JChem Cartridge issue

Hi,





We are using the 3.1.1 version of the cartridge and are finding that the cartridge periodically stops working. The only thing which makes it work again is restarting Tomcat. The query I'm running is a simple one (SELECT compound_ID FROM compound where JC_Contains(structure, 'c1ccccc1') = 1) Initially what tends to happen is that the query is run and no results are returned. Generally, the query runs for several minutes before being cancelled. However, this morning the query actually returned after approximately 3 minutes with no results and no error message.





Then what happens is, I run the query again and get the error message:





ORA-29902: error in executing ODCIIndexStart() routine


ORA-29532: Java call terminated by uncaught Java exception: java.lang.RuntimeException: The following exception has been thrown by the servlet:


Exception: null


ORA-06512: at "JCHEM.JCHEM_CORE_PKG", line 121


ORA-06512: at "JCHEM.JC_IDXTYPE_IM", line 167


ORA-06512: at line 1





This will continue until such time as Tomcat is restarted. It's unclear to me as to how or why this is happening, as the cartridge works for at least a day after the restart but will always eventually come around to the same error message again. Could somebody please take a look at this and tell me what I need to do to make it stop happening?





Regards,





Phil.

Hi Phil,





Please, could you specify the operating system and Oracle version you are using JChem Cartridge with.





Please, could you also post the Java stack trace from <tomcat-home>/logs/catalina.out related to this problem





Thank you,





Peter

Hi Peter,





The operating system is Red Hat Enterprise Server version 3.0, and the database is Oracle 10g (release one I'm told). The operating system has been patched, etc. to allow for the installation of Oracle (so I believe that requires a couple of updates to the kernel for example, plus other software to be installed). The error message is in the attached file. I've included the whole log from the last time Tomcat was restarted. I hope that helps.





Regards,





Phil.

Hi Phil,





This seems to be a problem between the Oracle JDBC client and the database. There are a lot of problem reports on Metalink with the "java.sql.SQLException: No more data to read from socket" error message which seems to be the most immediate cause of the problem. Some of the reports seem to suggest that this problem may be caused by the database session process encountering an error. Can you see any error messages in the alert.log in $ORACLE_BASE/admin/<your-db-name>/bdump or in the session trace files in $ORACLE_BASE/admin/<your-db-name>/udump?





Did you observe an increase in frequency of this error message recently? Is there anything in the pattern of how the JChem Cartridge is used that seems to correlate with the frequency of this problem (such as the number of concurrent users of JChem Cartridge, level of overall system load)? (I am going to try to reproduce this problem and I would like to maximize the likelihood of its occurence.)





Thank you,





Peter