the more I am working through this issue, the more I get convinced that 
it's a Derby issue.
When the select statement is modified slightly (not using joining of 
tables on themselves, but rather using IN), then everything works without 
a hiccup:

SELECT 
    P1.ID ,
    R1.description
    P1.BOOK
    P1.NOMINAL
    P1.NOMINAL * R1.Factor
FROM
    P_TABLE P1,
    R_TABLE R1
WHERE
    P1.IN_ID = R1.IN_ID  AND
    R1.IN_ID in (
      select 
        R2.IN_ID
      from 
        P_TABLE P2,
        R_TABLE R2
      where 
        P2.IN_ID = R2.IN_ID AND
        P2.NOMINAL <> 0  AND
        R2.IType='X'
      GROUP BY R2.IN_ID 
      HAVING COUNT(*) >1
    )


So, this leads me to believe that SELECT statements such as this causes a 
problem within Derby:

select
    *
from
    TABLE T1,
     (
         select <field> from TABLE T2
     ) as M
where
    M.<field> = T1.<field>

----- Forwarded by Pavel Bortnovskiy/JEFCO on 01/20/2011 03:55 PM -----

From:
Pavel Bortnovskiy/JEFCO
To:
Derby Discussion <derby-user@db.apache.org>
Date:
01/20/2011 01:28 PM
Subject:
Can it be that Derby (in-memory) is deadlocking on this query?


Hello:

while running my application, I noticed that when the following query 
(which uses a subquery with tables joining on themselves) is executed, the 
application processes 185 records and then sits indefinitely in 
ResultSet.next() method:

SELECT 
    P1.ID ,
    R1.description
    P1.BOOK
    P1.NOMINAL
    P1.NOMINAL * R1.Factor
FROM
    P_TABLE P1,
    R_TABLE R1,
    (
      select 
        R2.IN_ID
      from 
        P_TABLE P2,
        R_TABLE R2
      where 
        P2.IN_ID = R2.IN_ID AND
        P2.NOMINAL <> 0  AND
        R2.IType='X'
      GROUP BY R2.IN_ID 
      HAVING COUNT(*) >1
    ) as MULTI
WHERE
    P1.IN_ID = R1.IN_ID  AND
    MULTI.IN_ID = R1.IN_ID


Then I tried running AquaDataStudio with this query and it's been over 16 
minutes without any results back:



However, when I run the subquery itself, it executes practically 
instanteneously:



And if I replace the subquery with where R1.IN in ('P32764', 'P32765', ... 
[all results from subquery]), it executes in a few ms:



I have a suspicion that Derby (which is running in in-memory only mode) is 
deadlocking.
What can I do on my end (without exposing our data) to help you diagnose 
this.

Please respond as soon as you can, since this is quite important and 
urgent.

Thank you,
Pavel.




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