I got this error when restarting graphdb

./bin/graphdb [INFO ] 2016-10-14 12:56:49,848 [main | c.o.g.Config] Using 'file:/home/samur/tools/graphdb-se-7.1.0/conf/logback.xml' as logback's configuration file for graphdb [INFO ] 2016-10-14 12:56:49,918 [main | c.o.g.s.GraphDB] Starting GraphDB in workbench mode. [INFO ] 2016-10-14 12:56:52,750 [localhost-startStop-1 | c.o.g.Config] GraphDB Home directory: /home/samur/tools/graphdb-se-7.1.0 [INFO ] 2016-10-14 12:56:52,750 [localhost-startStop-1 | c.o.g.Config] GraphDB Config directory: /home/samur/tools/graphdb-se-7.1.0/conf [INFO ] 2016-10-14 12:56:52,750 [localhost-startStop-1 | c.o.g.Config] GraphDB Data directory: /home/samur/tools/graphdb-se-7.1.0/data [INFO ] 2016-10-14 12:56:52,750 [localhost-startStop-1 | c.o.g.Config] GraphDB Work directory: /home/samur/tools/graphdb-se-7.1.0/work [INFO ] 2016-10-14 12:56:52,750 [localhost-startStop-1 | c.o.g.Config] GraphDB Logs directory: /home/samur/tools/graphdb-se-7.1.0/logs [INFO ] 2016-10-14 12:56:55,375 [main | c.o.g.s.GraphDB] Started GraphDB in workbench mode at port 7200. [WARN ] 2016-10-14 12:57:04,281 [http-nio-7200-exec-10 | o.o.s.h.DirectoryLockManager] Removing invalid lock 24422@samur-desktop [INFO ] 2016-10-14 12:57:05,662 [repositories/geophy | c.o.t.OwlimSchemaRepository] Version: 7.1, revision: -684725095 [INFO ] 2016-10-14 12:57:05,663 [repositories/geophy | c.o.t.OwlimSchemaRepository] Build date: Tue Aug 09 20:30:24 CEST 2016 [INFO ] 2016-10-14 12:57:05,665 [repositories/geophy | c.o.t.OwlimSchemaRepository] License configuration: Set through Workbench or API [INFO ] 2016-10-14 12:57:05,665 [repositories/geophy | c.o.t.OwlimSchemaRepository] License file: /home/samur/tools/graphdb-se-7.1.0/work/graphdb.license [INFO ] 2016-10-14 12:57:05,669 [repositories/geophy | c.o.t.OwlimSchemaRepository] Product: GRAPHDB_SE [INFO ] 2016-10-14 12:57:05,669 [repositories/geophy | c.o.t.OwlimSchemaRepository] Licensee: geophy [INFO ] 2016-10-14 12:57:05,670 [repositories/geophy | c.o.t.OwlimSchemaRepository] Permitted use: This is an evaluation license for GraphDB SE, Copyright (c) 2016 Ontotext AD, Sofia, Bulgaria. This software can be used for evaluation purposes only and will expire on 26-11-2016. Any commercial use of this software is expressly forbidden. [INFO ] 2016-10-14 12:57:05,670 [repositories/geophy | c.o.t.OwlimSchemaRepository] Version: null [INFO ] 2016-10-14 12:57:05,670 [repositories/geophy | c.o.t.OwlimSchemaRepository] Expiry date: 26-11-2016 [INFO ] 2016-10-14 12:57:05,670 [repositories/geophy | c.o.t.OwlimSchemaRepository] Latest publication date: none [INFO ] 2016-10-14 12:57:05,670 [repositories/geophy | c.o.t.OwlimSchemaRepository] Max CPU cores: null [INFO ] 2016-10-14 12:57:05,679 [repositories/geophy | c.o.t.OwlimSchemaRepository] Started in READ/WRITE mode. [INFO ] 2016-10-14 12:57:05,679 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'partialRDFS' to default value 'false' [INFO ] 2016-10-14 12:57:05,679 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'enable-optimization' to default value 'true' [INFO ] 2016-10-14 12:57:05,680 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'checkForValidPropertiesAndClasses' to default value 'false' [INFO ] 2016-10-14 12:57:05,680 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'entity-pool-implementation' to default value 'classic' [INFO ] 2016-10-14 12:57:05,680 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'useShutdownHooks' to default value 'true' [INFO ] 2016-10-14 12:57:05,680 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'index-compression-ratio' to default value '-1' [INFO ] 2016-10-14 12:57:05,680 [repositories/geophy | c.o.GraphDBConfigParameters] Cache pages for tuples: 141487 [INFO ] 2016-10-14 12:57:05,681 [repositories/geophy | c.o.GraphDBConfigParameters] Cache pages for predicates: 70743 [INFO ] 2016-10-14 12:57:05,681 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'parallelInsertionThreadPoolSize' to default value '10' [INFO ] 2016-10-14 12:57:05,681 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'parallelInsertionBufferSize' to default value '1000000' [INFO ] 2016-10-14 12:57:05,687 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'graphdb.epool.onheap' to default value 'false' [INFO ] 2016-10-14 12:57:05,688 [repositories/geophy | c.o.t.e.EntityPoolFactory] Using entity pool implementation: classic [INFO ] 2016-10-14 12:57:05,693 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'allow-system-entities-as-data' to default value 'false' [INFO ] 2016-10-14 12:57:05,698 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'graphdb.epool.onheap' to default value 'false' [INFO ] 2016-10-14 12:57:05,698 [repositories/geophy | c.o.t.e.i.m.HashEntityMapVersion5] Restoring entity hash table... [INFO ] 2016-10-14 12:57:06,163 [repositories/geophy | c.o.t.e.i.m.HashEntityMapVersion5] Done in 464 ms. [INFO ] 2016-10-14 12:57:06,188 [repositories/geophy | c.o.c.AbstractParameter] Configured parameter 'enable-pool-reversecache' to default value 'true' [INFO ] 2016-10-14 12:57:06,228 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] Begin restoring from persistence: hashmap types array [INFO ] 2016-10-14 12:57:07,790 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 1000000 entities so far. [INFO ] 2016-10-14 12:57:09,102 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 2000000 entities so far. [INFO ] 2016-10-14 12:57:10,230 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 3000000 entities so far. [INFO ] 2016-10-14 12:57:11,236 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 4000000 entities so far. [INFO ] 2016-10-14 12:57:12,317 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 5000000 entities so far. [INFO ] 2016-10-14 12:57:13,833 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 6000000 entities so far. [INFO ] 2016-10-14 12:57:14,996 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 7000000 entities so far. [INFO ] 2016-10-14 12:57:16,136 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 8000000 entities so far. [INFO ] 2016-10-14 12:57:17,059 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 9000000 entities so far. [INFO ] 2016-10-14 12:57:17,985 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 10000000 entities so far. [INFO ] 2016-10-14 12:57:19,218 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 11000000 entities so far. [INFO ] 2016-10-14 12:57:20,664 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] 12000000 entities so far. [ERROR] 2016-10-14 12:57:21,458 [repositories/geophy | c.o.t.e.i.EntityPoolHelper] Could not rebuild hashmap from persistence. java.lang.RuntimeException: Duplicate entity "-0.343014"^^<http://www.w3.org/2001/XMLSchema#decimal>' found with ids 12582915 and 12582915 at com.ontotext.trree.entitypool.impl.EntityPoolHelper.<init>(EntityPoolHelper.java:295) at com.ontotext.trree.entitypool.impl.EntityPoolBase.createHashEntityPool(EntityPoolBase.java:46) at com.ontotext.trree.entitypool.impl.EntityPoolBase.<init>(EntityPoolBase.java:38) at com.ontotext.trree.entitypool.impl.DummieMappingToOldEntityPool.<init>(DummieMappingToOldEntityPool.java:21) at com.ontotext.trree.entitypool.EntityPoolFactory.getEntityPool(EntityPoolFactory.java:91) at com.ontotext.trree.OwlimSchemaRepository.initEntityPool(OwlimSchemaRepository.java:1299) at com.ontotext.trree.OwlimSchemaRepository.initializeInternal(OwlimSchemaRepository.java:174) at org.openrdf.sail.helpers.SailBase.initialize(SailBase.java:194) at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:163) at org.openrdf.repository.base.RepositoryBase.initialize(RepositoryBase.java:40) at org.openrdf.repository.manager.LocalRepositoryManager.createRepository(LocalRepositoryManager.java:225) at org.openrdf.repository.manager.RepositoryManager.getRepository(RepositoryManager.java:404) at org.openrdf.http.server.repository.RepositoryInterceptor.setRequestAttributes(RepositoryInterceptor.java:118) at org.openrdf.http.server.ServerInterceptor.preHandle(ServerInterceptor.java:45) at org.openrdf.http.server.repository.RepositoryInterceptor.preHandle(RepositoryInterceptor.java:98) at com.ontotext.forest.sesame.ForestRepositoryInterceptor.preHandle(ForestRepositoryInterceptor.java:41) at com.ontotext.forest.sesame.ForestRepositoryInterceptor$$FastClassBySpringCGLIB$$d99bcd9f.invoke(<generated>) at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:717) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:133) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:653) at com.ontotext.forest.sesame.ForestRepositoryInterceptor$$EnhancerBySpringCGLIB$$a1909988.preHandle(<generated>) at org.springframework.web.servlet.HandlerExecutionChain.applyPreHandle(HandlerExecutionChain.java:134) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:954) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:966) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:857) at javax.servlet.http.HttpServlet.service(HttpServlet.java:622) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:842) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at com.ontotext.forest.core.request.RequestFilter.doFilterInternal(RequestFilter.java:41) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:85) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at com.ontotext.forest.security.AdminDelegatingFilterProxy.doFilter(AdminDelegatingFilterProxy.java:29) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:522) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1095) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:672) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1500) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1456) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) [ERROR] 2016-10-14 12:57:21,460 [repositories/geophy | o.o.h.s.ProtocolExceptionResolver] Error while handling request (500) org.openrdf.http.server.ServerHTTPException: org.openrdf.repository.RepositoryException: java.lang.RuntimeException: Could not rebuild hashmap from persistence. at org.openrdf.http.server.repository.RepositoryInterceptor.setRequestAttributes(RepositoryInterceptor.java:146) at org.openrdf.http.server.ServerInterceptor.preHandle(ServerInterceptor.java:45) at org.openrdf.http.server.repository.RepositoryInterceptor.preHandle(RepositoryInterceptor.java:98) at com.ontotext.forest.sesame.ForestRepositoryInterceptor.preHandle(ForestRepositoryInterceptor.java:41) at com.ontotext.forest.sesame.ForestRepositoryInterceptor$$FastClassBySpringCGLIB$$d99bcd9f.invoke(<generated>) at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:717) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:133) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:653) at com.ontotext.forest.sesame.ForestRepositoryInterceptor$$EnhancerBySpringCGLIB$$a1909988.preHandle(<generated>) at org.springframework.web.servlet.HandlerExecutionChain.applyPreHandle(HandlerExecutionChain.java:134) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:954) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:966) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:857) at javax.servlet.http.HttpServlet.service(HttpServlet.java:622) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:842) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at com.ontotext.forest.core.request.RequestFilter.doFilterInternal(RequestFilter.java:41) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:85) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at com.ontotext.forest.security.AdminDelegatingFilterProxy.doFilter(AdminDelegatingFilterProxy.java:29) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:522) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1095) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:672) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1500) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1456) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) Caused by: org.openrdf.repository.RepositoryException: java.lang.RuntimeException: Could not rebuild hashmap from persistence. at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:172) at org.openrdf.repository.base.RepositoryBase.initialize(RepositoryBase.java:40) at org.openrdf.repository.manager.LocalRepositoryManager.createRepository(LocalRepositoryManager.java:225) at org.openrdf.repository.manager.RepositoryManager.getRepository(RepositoryManager.java:404) at org.openrdf.http.server.repository.RepositoryInterceptor.setRequestAttributes(RepositoryInterceptor.java:118) ... 50 common frames omitted Caused by: org.openrdf.sail.SailException: java.lang.RuntimeException: Could not rebuild hashmap from persistence. at com.ontotext.trree.OwlimSchemaRepository.initializeInternal(OwlimSchemaRepository.java:276) at org.openrdf.sail.helpers.SailBase.initialize(SailBase.java:194) at org.openrdf.repository.sail.SailRepository.initializeInternal(SailRepository.java:163) ... 54 common frames omitted Caused by: java.lang.RuntimeException: Could not rebuild hashmap from persistence. at com.ontotext.trree.entitypool.impl.EntityPoolHelper.<init>(EntityPoolHelper.java:333) at com.ontotext.trree.entitypool.impl.EntityPoolBase.createHashEntityPool(EntityPoolBase.java:46) at com.ontotext.trree.entitypool.impl.EntityPoolBase.<init>(EntityPoolBase.java:38) at com.ontotext.trree.entitypool.impl.DummieMappingToOldEntityPool.<init>(DummieMappingToOldEntityPool.java:21) at com.ontotext.trree.entitypool.EntityPoolFactory.getEntityPool(EntityPoolFactory.java:91) at com.ontotext.trree.OwlimSchemaRepository.initEntityPool(OwlimSchemaRepository.java:1299) at com.ontotext.trree.OwlimSchemaRepository.initializeInternal(OwlimSchemaRepository.java:174) ... 56 common frames omitted Caused by: java.lang.RuntimeException: Duplicate entity"-0.343014"^^http://www.w3.org/2001/XMLSchema#decimal' found with ids 12582915 and 12582915 at com.ontotext.trree.entitypool.impl.EntityPoolHelper.<init>(EntityPoolHelper.java:295) ... 62 common frames omitted [INFO ] 2016-10-14 12:57:21,478 [repositories/geophy | c.o.t.OwlimSchemaRepository] Version: 7.1, revision: -684725095

asked 14 Oct '16, 07:00

samur's gravatar image

samur
123
accept rate: 0%


Hi, That error is strange. You probably haven't performed a clean shutdown which has caused the rebuild of the hashmap during initialization, but still the duplication of the ids whcih are equal is a new one. Have you tried to replace over an exiting repository withouth deleting the storage first?

link

answered 17 Oct '16, 10:54

Venelin%20Kotsev's gravatar image

Venelin Kotsev
4212
accept rate: 20%

Your answer
toggle preview

Follow this question

By Email:

Once you sign in you will be able to subscribe for any updates here

By RSS:

Answers

Answers and Comments

Markdown Basics

  • *italic* or _italic_
  • **bold** or __bold__
  • link:[text](http://url.com/ "title")
  • image?![alt text](/path/img.jpg "title")
  • numbered list: 1. Foo 2. Bar
  • to add a line break simply add two spaces to where you would like the new line to be.
  • basic HTML tags are also supported

Tags:

×13

Asked: 14 Oct '16, 07:00

Seen: 223 times

Last updated: 17 Oct '16, 10:54

powered by BitNami OSQA