ChemAxon Forum Archive » Storage & search: JChem Base and JChem Oracle Cartridge

problem in repetitive calculate/update

User bf3dbc99cf

07-09-2015 14:35:35

Dear ChemAxon,


I am using jchem cartridge 15.8.17 on Oracle11g, Centos 64-bit.


 


JCHEM_CORE_PKG.GETENVIRONMENT()


--------------------------------------------------------------------------------


Oracle environment:


Oracle Database 11g Enterprise Edition Release 11.2.0.1.0 - 64bit Production


PL/SQL Release 11.2.0.1.0 - Production


CORE    11.2.0.1.0      Production


TNS for Linux: Version 11.2.0.1.0 - Production


NLSRTL Version 11.2.0.1.0 - Production




JChem owner: JCHEM




JChem Server environment:


Java VM vendor: Oracle Corporation




JCHEM_CORE_PKG.GETENVIRONMENT()


--------------------------------------------------------------------------------


Java version: 1.8.0_05


Java VM version: 25.5-b02


JChem version: 15.8.17.0


JChem index version: 15071300


JDBC driver version: 11.2.0.3.0


JChem Server start directory: /home/chemaxon/jchem-150817/cartridge


JChem Server host:port : localhost:1099


 


 


 


When I calculate some property and update a column, it works for several times.


But after repetitive calculation and update, it fails as follows.


 


update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;




1 row updated.




update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;




1 row updated.




update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;




1 row updated.




update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;


update compound_record r


*


ERROR at line 1:


ORA-00600: internal error code, arguments: [kdddgb:clsviol_kcbgcur_9], [0],


[4194971], [1], [4294967250], [2], [], [], [], [], [], []


ORA-06512: at "JCHEM.JCHEM_DEFRIGHT_PKG", line 6


ORA-06512: at "JCHEM.EXEC_FUNCB", line 16


ORA-06512: at "JCHEM.EVALUATE_FUNCB", line 7


 


 


 


To enable the calculation and update again, I have to success some jchem calculation as follows:


 


select to_number( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = 320437;


      LOGP


----------


5.42543317


 


 


Now, the calculate/update runs OK, but only for several times.


 


 


update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;




1 row updated.




update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;




1 row updated.




update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;




1 row updated.




update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


where r.corp_id = 320437;


update compound_record r


*


ERROR at line 1:


ORA-00600: internal error code, arguments: [kdddgb:clsviol_kcbgcur_9], [0],


[4194971], [1], [4294967250], [2], [], [], [], [], [], []


ORA-06512: at "JCHEM.JCHEM_DEFRIGHT_PKG", line 6


ORA-06512: at "JCHEM.EXEC_FUNCB", line 16


ORA-06512: at "JCHEM.EVALUATE_FUNCB", line 7


 


Can you help me to cope with this problem?



Chong Hak Chae,

ChemAxon abe887c64e

08-09-2015 07:47:12

Dear Chong Hak Chae,


We have not experienced this kind of error yet. Would you check and send us the trace log file(s) generated during the error? (The log files are available in the <jchem_home>/cartridge/logs/ folder.)


Thank you,


Krisztina

User bf3dbc99cf

08-09-2015 09:48:05

Dear,


I made the error intentionally, and tried to find the corresponding error log file.


But I cannot find the newly generated, corresponding log file.


Which log file do you want?


Regards,


 


 




pims:/home/chemaxon/jchem/cartridge/logs$sqlplus cims_new/cims4bank




SQL*Plus: Release 11.2.0.1.0 Production on Tue Sep 8 18:32:55 2015




Copyright (c) 1982, 2009, Oracle.  All rights reserved.






Connected to:


Oracle Database 11g Enterprise Edition Release 11.2.0.1.0 - 64bit Production


With the Partitioning, OLAP, Data Mining and Real Application Testing options




update compound_record r


set   cd_logp         = (select ( jc_evaluate( cd_structure, 'logp()' ) ) logp from compound c where c.corp_id = r.corp_id)


  3  where r.corp_id = 320437;


update compound_record r


*


ERROR at line 1:


ORA-00600: internal error code, arguments: [kdddgb:clsviol_kcbgcur_9], [0],


[4194971], [1], [4294967250], [2], [], [], [], [], [], []


ORA-06512: at "JCHEM.JCHEM_DEFRIGHT_PKG", line 6


ORA-06512: at "JCHEM.EXEC_FUNCB", line 16


ORA-06512: at "JCHEM.EVALUATE_FUNCB", line 7






SQL> quit


Disconnected from Oracle Database 11g Enterprise Edition Release 11.2.0.1.0 - 64bit Production


With the Partitioning, OLAP, Data Mining and Real Application Testing options


pims:/home/chemaxon/jchem/cartridge/logs$date


Tue Sep  8 18:33:11 KST 2015


pims:/home/chemaxon/jchem/cartridge/logs$dir


total 280


-rw-rw-r--. 1 chemaxon chemaxon    405 Sep  8 14:32 jcart0.log


-rw-r--r--. 1 root     root          0 Sep  8 14:32 jcart0.log.lck


-rw-rw-r--. 1 chemaxon chemaxon 146252 Sep  8 18:03 jcart1.log


-rw-r--r--. 1 root     root          0 Sep  8 14:32 jcart1.log.lck


-rw-r--r--. 1 root     root        404 Sep  8 14:32 jcart2.log


-rw-r--r--. 1 root     root        127 Sep  8 14:32 jcart3.log


-rw-rw-r--. 1 chemaxon chemaxon      0 Aug 24 21:19 null


-rw-rw-r--. 1 chemaxon chemaxon      0 Aug 24 21:19 null.lck


-rw-rw-r--. 1 chemaxon chemaxon      0 Sep  8 14:32 trace0.log


-rw-r--r--. 1 root     root          0 Sep  8 14:32 trace0.log.lck


-rw-rw-r--. 1 chemaxon chemaxon 116525 Sep  8 16:53 trace1.log


-rw-r--r--. 1 root     root          0 Sep  8 14:32 trace1.log.lck


-rw-r--r--. 1 root     root          0 Sep  8 14:32 trace2.log


-rw-r--r--. 1 root     root          0 Sep  7 09:42 trace3.log


-rw-r--r--. 1 root     root          0 Sep  7 09:42 trace3.log.lck


-rw-r--r--. 1 root     root          0 Sep  7 11:42 trace4.log


-rw-r--r--. 1 root     root          0 Sep  7 11:42 trace4.log.lck


-rw-r--r--. 1 root     root          0 Sep  8 13:12 trace5.log


-rw-r--r--. 1 root     root          0 Sep  8 13:12 trace5.log.lck


-rw-r--r--. 1 root     root          0 Sep  8 14:18 trace6.log


-rw-r--r--. 1 root     root          0 Sep  8 14:18 trace6.log.lck


-rw-r--r--. 1 root     root          0 Sep  8 14:26 trace7.log


-rw-r--r--. 1 root     root          0 Sep  8 14:26 trace7.log.lck


-rw-r--r--. 1 root     root          0 Sep  8 14:27 trace8.log


-rw-r--r--. 1 root     root          0 Sep  8 14:27 trace8.log.lck


-rw-r--r--. 1 root     root          0 Sep  8 14:32 trace9.log


-rw-r--r--. 1 root     root          0 Sep  8 14:32 trace9.log.lck


pims:/home/chemaxon/jchem/cartridge/logs$





ChemAxon abe887c64e

08-09-2015 12:17:30

It seems you sent the appropriate log files from /home/chemaxon/jchem-150817/cartridge/logs. However, in these log files there were not any relevant information in connection with the source of the ORA error, indeed. As ORA-00600 is the code of an internal Oracle error, it might help to check the relevant Oracle logs of the database as well.


Best regards,


Krisztina

User bf3dbc99cf

08-09-2015 15:54:43

Dear Krisztina,


As you have said, I am attaching the relevant trace log file of oracle.


It says that there are some kind of write fail error, but I cannot understand.


I think I have plenty of free disk space. (over 64GB)


 


Filesystem     1M-blocks   Used Available Use% Mounted on


/dev/sda2         177370 103109     65251  62% /


tmpfs              32196  15080     17116  47% /dev/shm


/dev/sdb1         938899 234665    656541  27% /home1



Can you give me some idea?


Best regards,



ChemAxon 61b4fee994

09-09-2015 11:50:22

Dear Chong Hak Chae,


We checked your log files and the internal sql command that raises the ORA-600 exception is this call:


SELECT JCHEM.jchem_sessionid_sq.nextval FROM dual


We checked the Oracel knowledge base about the exception message "kdddgb:clsviol_kcbgcur_9" and we found different kind of bugs which resulted in the message, but none of them seems to be connected to a nextval call on a sequence.


I suggest upgrading the database (the 11.3 version solved some similar issues) or contacting Oracle support with your bug report.


Best regards,


Tamas

User bf3dbc99cf

10-09-2015 08:42:12

Dear Mr. Tamas,


Thank you very much for your efforts.


I will try on the upgraded oracle version.


Regards,