ORA-03114: not connected to ORACLE and markush smiles

Two issues here:


Looks like Oracle 10g on linux (Redhat ES 4.0) is having some problems with JChem cartridge 3.2.3 upgrade from 3.1.7. Upgrade of JChem was uneventful. Indexes were no longer valid, so drop and create (rebuild did not work). Dropping of index behaved as expected. Upon attempting to create new index (jc_idxtype), Oracle throws the following error:


ORA-03114: not connected to ORACLE


create index jc_cis_idx on cis_chemstruct(smiles)


*


ERROR at line 1:


ORA-03113: end-of-file on communication channel





SQL Plus session terminated unexpectly.





Log from catalina.out by Tomcat:


2007-01-17 11:17:07.015 [null] [http-8000-Processor23]: JDBC driver version: 10.2.0.1.0


2007-01-17 11:17:07.372 [UNKNOWN]: Failing statement: DROP TABLE CIS.JC_CIS_IDX_jcx


2007-01-17 11:17:07.380 [UNKNOWN]: Failing statement: DROP SEQUENCE CIS.JC_CIS_IDX_jcx_SQ


2007-01-17 11:17:07.388 [UNKNOWN]: Failing statement: DROP TRIGGER CIS.JC_CIS_IDX_jcx_TR


2007-01-17 11:17:07.396 [UNKNOWN]: Failing statement: DROP TABLE CIS.JC_CIS_IDX_jcx_UL


2007-01-17 11:17:07.405 [UNKNOWN]: Failing statement: DROP SEQUENCE CIS.JC_CIS_IDX_jcx_USQ


2007-01-17 11:17:07.413 [UNKNOWN]: Failing statement: DROP TABLE CIS.JC_CIS_IDX_jsu


2007-01-17 11:17:08.985 [UNKNOWN]: prop_name column in CIS.JC_IDX_PROPERTY has been increased.





I attempted to do this same upgrade on Solaris and Oracle 9i and index creation was successful. I'm lead to believe this may have something to do with linux and Oracle 10g.





Second issue:


Markush smiles breaks index creation. While attempting to do the upgrade (see above) we also encountered failure of index creation when a markush smiles is encountered. Upon removing any markush smiles index creation was successful. This is a change in behavior from 3.1.7 from 3.2.3. Please advise as to the direction we should move ahead. Should we set the smiles to null if we encounter a markus structure or will you ignore markush structures during index creation as observed in 3.1.7?

Hi Matt,





I am addressing the second issue now, my colleagues will follow up the other one.





In 3.2, we introduced table types to allow type-specific operations, and the default is that the table contains molecules only. To get the same behaviour as in 3.1.7, I recommend to use index option "tableType:anyStructures".





See the corresponding documentation:





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


http://www.chemaxon.com/jchem/doc/admin/index.html#tableTypes





In the future, we plan additional table types, like query and Markush tables.





Szabolcs

Quote:

ORA-03114: not connected to ORACLE create index jc_cis_idx on cis_chemstruct(smiles) * ERROR at line 1: ORA-03113: end-of-file on communication channel

There are various stability issues with running JChem Cartridge on Oracle 10gR2 x86_64 (http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html#issues_64bit) -- all of them probably having the same underlying low-level Oracle problem. In your case, the Oracle backend session process dies with a core dump. Oracle is currently researching the issue.





Note that this problem affects neither Oracle 10gR1 on x86_64 systems nor 64-bit Oracle 10gR2 running on Sparc processors.





Peter

Do you have any idea what the status with Oracle or when they will release a patch? This is a major show stopper. If no timely patch is available then we will be forced to use MDL Direct 6 instead of JChem.

We have traced this problem to SQL Plus session (might be related to session variables). We used different clients on different platforms and where able to reproduce this same error (all going against Oracle 10g R2 on Linux Redhat 4.0 server):


9.2.0.4 window xp sqlplus client (remote sql net) - error


10.2.0.1 Linux Fedora 5 sqlplus client (remote sql net) - error


10.2.0.1 Linux Redhat 4 sqlplus client (local sql net) - error


10.2.0.1 Linux Redhat 4 sqlplus client (local no sql net) - error





Work around use Oracle SQL Developer instead of SQL Plus on your preferred platform (I tested on Windows XP and Linux). My theory is that because SQL Developer is Java based it is connecting through via JDBC which uses a different protocol than SQL Plus. This will allow us to continue with Linux/Oracle 10g R2 JChem 3.2.3 upgrade.

Quote:

Work around use Oracle SQL Developer instead of SQL Plus on your preferred platform

Doesn't work for me with Oracle SQL Developer on Windows 2003 Server and Oracle 10.2 on Enterprise ("Unbreakable") Linux. (I used default connection properties with Oracle SQL Developer.)





P.

Core dump of the crashed Oracle backend process shows that there is an invalid memory reference problem (segmentation violation) within the Oracle JVM. We have started work to move away from the Oracle JVM. (Though the source of the problem may theoretically reside outside the Oracle JVM.)

Quote:

Oracle is currently researching the issue.

We raised the following service request with Oracle for this problem:





Service Request 5951457.992 - BACKEND SERVER PROCESS DIES WITH CERTAIN JSP CALLS, NO TRACE FILE GENERATED

I could finally get it work by installing Oracle Database 10g Products from the Oracle Database Companion CD.