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Unable to start server: (javax.transaction.SystemExcep tion: TM has encountered some problem)
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Justin Pincar  
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 More options Aug 9 2012, 7:08 pm
From: Justin Pincar <justinpin...@gmail.com>
Date: Thu, 9 Aug 2012 16:08:30 -0700 (PDT)
Local: Thurs, Aug 9 2012 7:08 pm
Subject: Unable to start server: (javax.transaction.SystemException: TM has encountered some problem)
Print | Individual message | Show original | Report this message | Find messages by this author

I'm just starting with neo4j and running into some issues, and was hoping
to get some help here.

I created a graph with about 600k nodes and 11M relationships - I have
plenty of disk space left. I have three types of nodes and two indices. My
data import script seemed to be running fine, and then inexplicably
starting returning 400s.

I googled parts of the stack trace but couldn't find any relevant details.
Every time I try to start the server I get the trace below.

Any help would be greatly appreciated. Thanks!

- Justin

21:14:04.884 [18183221@qtp-11467963-4103] ERROR org.mortbay.log -
/db/data/node
org.neo4j.graphdb.TransactionFailureException: Unable to begin transaction
        at
org.neo4j.kernel.InternalAbstractGraphDatabase.beginTx(InternalAbstractGrap hDatabase.java:747)
~[neo4j-kernel-1.8.M06.jar:1.8.M06]
        at
org.neo4j.kernel.TransactionBuilderImpl.begin(TransactionBuilderImpl.java:3 9)
~[neo4j-kernel-1.8.M06.jar:1.8.M06]
        at
org.neo4j.server.rest.web.DatabaseActions.beginTx(DatabaseActions.java:228)
~[neo4j-server-1.8.M06.jar:1.8.M06]
        at
org.neo4j.server.rest.web.DatabaseActions.createNode(DatabaseActions.java:2 10)
~[neo4j-server-1.8.M06.jar:1.8.M06]
        at
org.neo4j.server.rest.web.RestfulGraphDatabase.createNode(RestfulGraphDatab ase.java:195)
~[neo4j-server-1.8.M06.jar:1.8.M06]
        at sun.reflect.GeneratedMethodAccessor83.invoke(Unknown Source)
~[na:na]
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImp l.java:43)
~[na:1.6.0_20]
        at java.lang.reflect.Method.invoke(Method.java:616) ~[na:1.6.0_20]
        at
com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodIn vokerFactory.java:60)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDisp atchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchPro vider.java:205)
~[jersey-server-1.9.jar:1.9]        at
com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatch er.dispatch(ResourceJavaMethodDispatcher.java:75)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.j ava:288)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPath Rule.java:147)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClass Rule.java:108)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPath Rule.java:147)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootRes ourceClassesRule.java:84)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(We bApplicationImpl.java:1469)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(We bApplicationImpl.java:1400)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(Web ApplicationImpl.java:1349)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(Web ApplicationImpl.java:1339)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java :416)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContai ner.java:537)
~[jersey-server-1.9.jar:1.9]
        at
com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContai ner.java:699)
~[jersey-server-1.9.jar:1.9]
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:820)
~[servlet-api-2.5-20081211.jar:na]
        at
org.mortbay.jetty.servlet.ServletHolder.handle(ServletHolder.java:511)
~[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandle r.java:1166)
~[jetty-6.1.25.jar:6.1.25]
        at
org.neo4j.server.statistic.StatisticFilter.doFilter(StatisticFilter.java:62 )
~[neo4j-server-1.8.M06.jar:1.8.M06]
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandle r.java:1157)
~[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
~[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:1 14)
[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
[jetty-6.1.25.jar:6.1.25]
        at org.mortbay.jetty.Server.handle(Server.java:326)
[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.jetty.HttpConnection$RequestHandler.content(HttpConnection.java :943)
[jetty-6.1.25.jar:6.1.25]
        at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:756)
[jetty-6.1.25.jar:6.1.25]
        at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
[jetty-6.1.25.jar:6.1.25]
        at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:410 )
[jetty-6.1.25.jar:6.1.25]
        at
org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:58 2)
[jetty-util-6.1.25.jar:6.1.25]
Caused by: javax.transaction.SystemException: TM has encountered some
problem, please perform neccesary action (tx recovery/restart)
        at
org.neo4j.kernel.impl.transaction.TxManager.assertTmOk(TxManager.java:362)
~[neo4j-kernel-1.8.M06.jar:1.8.M06]
        at
org.neo4j.kernel.impl.transaction.TxManager.begin(TxManager.java:339)
~[neo4j-kernel-1.8.M06.jar:1.8.M06]
        at
org.neo4j.kernel.InternalAbstractGraphDatabase.beginTx(InternalAbstractGrap hDatabase.java:742)
~[neo4j-kernel-1.8.M06.jar:1.8.M06]
        ... 40 common frames omitted


 
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Michael Hunger  
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 More options Aug 9 2012, 10:01 pm
From: Michael Hunger <michael.hun...@neotechnology.com>
Date: Fri, 10 Aug 2012 04:01:11 +0200
Local: Thurs, Aug 9 2012 10:01 pm
Subject: Re: [Neo4j] Unable to start server: (javax.transaction.SystemException: TM has encountered some problem)
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Justin,

could you please share your servers data/graph.db/messages.log
as well as the logs in data/log ?

And please don't delete the database (yet) we might ask you for it.

Thanks a lot

Michael

Am 10.08.2012 um 01:08 schrieb Justin Pincar:


 
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Justin Pincar  
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 More options Aug 12 2012, 1:07 pm
From: Justin Pincar <justinpin...@gmail.com>
Date: Sun, 12 Aug 2012 10:07:50 -0700 (PDT)
Local: Sun, Aug 12 2012 1:07 pm
Subject: Re: [Neo4j] Unable to start server: (javax.transaction.SystemException: TM has encountered some problem)
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Hi Michael,

I've uploaded the logs to S3:

http://justinpincar-public.s3.amazonaws.com/neo4j/console.log
http://justinpincar-public.s3.amazonaws.com/neo4j/messages.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.0.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.1.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.2.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.3.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.4.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.5.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.6.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.7.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.8.log
http://justinpincar-public.s3.amazonaws.com/neo4j/neo4j.0.9.log

Let me know if there's anything else you need. Thanks for taking a look!

- Justin


 
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Jacob Hansson  
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 More options Aug 28 2012, 6:12 am
From: Jacob Hansson <jacob.hans...@neotechnology.com>
Date: Tue, 28 Aug 2012 03:12:23 -0700 (PDT)
Local: Tues, Aug 28 2012 6:12 am
Subject: Re: [Neo4j] Unable to start server: (javax.transaction.SystemException: TM has encountered some problem)
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Hey Justin, thanks for uploading the logs.

Looking at the messages.log, two items stick out. One is the amount of GC
pauses you are seeing, you might want to look into tuning your garbage
collector. Specifically, try and make sure there are available cores for
the GC thread (by for instance limiting the number of threads given to
jetty in the neo4j server config), it seems it is getting paused by the OS
almost constantly.

The other issue, which appears to be the cause of your Transaction Manager
(TM) problems, is that Lucene has broken with this exception:

java.io.IOException: Illegal seek:
NIOFSIndexInput(path="/mnt/neo4j-community-1.8.M06/data/graph.db/index/luce ne/node/users/_7j5r.cfs")

I've googled to try and find anyone else seeing this issue, and haven't had
any luck. One hypothesis is that the shaky environment created by
the continuous GC pauses has rustled up a race condition that hasn't been
noticed in Lucene before.

You can try running the Lucene checkindex tool to make sure your indexes
are intact. The various indexes are stored under
graph.db/index/lucene/node|relationship/. Take a look here for how to use
checkindex:

http://solr.pl/en/2011/01/17/checkindex-for-the-rescue/

Please let us know what checkindex tells you and if you were able to
resolve the issue with it, it will help tracing down what caused this in
the first place.

/jake

Den söndagen den 12:e augusti 2012 kl. 19:07:50 UTC+2 skrev Justin Pincar:


 
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Justin Pincar  
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 More options Aug 29 2012, 11:58 am
From: Justin Pincar <justinpin...@gmail.com>
Date: Wed, 29 Aug 2012 08:58:19 -0700
Local: Wed, Aug 29 2012 11:58 am
Subject: Re: [Neo4j] Unable to start server: (javax.transaction.SystemException: TM has encountered some problem)
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Thanks Jake, I'll try these things tonight and let you know how it turns
out.
- Justin
On Aug 28, 2012 3:12 AM, "Jacob Hansson" <jacob.hans...@neotechnology.com>
wrote:

...

read more »


 
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Justin Pincar  
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 More options Sep 6 2012, 2:56 pm
From: Justin Pincar <justinpin...@gmail.com>
Date: Thu, 6 Sep 2012 11:55:52 -0700
Local: Thurs, Sep 6 2012 2:55 pm
Subject: Re: [Neo4j] Unable to start server: (javax.transaction.SystemException: TM has encountered some problem)
Print | Individual message | Show original | Report this message | Find messages by this author

The garbage collection seems very likely - I switched to a higher memory
instance and things seem like they're going faster and smoother.

The index seems to be fine, output below.

At this point I'm just moving on with the new setup and making sure to
backup frequently, so I'm not going to worry about this issue too much.
Thanks for all the help!

- Justin

ubuntu@ip-10-170-99-9:/mnt/neo4j-community-1.8.M06/data-old/graph.db$ java
-cp ../../lib/lucene-core-3.5.0.jar -ea:org.apache.lucene...
org.apache.lucene.index.CheckIndex index/lucene/node/apps/ -fix

Opening index @ index/lucene/node/apps/

Segments file=segments_3 numSegments=2 version=3.5 format=FORMAT_3_1
[Lucene 3.1+]
  1 of 2: name=_2xr8 docCount=123355
    compound=false
    hasProx=true
    numFiles=8
    size (MB)=7.114
    diagnostics = {mergeFactor=10, os.version=2.6.32-345-ec2, os=Linux,
lucene.version=3.5.0 1204988 - simon - 2011-11-22 14:46:51, source=merge,
os.arch=i386, mergeMaxNumSegments=-1, java.version=1.6.0_20,
java.vendor=Sun Microsystems Inc.}
    no deletions
    test: open reader.........OK
    test: fields..............OK [2 fields]
    test: field norms.........OK [2 fields]
    test: terms, freq, prox...OK [246705 terms; 246710 terms/docs pairs;
246710 tokens]
    test: stored fields.......OK [246710 total field count; avg 2 fields
per doc]
    test: term vectors........OK [0 total vector count; avg 0 term/freq
vector fields per doc]

  2 of 2: name=_2xr9 docCount=1
    compound=true
    hasProx=true
    numFiles=1
    size (MB)=0
    diagnostics = {os.version=2.6.32-345-ec2, os=Linux,
lucene.version=3.5.0 1204988 - simon - 2011-11-22 14:46:51, source=flush,
os.arch=i386, java.version=1.6.0_20, java.vendor=Sun Microsystems Inc.}
    no deletions
    test: open reader.........OK
    test: fields..............OK [2 fields]
    test: field norms.........OK [2 fields]
    test: terms, freq, prox...OK [2 terms; 2 terms/docs pairs; 2 tokens]
    test: stored fields.......OK [2 total field count; avg 2 fields per doc]
    test: term vectors........OK [0 total vector count; avg 0 term/freq
vector fields per doc]

No problems were detected with this index.

On Wed, Aug 29, 2012 at 8:58 AM, Justin Pincar <justinpin...@gmail.com>wrote:

...

read more »


 
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