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Posted to dev@jena.apache.org by "Andy Seaborne (Created) (JIRA)" <ji...@apache.org> on 2011/11/11 12:14:51 UTC
[jira] [Created] (JENA-163) TDBException: Different ids for :
allocated: expected [...], got [...]
TDBException: Different ids for <uri>: allocated: expected [...], got [...]
----------------------------------------------------------------------------
Key: JENA-163
URL: https://issues.apache.org/jira/browse/JENA-163
Project: Jena
Issue Type: Bug
Components: TDB
Reporter: Andy Seaborne
Assignee: Andy Seaborne
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[jira] [Issue Comment Edited] (JENA-163) TDBException: Different
ids for : allocated: expected [...], got [...]
Posted by "Andy Seaborne (Issue Comment Edited) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13155294#comment-13155294 ]
Andy Seaborne edited comment on JENA-163 at 11/22/11 6:28 PM:
--------------------------------------------------------------
ReportJena163_TDBDifferentIds.java ==> Jena163_TDBDifferentIds.java
Now shows (used with TDB svn) that the object file storage for the transaction is not initially empty as expected.
was (Author: andy.seaborne):
ReportJena163_TDBDifferentIds.java ==> Jena163_TDBDifferentIds.java
Now shows (used with TDB svn) that the object file storage for the transaction is not initially empty as expected.
I have not seen this happen with a memory dataset. Suggest it's either the impl of a disk file or the way the file is reused across transactions.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Simon Helsen (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13150832#comment-13150832 ]
Simon Helsen commented on JENA-163:
-----------------------------------
after straightening my builds, I was not able to reproduce the problem so easily anymore, but I did notice that I ran in the deadlock of JENA-161 again. This does not mean the defect is invalid of course. More effort is need to reproduce the problem reliably
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13164254#comment-13164254 ]
Andy Seaborne commented on JENA-163:
------------------------------------
Even when the multiple file open issue is fixed, there is still a problem - it occurs (typically) after a longer run.
The current Jena163_TDBDifferentIds prints out every file open/sync/close on the journalled files so I check that the right sequence of file operations and ownership is happening. Therefore, it might be that file operations from different threads do not provide the necessary guarantees of consistency. This is fixable by simply initializing the state of the file when it is started to be used, rather than when it is finished with. When this is done, the test case runs for much longer. Other, unrelated problems sometimes occur but on checking all these, they are not connected with file management.
Next step: central file management (avoids repeated open/close), initialize the state of a temporary journal file explicitly at point of use. These will affect,positively, the test case and are generally better design anyway.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Simon Helsen (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13149997#comment-13149997 ]
Simon Helsen commented on JENA-163:
-----------------------------------
Given Andy's comments about my build state, I need to see if I can still reproduce the problem after pulling this straight
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13179413#comment-13179413 ]
Andy Seaborne commented on JENA-163:
------------------------------------
Good to hear that your tests worked.
The "rare" problem was another bug that didn't show because the first one was so much more frequent. Its symptom was missing nodes in the node table (but that is one of those things that has been the result of other errors leading to the same visible defect) that made DESCRIBE unstable. Having run the test programs repeatedly (in memory, SSD, and rotating disk; direct and mapped) I have some confidence although real use is going to throw up new deployment assumptions.
I'm a bit surprised about Xerces 2.10.0 -- in fact, all we did was upgrade Xerces, no code changes as far as I know, so other versions right back to the old one were depending on should work. Using the quite old one was causing some people problems with clashes with other libraries.
(not relevant to Simon) Fuseki is updated to use transactions.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
> Fix For: TDB 0.9.0
>
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Simon Helsen (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13149958#comment-13149958 ]
Simon Helsen commented on JENA-163:
-----------------------------------
not sure if this was already known, but I can reproduce this by simply running T_TransSystem on disk (direct). Tested on windows 7/64 bit
START (disk[direct], 100 iterations)
000: ..........
010: ..........
020: ...com.hp.hpl.jena.tdb.TDBException: Different ids for S: allocated: expected [000000000000000E], got [0000000000000000]
at com.hp.hpl.jena.tdb.transaction.NodeTableTrans.append(NodeTableTrans.java:178)
at com.hp.hpl.jena.tdb.transaction.NodeTableTrans.writeNodeJournal(NodeTableTrans.java:210)
at com.hp.hpl.jena.tdb.transaction.NodeTableTrans.commitPrepare(NodeTableTrans.java:190)
at com.hp.hpl.jena.tdb.transaction.Transaction.prepare(Transaction.java:108)
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:92)
at com.hp.hpl.jena.tdb.DatasetGraphTxn.commit(DatasetGraphTxn.java:38)
at com.hp.hpl.jena.tdb.transaction.T_TransSystem$Writer.call(T_TransSystem.java:213)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:314)
at java.util.concurrent.FutureTask.run(FutureTask.java:149)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:897)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:919)
at java.lang.Thread.run(Thread.java:736)
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Simon Helsen (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13179120#comment-13179120 ]
Simon Helsen commented on JENA-163:
-----------------------------------
I deployed Jena 2.7.0 + jena-tdb-0.9.0-incubating-20111229.215747-88. I am not seeing the reported error anymore both in our regular functional suite as well as in our stress/scale test suite. (I tested on win7/64bit/ibm jre) The scale test instance was set up with 30 clients, each executing multiple queries and writing resources with a ratio of 7/1 where the actions are set to be half a second apart. Now, I must say that the inclusion of Xerces 2.10.0 has caused some issues which inhibit me from executing all my functional tests, but most of the tests which suffer were not showing the problem originally reported.
So, it is looking good. Now, Andy, from your previous post, you seem to suggest that you still expect something very rare. Reading your comment from December 7, I am not sure with what version of TDB/ARQ you saw the "rare" problem.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13155294#comment-13155294 ]
Andy Seaborne commented on JENA-163:
------------------------------------
ReportJena163_TDBDifferentIds.java ==> Jena163_TDBDifferentIds.java
Now shows (used with TDB svn) that the object file storage for the transaction is not initially empty as expected.
I have not seen this happen with a memory dataset. Suggest it's either the impl of a disk file or the way the file is reused across transactions.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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Re: [jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by Paolo Castagna <ca...@googlemail.com>.
Andy Seaborne (Commented) (JIRA) wrote:
> Progress. At least one cause of this (or at least a problem which needed fixing) identified. Files could be open multiple times and so have kernel or JVM state that was inconsistent - one might be flushed on close resulting in potnetially bad information later. Highly dependent on the exact order between threads that occurs.
Great news, thanks Andy.
> Running on an SSD makes the test catch things earlier (based on number of transactions needed before problems show up) and make transactional TDB run much faster anyway.
Good to know. :-)
Thanks,
Paolo
[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13163763#comment-13163763 ]
Andy Seaborne commented on JENA-163:
------------------------------------
Progress. At least one cause of this (or at least a problem which needed fixing) identified. Files could be open multiple times and so have kernel or JVM state that was inconsistent - one might be flushed on close resulting in potnetially bad information later. Highly dependent on the exact order between threads that occurs.
Running on an SSD makes the test catch things earlier (based on number of transactions needed before problems show up) and make transactional TDB run much faster anyway.
Jena163_TDBDifferentIds.java in Jena2/Jena-Dev
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Simon Helsen (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13179521#comment-13179521 ]
Simon Helsen commented on JENA-163:
-----------------------------------
Andy, although getting off topic for this issue, the problems I am facing with Xerces are class-loading related and typically caused by clashes with other libraries. Xerces is highly sensitive to this. I wonder if it would be safe to keep using Xerces 2.7.1 in our deployment
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
> Fix For: TDB 0.9.0
>
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13154232#comment-13154232 ]
Andy Seaborne commented on JENA-163:
------------------------------------
The same node (here, <S>) is sending up in the nodes.dat-jrnl file twice, which is wrong.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13148508#comment-13148508 ]
Andy Seaborne commented on JENA-163:
------------------------------------
Another one:
http://markmail.org/message/wg3ho7mrdutecjum
com.hp.hpl.jena.tdb.TDBException: Different ids for http://covers.openlibrary.org/b/id/609263-M.jpg: allocated: expected [00000000081BBA4B], got [00000000081B5C58]
com.hp.hpl.jena.tdb.transaction.NodeTableTrans.append(NodeTableTrans.java:178) com.hp.hpl.jena.tdb.transaction.NodeTableTrans.writeNodeJournal(NodeTableTrans.java:210) com.hp.hpl.jena.tdb.transaction.NodeTableTrans.commitPrepare(NodeTableTrans.java:190) com.hp.hpl.jena.tdb.transaction.Transaction.prepare(Transaction.java:105) com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:89)
com.hp.hpl.jena.tdb.DatasetGraphTxn.commit(DatasetGraphTxn.java:38)
Same stack trace.
But this is a point where different problems tend to manifest themselves (e.g. JENA-91) and it's a pretty sensitive internal consistency test.
where it's found first, not the cause.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13148428#comment-13148428 ]
Andy Seaborne commented on JENA-163:
------------------------------------
Copied from JENA-131: Simon Helson writes:
Ok, so I verified the fix. The problem described in this defect is certainly gone. My multi-client scale test went through, mostly. My log at some point indicated the following
15:08:39,977 [jazz.jfs.indexer.jfs_tests_default_consumer_name.triple] ERROR com.ibm.team.jfs - Originating Exception:
com.hp.hpl.jena.tdb.TDBException: Different ids for https://localhost:9443/jazz/storage/RequirementsArea_356f61ce-2959-4100-a758-37e3fa82d1b0/requirement1065.xml: allocated: expected [00000000003B594E], got [00000000003B4D08]
at com.hp.hpl.jena.tdb.transaction.NodeTableTrans.append(NodeTableTrans.java:178)
at com.hp.hpl.jena.tdb.transaction.NodeTableTrans.writeNodeJournal(NodeTableTrans.java:210)
at com.hp.hpl.jena.tdb.transaction.NodeTableTrans.commitPrepare(NodeTableTrans.java:190)
at com.hp.hpl.jena.tdb.transaction.Transaction.prepare(Transaction.java:109)
at com.hp.hpl.jena.tdb.transaction.Transaction.commit(Transaction.java:93)
at com.hp.hpl.jena.tdb.DatasetGraphTxn.commit(DatasetGraphTxn.java:38)
at com.ibm.team.jfs.rdf.internal.jena.tdb.JenaTdbTxProvider.storeOperation(JenaTdbTxProvider.java:321)
...
15:08:39,983 [jazz.jfs.indexer.jfs_tests_default_consumer_name.triple] ERROR com.ibm.team.jfs - com.hp.hpl.jena.tdb.transaction.TDBTransactionException: Transaction has already committed or aborted
But only once and this test was running 10 clients who were performing both queries and write actions (ration 7 to 1). I don't know under what circumstances I might be able to reproduce this, but did Paolo also not see something like this recently? Having said this, this should probably become a separate issue
(I still have to check JENA-143)
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Resolved] (JENA-163) TDBException: Different ids for :
allocated: expected [...], got [...]
Posted by "Andy Seaborne (Resolved) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Andy Seaborne resolved JENA-163.
--------------------------------
Resolution: Fixed
Fix Version/s: TDB 0.9.0
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
> Fix For: TDB 0.9.0
>
>
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[jira] [Issue Comment Edited] (JENA-163) TDBException: Different
ids for : allocated: expected [...], got [...]
Posted by "Andy Seaborne (Issue Comment Edited) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13154232#comment-13154232 ]
Andy Seaborne edited comment on JENA-163 at 11/21/11 3:18 PM:
--------------------------------------------------------------
(in my version of the testing code in Jena-Dev - which currently does not have the query abort of JENA-143 because it sets the timeout so large it never happens
https://svn.apache.org/repos/asf/incubator/jena/Scratch/AFS/Jena-Dev/trunk/src/dev/ReportJena163_TDBDifferentIds.java
)
The same node (here, <S>) is sending up in the nodes.dat-jrnl file twice, which is wrong.
was (Author: andy.seaborne):
The same node (here, <S>) is sending up in the nodes.dat-jrnl file twice, which is wrong.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13179572#comment-13179572 ]
Andy Seaborne commented on JENA-163:
------------------------------------
Probably. Try it. Xerces was only changed late in the cycle because we did a sweep of upgrades; v2.7.1 was used up until them as per usual and all dev builds.
(Off-topic suggests email to jena-users)
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
> Fix For: TDB 0.9.0
>
>
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[jira] [Commented] (JENA-163) TDBException: Different ids for
: allocated: expected [...], got [...]
Posted by "Andy Seaborne (Commented) (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/JENA-163?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13175768#comment-13175768 ]
Andy Seaborne commented on JENA-163:
------------------------------------
The current development version of TDB has not exhibited the recurring issue previously reported. It was a different issue to the multiple file - once the multiple files issue was fixed, then it unmasked a rarer situation.
At this point, I'm getting no TDB errors for the high-load, long-run tests (memory, direct or mapped modes).
Next: testing more generally. I would appreciate people running tests in their environments so we get the greatest diversity of setups.
> TDBException: Different ids for <uri>: allocated: expected [...], got [...]
> ----------------------------------------------------------------------------
>
> Key: JENA-163
> URL: https://issues.apache.org/jira/browse/JENA-163
> Project: Jena
> Issue Type: Bug
> Components: TDB
> Reporter: Andy Seaborne
> Assignee: Andy Seaborne
>
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