"Page type mismatch" after removing index #109

tzaeschke · 2018-01-08T18:02:11Z

A lengthy combination of repeatedly creating/removing an index an dropping all associated instances can result in a "page type mismatch error", see Test_092_xxx:

javax.jdo.JDOFatalInternalException: Page type mismatch, expected 4/OID_INDEX (tx=0) but got 5 (tx=10). PageId=7
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
	at org.zoodb.internal.util.ReflTools.newInstance(ReflTools.java:211)
	at org.zoodb.internal.util.DBLogger.newEx(DBLogger.java:111)
	at org.zoodb.internal.util.DBLogger.newEx(DBLogger.java:102)
	at org.zoodb.internal.util.DBLogger.newFatalInternal(DBLogger.java:173)
	at org.zoodb.internal.util.DBLogger.newFatalInternal(DBLogger.java:169)
	at org.zoodb.internal.server.StorageReader.readHeader(StorageReader.java:334)
	at org.zoodb.internal.server.StorageReader.seekPage(StorageReader.java:104)
	at org.zoodb.internal.server.StorageReader.seekPageForRead(StorageReader.java:80)
	at org.zoodb.internal.server.index.AbstractPagedIndex.readPage(AbstractPagedIndex.java:173)
	at org.zoodb.internal.server.index.AbstractIndexPage.readOrCreatePage(AbstractIndexPage.java:160)
	at org.zoodb.internal.server.index.LLIndexPage.locatePageForKey(LLIndexPage.java:195)
	at org.zoodb.internal.server.index.LLIndexPage.locatePageForKeyUnique(LLIndexPage.java:167)
	at org.zoodb.internal.server.index.PagedUniqueLongLong.findValue(PagedUniqueLongLong.java:117)
	at org.zoodb.internal.server.index.PagedOidIndex.findOid(PagedOidIndex.java:224)
	at org.zoodb.internal.server.DiskAccessOneFile.readObject(DiskAccessOneFile.java:393)
	at org.zoodb.internal.server.DiskAccessOneFile.readObject(DiskAccessOneFile.java:330)
	at org.zoodb.internal.server.index.SchemaIndex.readSchemaAll(SchemaIndex.java:532)
	at org.zoodb.internal.server.DiskAccessOneFile.readSchemaAll(DiskAccessOneFile.java:177)
	at org.zoodb.internal.model1p.Node1P.connect(Node1P.java:77)
	at org.zoodb.internal.Session.<init>(Session.java:111)
	at org.zoodb.jdo.impl.PersistenceManagerImpl.<init>(PersistenceManagerImpl.java:101)
	at org.zoodb.jdo.impl.PersistenceManagerFactoryImpl.getPersistenceManager(PersistenceManagerFactoryImpl.java:97)
	at org.zoodb.test.testutil.TestTools.openPM(TestTools.java:150)
	at org.zoodb.test.testutil.TestTools.openPM(TestTools.java:144)
	at org.zoodb.test.jdo.Test_092_IndexQueryBug.test(Test_092_IndexQueryBug.java:84)
	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:497)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
	at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
	at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:538)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:760)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:460)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:206)
NestedThrowablesStackTrace:

java.lang.IllegalStateException: Some files were not closed: 1
	at org.zoodb.tools.ZooDebug.closeOpenFiles(ZooDebug.java:69)
	at org.zoodb.test.testutil.TestTools.closePM(TestTools.java:193)
	at org.zoodb.test.jdo.Test_092_IndexQueryBug.afterTest(Test_092_IndexQueryBug.java:64)
	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:497)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:33)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
	at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
	at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:538)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:760)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:460)
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:206)

The text was updated successfully, but these errors were encountered:

tzaeschke · 2018-12-18T17:30:27Z

Scheduled for 0.5.2 / 0.6.0

dominik-kopczynski · 2020-01-12T14:48:03Z

Hi there, we are running exactly into this problem. So is there any solution, because here I can't see anyone? Or are we supposed to wait until version 0.6? If we have so, what is the expected release time?

dominik-kopczynski · 2020-01-12T15:03:16Z

Ahh, it was fixed from version 0.5.1 to 0.5.2, isn't it? We still use 0.5.1.

tzaeschke · 2020-01-12T22:38:14Z

Yes, this particular issue was fixed in 0.5.2. If you are removing indexes, this may very well be fixed by using 0.5.2. Let me know if it does not.

Btw, I am currently preparing a 0.6.0, it will mainly fix issues with multiple concurrent PersistentManagers: #114 and #103 .

dominik-kopczynski · 2020-01-22T14:27:48Z

Sorry, but unfortunately we have to reopen the issue again. After recompiling our tool with ZooDB 0.5.2 we still get the "Page type mismatch" error. How can we proceed, should I provide you the corrupted database file?

The exception stack trace is:
javax.jdo.JDOFatalInternalException: Page type mismatch, expected 4/OID_INDEX (tx=0) but got 0 (tx=0). PageId=718102
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.zoodb.internal.util.ReflTools.newInstance(ReflTools.java:211)
at org.zoodb.internal.util.DBLogger.newEx(DBLogger.java:108)
at org.zoodb.internal.util.DBLogger.newEx(DBLogger.java:99)
at org.zoodb.internal.util.DBLogger.newFatalInternal(DBLogger.java:162)
at org.zoodb.internal.util.DBLogger.newFatalInternal(DBLogger.java:158)
at org.zoodb.internal.server.StorageReader.readHeader(StorageReader.java:334)
at org.zoodb.internal.server.StorageReader.seekPage(StorageReader.java:104)
at org.zoodb.internal.server.StorageReader.seekPageForRead(StorageReader.java:80)
at org.zoodb.internal.server.index.AbstractPagedIndex.readPage(AbstractPagedIndex.java:173)
at org.zoodb.internal.server.index.AbstractPagedIndex.readRoot(AbstractPagedIndex.java:160)
at org.zoodb.internal.server.index.PagedUniqueLongLong.(PagedUniqueLongLong.java:57)
at org.zoodb.internal.server.index.PagedUniqueLongLong.(PagedUniqueLongLong.java:52)
at org.zoodb.internal.server.index.IndexFactory.loadUniqueIndex(IndexFactory.java:105)
at org.zoodb.internal.server.index.PagedOidIndex.(PagedOidIndex.java:190)
at org.zoodb.internal.server.SessionManager.(SessionManager.java:148)
at org.zoodb.internal.server.SessionFactory.getSession(SessionFactory.java:88)
at org.zoodb.internal.model1p.Node1P.connect(Node1P.java:74)
at org.zoodb.internal.Session.(Session.java:112)
at org.zoodb.jdo.impl.PersistenceManagerImpl.(PersistenceManagerImpl.java:101)
at org.zoodb.jdo.impl.PersistenceManagerFactoryImpl.getPersistenceManager(PersistenceManagerFactoryImpl.java:97)
at org.zoodb.jdo.ZooJdoHelper.openDB(ZooJdoHelper.java:54)
at org.zoodb.jdo.ZooJdoHelper.openOrCreateDB(ZooJdoHelper.java:81)

tzaeschke · 2020-01-22T20:11:47Z

Yes, the database file may be helpful.
However, it would be easiest if I had a program that reproduces the problem, or does it only happen with this database file?
Could you also describe how the database got into this state, e.g. were any special operations executed, concurrent sessions, ... .

Is this still compomics-utilities? Which branch?

tzaeschke · 2020-05-03T18:53:47Z

I created a new issue #122 to cover this problem.

tzaeschke added a commit that referenced this issue Jan 8, 2018

Test issue #109

32de2f7

tzaeschke self-assigned this Jan 8, 2018

tzaeschke added the bug label Jan 8, 2018

tzaeschke added a commit that referenced this issue Dec 18, 2018

Fixed index deletion issue #109 and #110

8041049

tzaeschke closed this as completed Dec 18, 2018

tzaeschke modified the milestones: 0.5.2, 0.6.0 Dec 18, 2018

tzaeschke reopened this Jan 22, 2020

tzaeschke mentioned this issue May 3, 2020

Page type mismatch, expected 4/OID_INDEX (tx=0) but got 0, PageId=718102 #122

Closed

tzaeschke closed this as completed May 3, 2020

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"Page type mismatch" after removing index #109

"Page type mismatch" after removing index #109

tzaeschke commented Jan 8, 2018

tzaeschke commented Dec 18, 2018

dominik-kopczynski commented Jan 12, 2020

dominik-kopczynski commented Jan 12, 2020

tzaeschke commented Jan 12, 2020

dominik-kopczynski commented Jan 22, 2020 •

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tzaeschke commented Jan 22, 2020

tzaeschke commented May 3, 2020

"Page type mismatch" after removing index #109

"Page type mismatch" after removing index #109

Comments

tzaeschke commented Jan 8, 2018

tzaeschke commented Dec 18, 2018

dominik-kopczynski commented Jan 12, 2020

dominik-kopczynski commented Jan 12, 2020

tzaeschke commented Jan 12, 2020

dominik-kopczynski commented Jan 22, 2020 • edited Loading

tzaeschke commented Jan 22, 2020

tzaeschke commented May 3, 2020

dominik-kopczynski commented Jan 22, 2020 •

edited

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