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unable to close store using batchinserter
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bin chen  
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 More options Sep 23 2012, 10:38 pm
From: bin chen <binchenindi...@gmail.com>
Date: Sun, 23 Sep 2012 19:38:43 -0700 (PDT)
Local: Sun, Sep 23 2012 10:38 pm
Subject: unable to close store using batchinserter
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Hi, I got the following error while using batchinserter. It works well for
a small set but does not work for a larger test set consisting of millions
of relationships. I suspected  it has something to do with the memory, but
havenot fixed it. Any hint would be appreciated.

Exception in thread "main"
org.neo4j.kernel.impl.nioneo.store.UnderlyingStorageException: Unable to
close store D:\....\data\test\neo4j-store1\neostore.relationshipstore.db
at
org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.close(CommonAbstract Store.java:699)
at
org.neo4j.kernel.impl.nioneo.store.RelationshipStore.close(RelationshipStor e.java:79)
at
org.neo4j.kernel.impl.nioneo.store.NeoStore.closeStorage(NeoStore.java:231)
at
org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.close(CommonAbstract Store.java:634)
at
org.neo4j.unsafe.batchinsert.BatchInserterImpl.shutdown(BatchInserterImpl.j ava:700)
at com.linkingpilot.app.BatchImporterImpl.finish(BatchImporterImpl.java:134)
at com.linkingpilot.app.ImporterImpl.buildNewDb(ImporterImpl.java:47)
at com.linkingpilot.app.ImporterTest.main(ImporterTest.java:35)
Caused by: java.io.IOException: The requested operation cannot be performed
on a file with a user-mapped section open
at sun.nio.ch.FileChannelImpl.truncate0(Native Method)
at sun.nio.ch.FileChannelImpl.truncate(FileChannelImpl.java:340)
at
org.neo4j.kernel.impl.nioneo.store.CommonAbstractStore.close(CommonAbstract Store.java:669)
... 7 more

Thanks.


 
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Peter Neubauer  
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 More options Sep 24 2012, 5:49 pm
From: Peter Neubauer <peter.neuba...@neotechnology.com>
Date: Mon, 24 Sep 2012 14:49:18 -0700
Local: Mon, Sep 24 2012 5:49 pm
Subject: Re: [Neo4j] unable to close store using batchinserter
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What neo4j version are you doing this on, Chen?

Cheers,

/peter neubauer

Neo4j 1.8.RC1 "Vindeln Vy" -
http://blog.neo4j.org/2012/09/neo4j-18rc1-really-careful-ftw.html

G:  neubauer.peter
S:  peter.neubauer
P:  +46 704 106975
L:   http://www.linkedin.com/in/neubauer
T:   @peterneubauer

Wanna learn something new? Come to @graphconnect.


 
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bin chen  
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 More options Sep 24 2012, 10:39 pm
From: bin chen <binchenindi...@gmail.com>
Date: Mon, 24 Sep 2012 19:39:17 -0700 (PDT)
Local: Mon, Sep 24 2012 10:39 pm
Subject: Re: [Neo4j] unable to close store using batchinserter
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I am using 1.8.RC1. Thanks.

Best, Bin


 
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bin chen  
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 More options Sep 25 2012, 12:51 am
From: bin chen <binchenindi...@gmail.com>
Date: Mon, 24 Sep 2012 21:51:06 -0700 (PDT)
Local: Tues, Sep 25 2012 12:51 am
Subject: Re: [Neo4j] unable to close store using batchinserter
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Hi, Peter,  here is an observation that sounds quite strange. If I am using
the debug model and set a breaking point at the db.shutdown(), it works
surprisingly...Any clue?


 
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Jacob Hansson  
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 More options Sep 27 2012, 4:15 am
From: Jacob Hansson <jacob.hans...@neotechnology.com>
Date: Thu, 27 Sep 2012 01:15:11 -0700 (PDT)
Local: Thurs, Sep 27 2012 4:15 am
Subject: Re: [Neo4j] unable to close store using batchinserter
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Hey Bin,

does this happen every time you try it? Would you be able to provide a test
case that exhibits this behavior?

/jake

Den tisdagen den 25:e september 2012 kl. 06:51:06 UTC+2 skrev bin chen:


 
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Mattias Persson  
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 More options Sep 27 2012, 10:43 am
From: Mattias Persson <matt...@neotechnology.com>
Date: Thu, 27 Sep 2012 16:43:45 +0200
Local: Thurs, Sep 27 2012 10:43 am
Subject: Re: [Neo4j] unable to close store using batchinserter
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There is a known problem on Windows regarding releasing memory mapped areas
of a file relying on garbage collection as there's no public* way of
forcing such a release. This effectively means that neo4j races against the
GC and sometimes such things happen. It's interesting that you can produce
it so often though.

* There are ways, but probably not supported on all jvms and platforms.

2012/9/27 Jacob Hansson <jacob.hans...@neotechnology.com>

--
Mattias Persson, [matt...@neotechnology.com]
Hacker, Neo Technology
www.neotechnology.com

 
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bin chen  
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 More options Sep 27 2012, 1:14 pm
From: bin chen <binc...@indiana.edu>
Date: Thu, 27 Sep 2012 10:14:37 -0700
Local: Thurs, Sep 27 2012 1:14 pm
Subject: Re: [Neo4j] unable to close store using batchinserter
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Thanks.

I modified the batchinserter class and added some other functions (e.g.,
indexing) there. It happened very often when I was using a larger dataset
(see 4m edges), but it may sometimes work if the dataset has hundreds of
thousands edges.... my pc has 4G ram, running Windows XP...

Bin

On Thu, Sep 27, 2012 at 7:43 AM, Mattias Persson
<matt...@neotechnology.com>wrote:

--
Bin Chen
PHD student, Informatics,
Indiana University at Bloomington
http://cheminfo.informatics.indiana.edu/~binchen

 
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