Hey Running the Fuseki server in direct mode worked !
Thank you ✌ MR > On Oct 3, 2015, at 2:48 AM, Andy Seaborne <[email protected]> wrote: > > On 02/10/15 22:17, Meghan Raul wrote: >> >> Alexandre has some things he noticed in [1]. >> >> [1] https://github.com/stain/jena-docker/issues/1#issuecomment-145130229 >> <https://github.com/stain/jena-docker/issues/1#issuecomment-145130229> >> >> ✌ MR > > Looks like there is a Virtual box issue with mmapped files on /Users (which > is automatically shared between VM and host OS). > > Workaround: > Run in direct mode: > > The command line argument to switch it is --set tdb:fileMode=direct > > Andy > > PS Please could someone report back if this works ... or not ... I don't have > a setup to test it. > >> >>> On Oct 2, 2015, at 2:59 AM, Andy Seaborne <[email protected]> wrote: >>> >>> Hi, >>> >>> The project for this is: >>> https://github.com/stain/jena-docker >>> >>> Looks like you have raised an issue there which is good. >>> >>> When used in Docker, what does the /fuseki area look like after fuseki has >>> started, before any operations? >>> >>> What are the file permissions? >>> >>>> Caused by: java.io.IOException: Invalid argument >>>> at sun.nio.ch.FileChannelImpl.map0(Native Method) >>>> at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:925) >>> >>> (Sigh - this must be one of the most unhelpful messages possible!) >>> >>> All I can say about this is that it is some low issue with the first time >>> TDB attempts to set up a file. It does look like it is the first thing TDB >>> will do, hence asking about file permissions. The database files must be >>> accessible read-write. >>> >>> Andy >>> >>> On 29/09/15 20:53, Meghan Raul wrote: >>>> Hi, >>>> >>>> >>>> I am trying to run stain/jena-fuseki with a shared volume [1] and run into >>>> a weird issue. >>>> >>>> [1] https://hub.docker.com/r/stain/jena-fuseki/#data-persistence >>>> >>>> First, I start fresh: >>>> >>>> [[ >>>> mkdir /Users/meghanraul/Projects/fuseki-test/ >>>> ]] >>>> >>>> Then I start the container: >>>> >>>> [[ >>>> docker run -it -p 3030:3030 -e ADMIN_PASSWORD=12345 -v >>>> /Users/meghanraul/Projects/fuseki-test:/fuseki --rm stain/jena-fuseki >>>> ]] >>>> >>>> Then when I try to create a dataset from the web interface, I get the >>>> following error : >>>> >>>> [[ >>>> ################################### >>>> Initializing Apache Jena Fuseki >>>> >>>> >>>> ################################### >>>> [2015-09-28 22:55:30] Server INFO Fuseki 2.3.0 >>>> 2015-07-25T17:11:28+0000 >>>> [2015-09-28 22:55:30] Config INFO FUSEKI_HOME=/jena-fuseki >>>> [2015-09-28 22:55:30] Config INFO FUSEKI_BASE=/fuseki >>>> [2015-09-28 22:55:30] Servlet INFO Initializing Shiro environment >>>> [2015-09-28 22:55:30] Config INFO Shiro file: file:///fuseki/shiro.ini >>>> [2015-09-28 22:55:31] Server INFO Started 2015/09/28 22:55:31 GMT on >>>> port 3030 >>>> [2015-09-28 22:55:38] Admin INFO [1] GET >>>> http://192.168.99.100:3030/$/server >>>> [2015-09-28 22:55:38] Admin INFO [1] 200 OK (15 ms) >>>> [2015-09-28 22:55:44] Admin INFO [2] POST >>>> http://192.168.99.100:3030/$/datasets >>>> [2015-09-28 22:55:44] Admin INFO [2] Create database : name = /foobar >>>> [2015-09-28 22:55:45] Admin WARN [2] RC = 500 : caught: >>>> BlockMgrMapped.segmentAllocate: Segment = 0 >>>> org.apache.jena.assembler.exceptions.AssemblerException: caught: >>>> BlockMgrMapped.segmentAllocate: Segment = 0 >>>> doing: >>>> root: http://base/#tdb_dataset_readwrite with type: >>>> http://jena.hpl.hp.com/2008/tdb#DatasetTDB assembler class: class >>>> org.apache.jena.tdb.assembler.DatasetAssemblerTDB >>>> >>>> at >>>> org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:138) >>>> at >>>> org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:117) >>>> at >>>> org.apache.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:81) >>>> at >>>> org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:37) >>>> at >>>> org.apache.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:33) >>>> at >>>> org.apache.jena.fuseki.build.Builder.buildDataService(Builder.java:74) >>>> at >>>> org.apache.jena.fuseki.build.Builder.buildDataAccessPoint(Builder.java:59) >>>> at >>>> org.apache.jena.fuseki.mgt.ActionDatasets.execPostContainer(ActionDatasets.java:188) >>>> at >>>> org.apache.jena.fuseki.mgt.ActionContainerItem.execPost(ActionContainerItem.java:87) >>>> at >>>> org.apache.jena.fuseki.mgt.ActionContainerItem.perform(ActionContainerItem.java:62) >>>> at >>>> org.apache.jena.fuseki.mgt.ActionCtl.executeLifecycle(ActionCtl.java:76) >>>> at org.apache.jena.fuseki.mgt.ActionCtl.executeAction(ActionCtl.java:67) >>>> at >>>> org.apache.jena.fuseki.mgt.ActionCtl.execCommonWorker(ActionCtl.java:57) >>>> at >>>> org.apache.jena.fuseki.servlets.ActionBase.doCommon(ActionBase.java:79) >>>> at >>>> org.apache.jena.fuseki.mgt.ActionContainerItem.doPost(ActionContainerItem.java:42) >>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:707) >>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) >>>> at >>>> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:717) >>>> at >>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1644) >>>> at >>>> org.apache.jena.fuseki.servlets.FusekiFilter.doFilter(FusekiFilter.java:80) >>>> at >>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1632) >>>> at >>>> org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) >>>> at >>>> org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) >>>> at >>>> org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) >>>> at >>>> org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) >>>> at >>>> org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) >>>> at >>>> org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) >>>> at >>>> org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) >>>> at >>>> org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) >>>> at >>>> org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) >>>> at >>>> org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449) >>>> at >>>> org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365) >>>> at >>>> org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) >>>> at >>>> org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) >>>> at >>>> org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) >>>> at >>>> org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362) >>>> at >>>> org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125) >>>> at >>>> org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1624) >>>> at >>>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:550) >>>> at >>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) >>>> at >>>> org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:568) >>>> at >>>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221) >>>> at >>>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1110) >>>> at >>>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:479) >>>> at >>>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:183) >>>> at >>>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1044) >>>> at >>>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) >>>> at >>>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) >>>> at org.eclipse.jetty.server.Server.handle(Server.java:459) >>>> at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:281) >>>> at >>>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:232) >>>> at >>>> org.eclipse.jetty.io.AbstractConnection$1.run(AbstractConnection.java:505) >>>> at >>>> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:607) >>>> at >>>> org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:536) >>>> at java.lang.Thread.run(Thread.java:745) >>>> Caused by: org.apache.jena.tdb.base.file.FileException: >>>> BlockMgrMapped.segmentAllocate: Segment = 0 >>>> at >>>> org.apache.jena.tdb.base.file.BlockAccessMapped.allocSegment(BlockAccessMapped.java:231) >>>> at >>>> org.apache.jena.tdb.base.file.BlockAccessMapped.getByteBuffer(BlockAccessMapped.java:157) >>>> at >>>> org.apache.jena.tdb.base.file.BlockAccessMapped.allocate(BlockAccessMapped.java:85) >>>> at >>>> org.apache.jena.tdb.base.block.BlockMgrFileAccess.allocate(BlockMgrFileAccess.java:50) >>>> at >>>> org.apache.jena.tdb.base.block.BlockMgrBase.allocate(BlockMgrBase.java:44) >>>> at >>>> org.apache.jena.tdb.base.block.BlockMgrWrapper.allocate(BlockMgrWrapper.java:46) >>>> at >>>> org.apache.jena.tdb.base.block.BlockMgrFreeChain.allocate(BlockMgrFreeChain.java:48) >>>> at >>>> org.apache.jena.tdb.base.page.PageBlockMgr.create(PageBlockMgr.java:51) >>>> at >>>> org.apache.jena.tdb.index.bplustree.BPTreeRecordsMgr.create(BPTreeRecordsMgr.java:79) >>>> at >>>> org.apache.jena.tdb.index.bplustree.BPTreeNodeMgr.createEmptyBPT(BPTreeNodeMgr.java:52) >>>> at >>>> org.apache.jena.tdb.index.bplustree.BPlusTree.createIfAbsent(BPlusTree.java:213) >>>> at >>>> org.apache.jena.tdb.index.bplustree.BPlusTree.create(BPlusTree.java:139) >>>> at >>>> org.apache.jena.tdb.index.BuilderStdIndex$RangeIndexBuilderStd.createBPTree(BuilderStdIndex.java:94) >>>> at >>>> org.apache.jena.tdb.index.BuilderStdIndex$RangeIndexBuilderStd.buildRangeIndex(BuilderStdIndex.java:65) >>>> at >>>> org.apache.jena.tdb.index.BuilderStdIndex$IndexBuilderStd.buildIndex(BuilderStdIndex.java:47) >>>> at >>>> org.apache.jena.tdb.setup.BuilderStdDB$NodeTableBuilderStd.buildNodeTable(BuilderStdDB.java:72) >>>> at >>>> org.apache.jena.tdb.setup.DatasetBuilderStd$NodeTableBuilderRecorder.buildNodeTable(DatasetBuilderStd.java:423) >>>> at >>>> org.apache.jena.tdb.setup.DatasetBuilderStd.makeNodeTable(DatasetBuilderStd.java:323) >>>> at >>>> org.apache.jena.tdb.setup.DatasetBuilderStd.buildWorker(DatasetBuilderStd.java:204) >>>> at >>>> org.apache.jena.tdb.setup.DatasetBuilderStd._build(DatasetBuilderStd.java:198) >>>> at >>>> org.apache.jena.tdb.setup.DatasetBuilderStd.build(DatasetBuilderStd.java:187) >>>> at >>>> org.apache.jena.tdb.setup.DatasetBuilderStd.create(DatasetBuilderStd.java:91) >>>> at org.apache.jena.tdb.StoreConnection.make(StoreConnection.java:228) >>>> at org.apache.jena.tdb.StoreConnection.make(StoreConnection.java:235) >>>> at >>>> org.apache.jena.tdb.transaction.DatasetGraphTransaction.<init>(DatasetGraphTransaction.java:73) >>>> at org.apache.jena.tdb.sys.TDBMaker._create(TDBMaker.java:58) >>>> at >>>> org.apache.jena.tdb.sys.TDBMaker.createDatasetGraphTransaction(TDBMaker.java:46) >>>> at >>>> org.apache.jena.tdb.TDBFactory._createDatasetGraph(TDBFactory.java:82) >>>> at org.apache.jena.tdb.TDBFactory.createDatasetGraph(TDBFactory.java:64) >>>> at >>>> org.apache.jena.tdb.assembler.DatasetAssemblerTDB.make(DatasetAssemblerTDB.java:57) >>>> at >>>> org.apache.jena.tdb.assembler.DatasetAssemblerTDB.createDataset(DatasetAssemblerTDB.java:48) >>>> at >>>> org.apache.jena.sparql.core.assembler.DatasetAssembler.open(DatasetAssembler.java:45) >>>> at >>>> org.apache.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:130) >>>> ... 54 more >>>> Caused by: java.io.IOException: Invalid argument >>>> at sun.nio.ch.FileChannelImpl.map0(Native Method) >>>> at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:925) >>>> at >>>> org.apache.jena.tdb.base.file.BlockAccessMapped.allocSegment(BlockAccessMapped.java:223) >>>> ... 86 more >>>> [2015-09-28 22:55:45] Admin INFO [2] 500 caught: >>>> BlockMgrMapped.segmentAllocate: Segment = 0 (625 ms) >>>> ]] >>>> >>>> The same operation works ok when using fuseki outside of the container. >>>> >>>> Note: I have the same problem when using stain/jena-fuseki:devel. >>>> >>>> Anybody has an idea of what's going on? >>>> >>>> Thanks, >>>> Meghan >>>> >>> >> >> >
