stardog-admin server start won't work after a reboot

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cla...@gmail.com

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Jan 14, 2014, 3:53:50 AM1/14/14
to sta...@clarkparsia.com
Hi,

I installed Stardog on a macbook air with OS X 10.9 and everything worked fine... until I hard reboot the machine. Then, when I want to launch the server, I have the following error:

MacBook-Air:stardog-2.0.3 look$ ./bin/stardog-admin server start

14 janv. 2014 09:46:11 com.complexible.stardog.index.disk.btree.impl.ArrayKeys <init>

ATTENTION: Invalid index metadata: 1 > 0

Guice provision errors:


1) Error injecting constructor, java.lang.ArrayIndexOutOfBoundsException: 0

  at com.complexible.stardog.security.shiro.StardogRealmURI.<init>(StardogRealmURI.java:96)

  at com.complexible.stardog.security.shiro.StardogRealmURI.class(StardogRealmURI.java:96)

  while locating com.complexible.stardog.security.shiro.StardogRealmURI

  at com.complexible.stardog.security.index.SecurityModule.configure(SecurityModule.java:91)

  while locating org.apache.shiro.realm.Realm

    for parameter 1 at com.complexible.stardog.StardogKernel.<init>(StardogKernel.java:195)

  at com.complexible.stardog.StardogKernel.class(StardogKernel.java:195)

  while locating com.complexible.stardog.StardogKernel

Caused by: java.lang.ArrayIndexOutOfBoundsException: 0

at com.complexible.stardog.index.disk.btree.impl.ArrayKeys.getFirstPage(ArrayKeys.java:185)

at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.getStartPageID(BPlusTreeImpl.java:450)

at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.iterator(BPlusTreeImpl.java:558)

at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.iterator(BPlusTreeImpl.java:442)

at com.complexible.stardog.index.AbstractNaryIndex.iterator(AbstractNaryIndex.java:79)

at com.complexible.stardog.index.IteratorBuilder$ContextFirstTernaryBuilder.build(IteratorBuilder.java:655)

at com.complexible.stardog.index.IteratorBuilder.iterator(IteratorBuilder.java:183)

at com.complexible.stardog.security.shiro.StardogRealmURI.getSecurityIndexVersion(StardogRealmURI.java:342)

at com.complexible.stardog.security.shiro.StardogRealmURI.initializeSecurityIndex(StardogRealmURI.java:243)

at com.complexible.stardog.security.shiro.StardogRealmURI.<init>(StardogRealmURI.java:109)

at com.complexible.stardog.security.shiro.StardogRealmURI.<init>(StardogRealmURI.java:96)

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)

at java.lang.reflect.Constructor.newInstance(Constructor.java:513)

at com.google.inject.internal.DefaultConstructionProxyFactory$2.newInstance(DefaultConstructionProxyFactory.java:85)

at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:85)

at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254)

at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031)

at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)

at com.google.inject.Scopes$1$1.get(Scopes.java:65)

at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)

at com.google.inject.internal.FactoryProxy.get(FactoryProxy.java:54)

at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031)

at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)

at com.google.inject.Scopes$1$1.get(Scopes.java:65)

at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)

at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38)

at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62)

at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84)

at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254)

at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031)

at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)

at com.google.inject.Scopes$1$1.get(Scopes.java:65)

at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)

at com.google.inject.internal.InjectorImpl$4$1.call(InjectorImpl.java:978)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1024)

at com.google.inject.internal.InjectorImpl$4.get(InjectorImpl.java:974)

at com.complexible.stardog.protocols.server.StardogServer.start(StardogServer.java:80)

at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:135)

at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:42)

at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55)

at com.complexible.stardog.cli.admin.CLI.main(CLI.java:230)


2) Error injecting constructor, java.lang.ArrayIndexOutOfBoundsException: 0

  at com.complexible.stardog.security.shiro.StardogRealmURI.<init>(StardogRealmURI.java:96)

  at com.complexible.stardog.security.shiro.StardogRealmURI.class(StardogRealmURI.java:96)

  while locating com.complexible.stardog.security.shiro.StardogRealmURI

    for parameter 3 at com.complexible.stardog.security.impl.SecureSystemSecurityManagerImpl.<init>(SecureSystemSecurityManagerImpl.java:81)

  while locating com.complexible.stardog.security.impl.SecureSystemSecurityManagerImpl

  at com.complexible.stardog.security.index.SecurityModule.configure(SecurityModule.java:97)

  while locating com.complexible.stardog.security.SecureSystemSecurityManager<org.openrdf.model.URI>

    for parameter 0 at com.complexible.stardog.security.impl.StardogSecurityManagerImpl.<init>(StardogSecurityManagerImpl.java:76)

  while locating com.complexible.stardog.security.impl.StardogSecurityManagerImpl

  at com.complexible.stardog.security.index.SecurityModule.configure(SecurityModule.java:99)

  while locating com.complexible.stardog.security.StardogSecurityManager

    for parameter 5 at com.complexible.stardog.StardogKernel.<init>(StardogKernel.java:195)

  at com.complexible.stardog.StardogKernel.class(StardogKernel.java:195)

  while locating com.complexible.stardog.StardogKernel

Caused by: java.lang.ArrayIndexOutOfBoundsException: 0

at com.complexible.stardog.index.disk.btree.impl.ArrayKeys.getFirstPage(ArrayKeys.java:185)

at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.getStartPageID(BPlusTreeImpl.java:450)

at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.iterator(BPlusTreeImpl.java:558)

at com.complexible.stardog.index.disk.btree.impl.BPlusTreeImpl.iterator(BPlusTreeImpl.java:442)

at com.complexible.stardog.index.AbstractNaryIndex.iterator(AbstractNaryIndex.java:79)

at com.complexible.stardog.index.IteratorBuilder$ContextFirstTernaryBuilder.build(IteratorBuilder.java:655)

at com.complexible.stardog.index.IteratorBuilder.iterator(IteratorBuilder.java:183)

at com.complexible.stardog.security.shiro.StardogRealmURI.getSecurityIndexVersion(StardogRealmURI.java:342)

at com.complexible.stardog.security.shiro.StardogRealmURI.initializeSecurityIndex(StardogRealmURI.java:243)

at com.complexible.stardog.security.shiro.StardogRealmURI.<init>(StardogRealmURI.java:109)

at com.complexible.stardog.security.shiro.StardogRealmURI.<init>(StardogRealmURI.java:96)

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)

at java.lang.reflect.Constructor.newInstance(Constructor.java:513)

at com.google.inject.internal.DefaultConstructionProxyFactory$2.newInstance(DefaultConstructionProxyFactory.java:85)

at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:85)

at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254)

at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031)

at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)

at com.google.inject.Scopes$1$1.get(Scopes.java:65)

at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)

at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38)

at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62)

at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84)

at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254)

at com.google.inject.internal.FactoryProxy.get(FactoryProxy.java:54)

at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031)

at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)

at com.google.inject.Scopes$1$1.get(Scopes.java:65)

at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)

at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38)

at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62)

at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84)

at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254)

at com.google.inject.internal.FactoryProxy.get(FactoryProxy.java:54)

at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031)

at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)

at com.google.inject.Scopes$1$1.get(Scopes.java:65)

at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)

at com.google.inject.internal.SingleParameterInjector.inject(SingleParameterInjector.java:38)

at com.google.inject.internal.SingleParameterInjector.getAll(SingleParameterInjector.java:62)

at com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:84)

at com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:254)

at com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1031)

at com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)

at com.google.inject.Scopes$1$1.get(Scopes.java:65)

at com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:40)

at com.google.inject.internal.InjectorImpl$4$1.call(InjectorImpl.java:978)

at com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1024)

at com.google.inject.internal.InjectorImpl$4.get(InjectorImpl.java:974)

at com.complexible.stardog.protocols.server.StardogServer.start(StardogServer.java:80)

at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:135)

at com.complexible.stardog.cli.impl.ServerStart.call(ServerStart.java:42)

at com.complexible.stardog.cli.CLIBase.execute(CLIBase.java:55)

at com.complexible.stardog.cli.admin.CLI.main(CLI.java:230)


2 errors


I tried to remove the lock file and to start the server on a different port with no luck. The only solution is to reinstall completely Stardog from scratch...

Any idea why I have this issue ?

Thanks,

N.

Mike Grove

unread,
Jan 16, 2014, 7:41:21 AM1/16/14
to stardog
It looks like your reboot happened mid-write, or there were changes in mem-mapped files which were not completely flushed to disk yet.

The upcoming 2.1 release has some auto-repair facilities that are able to recover from these types of checksum errors.

Cheers,

Mike
 

Thanks,

N.

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