User a7faa21887
28-09-2011 18:24:52
Hi,
We use
JChem Server environment:
Java VM vendor: Sun Microsystems Inc.
Java version: 1.6.0_23
Java VM version: 19.0-b09
JChem version: 5.6.0.0
JChem Index version: 5060000
JDBC driver version: 11.1.0.7.0-Production
on Oracle Database 10.2.0.5 x86_64
For several structures:
SELECT jc_molconvert(structure_as_mol, 'svg') FROM dual
failed with error: ORA-07445 [sjontlo_switch_to()+41].
But sometimes the same structures can be converted into svg without any errors.
ChemAxon aa7c50abf8
29-09-2011 16:02:07
Hi,
How do you set the value of structure_as_mol? Do you create a temporary LOB and assign it to structure_as_mol? What is the client environment: PL/SQL, Java, .NET, other?
Thanks
Peter
User a7faa21887
29-09-2011 20:27:09
pkovacs wrote: |
Hi,
How do you set the value of structure_as_mol? Do you create a temporary LOB and assign it to structure_as_mol? What is the client environment: PL/SQL, Java, .NET, other?
Thanks
Peter
|
Hi, Peter.
This column is just clob. There is PL/SQL function in package:
function lob2svg(
p_Structure clob,
p_UseClean varchar2 default 'F',
p_Options varchar2 default null)
return clob
as
l_SVG CLOB;
begin
SELECT jc_molconvert(p_Structure, 'svg:' || nvl(p_Options, 'H_off')) INTO l_SVG
FROM dual;
-- finally, remove DOCTYPE with dtd references
return regexp_replace(l_SVG, '<!DOCTYPE.*?>', null, 1, 1, 'imn');
exception when others then
return null;
end lob2svg;
Also there is a JChem index for table with column "structure_as_mol" (in real it is structure):
CREATE INDEX chem_structs_i_jchem ON chem_structs (structure) INDEXTYPE IS jchem.jc_idxtype
PARAMETERS ('fp_size=32,fp_bit=2,pat_length=6,duplicateFiltering=n');
Thanks
ChemAxon aa7c50abf8
30-09-2011 21:09:17
Thanks for the additional input.
We recently started to encounter the same error very sporadically (in scenarios different from yours, but similarily involving LOBs) after upgrading some of our test machines from Oracle 10.2.0.4 to 10.2.0.5. My gut feeling is that this is a bug introduced with 10.2.0.5, but this needs to be confirmed yet through further investigation. In the meantime, if you find the opportunity (and find it worthwhile), you could try and see whether using 10.2.0.4 instead of 10.2.0.5 is a work-around.
Peter
ChemAxon aa7c50abf8
05-10-2011 15:54:41
We can consistently reproduce the problem with Oracle 10.2.0.5. We can't reproduce it with 10.2.0.4. We will open an SR with Oracle Support ASAP.
Peter
ChemAxon aa7c50abf8
07-11-2011 10:45:22
I filed a bug report with Oracle. I was told that extended support license is required to raise a bug on 10.2.0.5. (I was not aware of this, but found nevertheless: https://blogs.oracle.com/stevenChan/entry/ecs_10gr2_10204 )
I could not reproduce this problem with 11.2.0.3. Is it not an option for you to upgrade to 11.2.0.3? (JChem Cartridge is also about 3 times faster on 11g than on 10g.)
Peter
User a7faa21887
07-11-2011 19:28:40
pkovacs wrote: |
I filed a bug report with Oracle. I was told that extended support license is required to raise a bug on 10.2.0.5. (I was not aware of this, but found nevertheless: https://blogs.oracle.com/stevenChan/entry/ecs_10gr2_10204 )
I could not reproduce this problem with 11.2.0.3. Is it not an option for you to upgrade to 11.2.0.3? (JChem Cartridge is also about 3 times faster on 11g than on 10g.)
Peter
|
Hi, Peter.
You knew it! - we are just now migrating all our 10g databases to 11.2.0.2 and 11.2.0.3 versions :-)
Pavel
ChemAxon aa7c50abf8
10-11-2011 10:19:33
Thank you, Pavel!
Let us know what you find after upgrading to 11.2.0.2 and/or 11.2.0.3, so we can pursue the issue with Oracle Support if needed.
Thanks
Peter
User a7faa21887
22-11-2011 18:13:42
Hi, Peter.
I tested such svg convertion on 11.2.02 and 11.2.0.3 (Single instances and for RAC databases) - there is no problems like this.
Pavel
ChemAxon aa7c50abf8
22-11-2011 20:03:48
Hi Pavel,
Many thanks for the feed back.
Peter