ERROR ORA-29877: ODCIINDEXUPDATE routine failure

User a68e2d9365

25-04-2007 09:39:40

Hello,





I'm trying to insert a set of molecules into our Oracle tables.





We installed jchem cartridge 3.2.3 on Oracle Database 10G (release 10.2.0.3). We store mol structure within a clob 'molstructure' in table named 'compound'. We build a jchem table called 'jcompstruct' with jchem manager option 'any structure' on. We created an index called 'JC_COMPOUND_IDX' that allows queries on column 'molstructure' such as :


select compound.id from compound


where jc_contains(molstructure, 'O1C=CC=C1') = 1


(works fine !)





When I tried to insert in one shot 20 structures I get the following error for item #7 :





*** Compound 'Batch of EDS|004ED0084' UNloadable *** [rank=7 in the list]


java.io.IOException: ORA-29877: failed in the execution of the ODCIINDEXUPDATE routine


ORA-29516: Aurora assertion failure: Assertion failure at eoamrk.c:234


EOA runtime assertion failure: eoamrk.c:234


ORA-06512: at "JCHEM.JCHEM_CORE_PKG", line 208


ORA-06512: at "JCHEM.JC_IDXTYPE_IM", line 663


ORA-06512: at line 2





at oracle.jdbc.driver.DatabaseError.SQLToIOException(DatabaseError.java:517)


at oracle.jdbc.driver.OracleClobWriter.flushBuffer(OracleClobWriter.java:206)


at oracle.jdbc.driver.OracleClobWriter.close(OracleClobWriter.java:176)


at hgx.hitdb.V02.COMPOUND_G._Create(Unknown Source)


at hgx.hitdb.V02.COMPOUND_G.Create(Unknown Source)


at hgx.hitdb.V02.COMPOUND_G.Create(Unknown Source)


at hgx.hitdb.V02.COMPOUND.Create(Unknown Source)


at hgx.hitdb.V02.COMPOUND.processAfterXMLLoading(Unknown Source)


at hgx.hitdb.V02.loader.ChemLibLoader.loads(Unknown Source)


at hgx.hitdb.V02.loader.ChemLibLoader.main(Unknown Source)





What is weird is when I try to insert this specific structure alone (#7) it works fine !





It seems to me that the problem is linked to 'JC_COMPOUND_IDX' index and not to 'JCOMPSTRUCT' table.





Alain.

ChemAxon aa7c50abf8

25-04-2007 09:53:37

Hello Alain,





Have you installed Oracle Database 10g Products from the Oracle Database Companion CD?





Thanks


Peter

User a68e2d9365

25-04-2007 11:39:23

We have 2 CD for Oracle Installation.





We installed Oracle 10G from CD #1 exclusively. We installed nothing from CD #2 ("companion").





Alain.

ChemAxon aa7c50abf8

25-04-2007 12:03:41

Please, apply the patch for Oracle bug No. 4655283, if available for your platform. (Last time I checked, it was not available for Windows. From the error message you reported, I infer that your Oracle runs on Windows.)





If this patch is not available for your platform, you have to install JAccelerator which provides a workaround for this bug. JAccelerator is included in the Companion CD (in Oracle Database 10g Products).





Thanks


Peter





PS:


The following steps can be used to check, if JAccelerator has been installed:





1.) start the Oracle Installer ($ORACLE_HOME/oui/bin/runInstaller)





2.) Click on the "Installed Products" button





3.) In the "Contents" tab, in the products' tree the following path


should be present:





Oracle Homes / <your-oracle-home> / Oracle Database 10g Products


10.2.0.1 / JAccelerator (COMPANION) 10.2.0.1.0 / JAccelerator


(COMPANION) patch 10.2.0.3.0

User a68e2d9365

25-04-2007 12:36:34

10.2.0.3 oracle version already contains the patch for Oracle bug #4655283. We are installing JAccelerator.





Alain.

User f48d010cc5

22-04-2010 15:46:09

Hi,


I have the same problem than Alain 3 years after. Here is the error message:


*** Compound 'Batch of XXXXXXXXXXX' UNloadable *** [rank=465 in the list]
java.io.IOException: ORA-29877: failed in the execution of the ODCIINDEXUPDATE routine
ORA-29516: Aurora assertion failure: Assertion failure at eoamrk.c:234
EOA runtime assertion failure: eoamrk.c:234
ORA-06512: at "JCHEM.JCHEM_CORE_PKG", line 208
ORA-06512: at "JCHEM.JC_IDXTYPE_IM", line 663
ORA-06512: at line 2


        at oracle.jdbc.driver.DatabaseError.SQLToIOException(DatabaseError.java:517)
        at oracle.jdbc.driver.OracleClobWriter.flushBuffer(OracleClobWriter.java:206)
        at oracle.jdbc.driver.OracleClobWriter.close(OracleClobWriter.java:176)
        at hgx.hitdb.V02.COMPOUND_G._Create(Unknown Source)
        at hgx.hitdb.V02.COMPOUND_G.Create(Unknown Source)
        at hgx.hitdb.V02.COMPOUND_G.Create(Unknown Source)
        at hgx.hitdb.V02.COMPOUND.Create(Unknown Source)
        at hgx.hitdb.V02.COMPOUND.processAfterXMLLoading(Unknown Source)
        at hgx.hitdb.V02.loader.ChemLibLoader.loads(Unknown Source)
        at hgx.hitdb.V02.loader.ChemLibLoader.main(Unknown Source)


Last time, you proposed to install Jaccelerator on Oracle which we did. I believe this has worked in 2007 but since probably 2008 we did not load again any other large compounds libraries (or small, apparently size does not matter for the crash!). Resuming this activity, it crashes with the above error message.  Retrying many times, it does not crash at the same compound showing an erratic behaviour and sometimes succeeding on a different development oracle database (example shown on our prod database).


I believe the best would be to upgrade the Jchem Cartridge but we can not perform this upgrade at the moment and we need a quick fix if possible.


 

ChemAxon aa7c50abf8

22-04-2010 16:25:51

Hi,


After installing JAccelerator, we could not reproduce the problem. (FS#1876) I suggest trying to upgrade to Oracle 10.2.0.4. Perhaps, that solves it.


Peter