOAction$$anon$1.$anonfun$run$1(DBIOAction.scala:186) | |
| at slick.dbio.DBIOAction$$anon$1$$Lambda$2704/0x000000080171ed68.apply(Unknown Source) | |
| at scala.collection.immutable.Vector.foreach(Vector.scala:1856) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:186) | |
| at slick.dbio.DBIOAction$$anon$1.run(DBIOAction.scala:183) | |
| at slick.dbio.SynchronousDatabaseAction$$anon$7.run(DBIOAction.scala:486) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.liftedTree1$1(BasicBackend.scala:276) | |
| at slick.basic.BasicBackend$DatabaseDef$$anon$3.run(BasicBackend.scala:276) | |
| at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) | |
| at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635 |
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