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Study database error #30

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axlbonnet opened this issue Jan 18, 2021 · 0 comments
Open

Study database error #30

axlbonnet opened this issue Jan 18, 2021 · 0 comments

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@axlbonnet
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Stack trace to study for workflow-72EMdP

2021-01-12 16:44:56,694 [Thread-48] WARN  org.hibernate.engine.jdbc.spi.SqlExceptionHelper.logExceptions(SqlExceptionHelper.java:143) - SQL Error: 23505, SQLState: 23505
2021-01-12 16:44:56,694 [Thread-48] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper.logExceptions(SqlExceptionHelper.java:144) - Unique index or primary key violation: "PRIMARY_KEY_4 ON PUBLIC.NODES(NODE_NAME, SITE)"; SQL statement:
/* insert fr.insalyon.creatis.gasw.bean.Node */ insert into PUBLIC.Nodes (cpu_bogomips, cpu_cache_size, cpu_mhz, cpu_model_name, mem_total, ncpus, node_name, site) values (?, ?, ?, ?, ?, ?, ?, ?) [23505-196]
2021-01-12 16:44:56,695 [Thread-48] ERROR fr.insalyon.creatis.gasw.dao.hibernate.NodeData.add(NodeData.java:70) - org.hibernate.exception.ConstraintViolationException: Unique index or primary key violation: "PRIMARY_KEY_4 ON PUBLIC.NODES(NODE_NAME, SITE)"; SQL statement:
/* insert fr.insalyon.creatis.gasw.bean.Node */ insert into PUBLIC.Nodes (cpu_bogomips, cpu_cache_size, cpu_mhz, cpu_model_name, mem_total, ncpus, node_name, site) values (?, ?, ?, ?, ?, ?, ?, ?) [23505-196]
2021-01-12 16:44:56,707 [Thread-48] ERROR fr.insalyon.creatis.gasw.execution.GaswOutputParser.parseStdOut(GaswOutputParser.java:337) - [GASW Parser] Error parsing stdout /var/www/html/workflows/workflow-72EMdP/./out/gate.sh-46576096063273489.sh.out
fr.insalyon.creatis.gasw.dao.DAOException: org.hibernate.exception.ConstraintViolationException: Unique index or primary key violation: "PRIMARY_KEY_4 ON PUBLIC.NODES(NODE_NAME, SITE)"; SQL statement:
/* insert fr.insalyon.creatis.gasw.bean.Node */ insert into PUBLIC.Nodes (cpu_bogomips, cpu_cache_size, cpu_mhz, cpu_model_name, mem_total, ncpus, node_name, site) values (?, ?, ?, ?, ?, ?, ?, ?) [23505-196]
	at fr.insalyon.creatis.gasw.dao.hibernate.NodeData.add(NodeData.java:71)
	at fr.insalyon.creatis.gasw.execution.GaswOutputParser.parseStdOut(GaswOutputParser.java:321)
	at fr.insalyon.creatis.gasw.plugin.executor.dirac.execution.DiracOutputParser.getGaswOutput(DiracOutputParser.java:81)
	at fr.insalyon.creatis.gasw.execution.GaswOutputParser.run(GaswOutputParser.java:112)
Caused by: org.hibernate.exception.ConstraintViolationException: Unique index or primary key violation: "PRIMARY_KEY_4 ON PUBLIC.NODES(NODE_NAME, SITE)"; SQL statement:
/* insert fr.insalyon.creatis.gasw.bean.Node */ insert into PUBLIC.Nodes (cpu_bogomips, cpu_cache_size, cpu_mhz, cpu_model_name, mem_total, ncpus, node_name, site) values (?, ?, ?, ?, ?, ?, ?, ?) [23505-196]
	at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:128)
	at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
	at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125)
	at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:110)
	at org.hibernate.engine.jdbc.internal.proxy.AbstractStatementProxyHandler.continueInvocation(AbstractStatementProxyHandler.java:129)
	at org.hibernate.engine.jdbc.internal.proxy.AbstractProxyHandler.invoke(AbstractProxyHandler.java:81)
	at com.sun.proxy.$Proxy16.executeUpdate(Unknown Source)
	at org.hibernate.engine.jdbc.batch.internal.NonBatchingBatch.addToBatch(NonBatchingBatch.java:56)
	at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2855)
	at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3296)
	at org.hibernate.action.internal.EntityInsertAction.execute(EntityInsertAction.java:88)
	at org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:362)
	at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:354)
	at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:275)
	at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:326)
	at org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:52)
	at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1181)
	at org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:379)
	at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.beforeTransactionCommit(JdbcTransaction.java:101)
	at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:175)
	at fr.insalyon.creatis.gasw.dao.hibernate.NodeData.add(NodeData.java:66)
	... 3 more
Caused by: org.h2.jdbc.JdbcSQLException: Unique index or primary key violation: "PRIMARY_KEY_4 ON PUBLIC.NODES(NODE_NAME, SITE)"; SQL statement:
/* insert fr.insalyon.creatis.gasw.bean.Node */ insert into PUBLIC.Nodes (cpu_bogomips, cpu_cache_size, cpu_mhz, cpu_model_name, mem_total, ncpus, node_name, site) values (?, ?, ?, ?, ?, ?, ?, ?) [23505-171]
	at org.h2.message.DbException.getJdbcSQLException(DbException.java:329)
	at org.h2.message.DbException.get(DbException.java:169)
	at org.h2.message.DbException.get(DbException.java:146)
	at org.h2.index.BaseIndex.getDuplicateKeyException(BaseIndex.java:82)
	at org.h2.index.PageBtree.find(PageBtree.java:121)
	at org.h2.index.PageBtreeLeaf.addRow(PageBtreeLeaf.java:147)
	at org.h2.index.PageBtreeLeaf.addRowTry(PageBtreeLeaf.java:100)
	at org.h2.index.PageBtreeIndex.addRow(PageBtreeIndex.java:102)
	at org.h2.index.PageBtreeIndex.add(PageBtreeIndex.java:93)
	at org.h2.index.MultiVersionIndex.add(MultiVersionIndex.java:50)
	at org.h2.table.RegularTable.addRow(RegularTable.java:122)
	at org.h2.command.dml.Insert.insertRows(Insert.java:124)
	at org.h2.command.dml.Insert.update(Insert.java:84)
	at org.h2.command.CommandContainer.update(CommandContainer.java:75)
	at org.h2.command.Command.executeUpdate(Command.java:230)
	at org.h2.server.TcpServerThread.process(TcpServerThread.java:334)
	at org.h2.server.TcpServerThread.run(TcpServerThread.java:150)
	at java.lang.Thread.run(Thread.java:748)

	at org.h2.engine.SessionRemote.done(SessionRemote.java:629)
	at org.h2.command.CommandRemote.executeUpdate(CommandRemote.java:209)
	at org.h2.jdbc.JdbcPreparedStatement.executeUpdateInternal(JdbcPreparedStatement.java:164)
	at org.h2.jdbc.JdbcPreparedStatement.executeUpdate(JdbcPreparedStatement.java:150)
	at sun.reflect.GeneratedMethodAccessor50.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.hibernate.engine.jdbc.internal.proxy.AbstractStatementProxyHandler.continueInvocation(AbstractStatementProxyHandler.java:122)
	... 19 more
2021-01-12 16:44:56,717 [Thread-44] INFO  fr.insalyon.creatis.gasw.plugin.listener.healing.execution.CommandState.computeJobErrorRate(CommandState.java:326) - [Healing] Updated the jobErrorRate to 15.533980582524272
2021-01-12 16:44:56,730 [Thread-50] INFO  fr.insalyon.creatis.gasw.plugin.listener.healing.execution.CommandState.computeInvocationPartialErrorRate(CommandState.java:341) - [Healing] Updated the invocationPartialErrorRate to 16.0
2021-01-12 16:44:56,732 [Thread-41] INFO  fr.insalyon.creatis.gasw.plugin.listener.healing.execution.CommandState.computeInvocationPartialErrorRate(CommandState.java:341) - [Healing] Updated the invocationPartialErrorRate to 16.0
2021-01-12 16:44:56,738 [Thread-48] ERROR fr.insalyon.creatis.gasw.execution.GaswOutputParser.parseStdErr(GaswOutputParser.java:417) - [GASW Parser] Error parsing stderr /var/www/html/workflows/workflow-72EMdP/./err/gate.sh-46576096063273489.sh.err
java.io.IOException: Stream closed
	at java.io.BufferedWriter.ensureOpen(BufferedWriter.java:116)
	at java.io.BufferedWriter.write(BufferedWriter.java:221)
	at java.io.Writer.write(Writer.java:157)
	at fr.insalyon.creatis.gasw.execution.GaswOutputParser.parseStdErr(GaswOutputParser.java:390)
	at fr.insalyon.creatis.gasw.plugin.executor.dirac.execution.DiracOutputParser.getGaswOutput(DiracOutputParser.java:82)
	at fr.insalyon.creatis.gasw.execution.GaswOutputParser.run(GaswOutputParser.java:112)
2021-01-12 16:44:56,739 [Thread-48] INFO  fr.insalyon.creatis.gasw.plugin.listener.healing.HealingListener.jobFinished(HealingListener.java:124) - [Healing] : job gate.sh-46576096063273489.jdl finished with exit code UNDEFINED
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