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
