Error during indexing with tdf=y option

User 7f33ec9a5c

04-11-2012 05:51:42

CREATE INDEX jc_idx ON structure(s_smiles) INDEXTYPE IS jchem.JC_IDXTYPE PARAMETERS('TABLESPACE=structure_indexes,tdf=y');

ORA-29855: error occurred in the execution of ODCIINDEXCREATE routine ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: java.rmi.RemoteException: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.Exception: Error while processing ROWID=AAAEbFABgAABp/qAAG: 4, CC(=O)OB1OC(CC(=[O+]1)c2ccccc2)c3ccccc3.C[Sb-](C)(C)(C)(C)C; nested exception is: java.util.concurrent.Exec

ChemAxon 9c0afc9aaf

04-11-2012 06:14:29

Hi,

I have split this to a different topic, as not related to the original question.

It seems there is a problem with a particular structure during indexing.

Could you please locate the corresponding full Java stack trace in the JChem Server log files and send it to us ?

(or the content of the whole cartridge/logs directory)

Please also remind us of your cartridge version :

select jchem_core_pkg.getenvironment() from dual;

We will try to reproduce this and get back to you soon.

Meanwhile you can re-try indexing with the haltOnError=nf option, where "nf" means "never fail".

In this case the indexing will be successful, but the few

structures with error can be missing from search results.

More details:

http://www.chemaxon.com/jchem/doc/dev/cartridge/index.html#create_index

Best regards,

Szilard

User 7f33ec9a5c

06-11-2012 02:02:34

Thanks Szilard,

The indexing worked when errors were ignored, as follows:

CREATE INDEX jc_idx ON structure(s_smiles) INDEXTYPE IS jchem.JC_IDXTYPE PARAMETERS(''TABLESPACE=structure_indexes,tdf=y,haltOnError=nf'')

------------------------ I believe the errors that caused the crash were: -------------------------------------

[pool-1-thread-239/4357]: 2012-11-04 19:59:42.650 chemaxon.jchem.cartridge.servlets.indexing.errorhandling.impl.IndexErrorImpl addError

SEVERE: Error while processing ROWID=AAAEbFABgAABp/qAAG: 4, CC(=O)OB1OC(CC(=[O+]1)c2ccccc2)c3ccccc3.C[Sb-](C)(C)(C)(C)C

[pool-1-thread-231/4349]: 2012-11-04 21:15:57.041 chemaxon.jchem.cartridge.servlets.indexing.errorhandling.impl.IndexErrorImpl addError

SEVERE: Error while processing ROWID=AAAEbFABhAAA1TsAAI: 4, O.O.O.O.[Na+].[Na+].C[Pt-2](C)(C)(C)(C)C

[pool-1-thread-247/4365]: 2012-11-04 23:21:22.564 chemaxon.jchem.cartridge.servlets.indexing.errorhandling.impl.IndexErrorImpl addError

SEVERE: Error while processing ROWID=AAAEbFABhAAA1TsAAI: 4, O.O.O.O.[Na+].[Na+].C[Pt-2](C)(C)(C)(C)C

----------------------------- this would have been an error from today.

[pool-1-thread-253/4371]: 2012-11-05 00:08:14.919 chemaxon.jchem.cartridge.servlets.indexing.errorhandling.impl.IndexErrorImpl addError

SEVERE: Error while processing ROWID=AAAEbFABgAABp/qAAG: 4, CC(=O)OB1OC(CC(=[O+]1)c2ccccc2)c3ccccc3.C[Sb-](C)(C)(C)(C)C

[RMI TCP Connection(188)-172.20.10.87/7335]: 2012-11-05 17:07:23.390 chemaxon.jchem.cartridge.util.Environment identifyJdbcDriverVersion

INFO: JDBC driver version: 11.1.0.7.0-Production

------------------------ end errors; -------------------------------------

SQL> select jchem_core_pkg.getenvironment() from dual;

JCHEM_CORE_PKG.GETENVIRONMENT()
--------------------------------------------------------------------------------
Oracle environment:
Oracle Database 11g Enterprise Edition Release 11.2.0.3.0 - 64bit Production
PL/SQL Release 11.2.0.3.0 - Production
CORE 11.2.0.3.0 Production
TNS for Linux: Version 11.2.0.3.0 - Production
NLSRTL Version 11.2.0.3.0 - Production

JChem owner: JCHEM

JChem Server environment:
Java VM vendor: Oracle Corporation

JCHEM_CORE_PKG.GETENVIRONMENT()
--------------------------------------------------------------------------------
Java version: 1.7.0_04
Java VM version: 23.0-b21
JChem version: 5.10.0
JChem Index version: 5100000
JDBC driver version: 11.1.0.7.0-Production

... LET ME KNOW IF YOU NEED MORE INFO :)

================== DON'T KNOW IF THIS IS OF INTEREST OR NOT?=======================

--Just wanted to let you know there are no structures missing from the index table.

select count(*) from structure;
--16521670

select count(*) from jc_idx_jcx;
--16521670

select s_Smiles
from structure
where rowid not in (SELECT RID FROM JC_IDX_JCX) ;
-- no rows returned.
================================================================================

ChemAxon 61b4fee994

06-11-2012 08:04:02

Thank you for the log. The problem I've seen in the log is that the database couldn't extend the tablespace:

ORA-01653: unable to extend table SENOBASE.JC_IDX_JCX by 8192 in tablespace DISCOVER_DATA1

ORA-01653: unable to extend table SENOBASE.JC_IDX_FLAT_JCX by 8192 in tablespace STRUCTURE_INDEXES

They are probably full or became too fragmented.

You can

- add or resize DATAFILE

- enable AUTOEXTEND for tablespace

-alter tablespace manually with the COALESCE clause to get larger free extents

Regards,

Tamas