hang during table JChem table regeneration - 5.0.6
ChemAxon 60ee1f1328
08-07-2008 09:44:20
Hello,
I have a JChem table (important "MOLECULES" table) which is hanging during the table regeneration after an upgrade to 5.0.6...
Can you advise what my course of action should be...
For starters does jcman produce any logged output in such a circumstance...
Could this be related to license keys (does the regenerate step need to check license keys?)
Many thanks,
Daniel.
ChemAxon aa7c50abf8
08-07-2008 09:48:40
Hi Daniel,
On what platform is your jcman running? (Windows, Linux, other?)
Thanks
Peter
ChemAxon 60ee1f1328
08-07-2008 09:52:21
Hi Peter,
Oracle unbreakable linux - which is a red hat flavour I think:
Kernel 2.6.18-53.el5PAE
Hope that helps,
Daniel.
ChemAxon 60ee1f1328
08-07-2008 09:53:35
By the way...
Other JCHEM tables have regenerated OK...so I think this could be down to particular data but the table was behaving correctly at previous version and so it is a bit of a mystery...
Cheers,
Daniel.
ChemAxon aa7c50abf8
08-07-2008 09:58:20
Is it the jcman GUI or command line?
Thanks
Peter
ChemAxon 60ee1f1328
08-07-2008 10:08:17
Hi Peter,
Via the GUI - I will go and try command line now and see if same behaviour apparent:
Cheers,
Daniel.
ChemAxon 60ee1f1328
08-07-2008 10:23:41
./jcman --login cspace --password cspace --dburl jdbc:Oracle:thin:@localhost:1521:cspace r moleculesv3baro
Above syntax is now running - difficult to tell if it is hanging or not though...
Daniel.
ChemAxon aa7c50abf8
08-07-2008 10:25:15
Is "top" showing any process activity?
Thanks
Peter
ChemAxon 60ee1f1328
08-07-2008 10:35:14
ps -ef shows the process is "on"
top shows that the equivalent pid is using no cpu - so presumably it is hanging...
ChemAxon aa7c50abf8
08-07-2008 11:03:28
It would helpful if you could send us a thread-dump of the process. Here are the steps how you can do it:
1. Establish the pid of the jcman process
2. In a command line window execute the following:
| Code: |
| strace -f -s 250 -p <pid> 2>thread.dump |
3. In another command line window execute the following command multiple times (say, 10 times) at about 1 second intervals:
| Code: |
| kill -SIGQUIT <pid> |
4. Terminate the strace command in the first command line window by pressing Ctrl-C.
<pid> is the pid of the jcman process.
The thread.dump file now should contain the string
multiple times and ChemAxon classnames:
in a slightly garbled format such as:
| Code: |
[pid 11685] write(1, "\tat chemaxon.jchem.JChemManager.init(JChemManager.java:89)\n", 59) = 59
[pid 11685] write(1, "\tat chemaxon.jchem.JChemManager.main(JChemManager.java:106)\n", 60) = 60
|
(Not necessarily exactly this class).
Please, post the thread.dump file.
Thanks
Peter
ChemAxon 60ee1f1328
08-07-2008 12:27:38
This now seems to have come up...
Error at molecule with cd_id: 407
java.sql.SQLException: ORA-00060: deadlock detected while waiting for resource
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:112)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:331)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:288)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:745)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:216)
at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:966)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1170)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3339)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3423)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2319)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2234)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:83)
ChemAxon aa7c50abf8
08-07-2008 12:42:08
Is not some other application locking rows of this table? Maybe a TOAD left open somewhere in transaction?
Thanks
Peter
ChemAxon 60ee1f1328
08-07-2008 12:48:23
i've just bounced oracle and this time get same error but with a different cd_id
Regenerating moleculesv3baro ... Error at molecule with cd_id: 562
java.sql.SQLException: ORA-00060: deadlock detected while waiting for resource
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:112)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:331)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:288)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:745)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:216)
at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:966)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1170)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3339)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3423)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2319)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2234)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:83)
ChemAxon 60ee1f1328
08-07-2008 13:01:03
Full thread dump Java HotSpot(TM) Server VM (10.0-b19 mixed mode):
"Thread-3" prio=10 tid=0xa3748800 nid=0xda6 waiting for monitor entry [0xa36ad000..0xa36ae030]
java.lang.Thread.State: BLOCKED (on object monitor)
at oracle.jdbc.driver.OraclePreparedStatement.executeQuery(OraclePreparedStatement.java:3379)
- waiting to lock <0xa8853dd0> (a oracle.jdbc.driver.T4CConnection)
at chemaxon.jchem.db.Regenerator.getNextMolData(Regenerator.java:127)
- locked <0xa863a878> (a chemaxon.jchem.db.Regenerator)
at chemaxon.jchem.db.Regenerator.access$100(Regenerator.java:25)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:78)
"Thread-2" prio=10 tid=0xa398bc00 nid=0xda5 runnable [0xa36fe000..0xa36fefb0]
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:129)
at oracle.net.ns.Packet.receive(Unknown Source)
at oracle.net.ns.DataPacket.receive(Unknown Source)
at oracle.net.ns.NetInputStream.getNextPacket(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.jdbc.driver.T4CMAREngine.unmarshalUB1(T4CMAREngine.java:1104)
at oracle.jdbc.driver.T4CMAREngine.unmarshalSB1(T4CMAREngine.java:1075)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:480)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:216)
at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:966)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1170)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3339)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3423)
- locked <0xa888d688> (a oracle.jdbc.driver.T4CPreparedStatement)
- locked <0xa88734e8> (a oracle.jdbc.driver.T4CConnection)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2319)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2234)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:83)
"Thread-1" prio=10 tid=0xa39d4000 nid=0xda4 waiting for monitor entry [0xa3892000..0xa3893130]
java.lang.Thread.State: BLOCKED (on object monitor)
at chemaxon.jchem.db.Regenerator.getNextMolData(Regenerator.java:121)
- waiting to lock <0xa863a878> (a chemaxon.jchem.db.Regenerator)
at chemaxon.jchem.db.Regenerator.access$100(Regenerator.java:25)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:78)
"Thread-0" prio=10 tid=0xa373ac00 nid=0xda3 runnable [0xa38e3000..0xa38e40b0]
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:129)
at oracle.net.ns.Packet.receive(Unknown Source)
at oracle.net.ns.DataPacket.receive(Unknown Source)
at oracle.net.ns.NetInputStream.getNextPacket(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.jdbc.driver.T4CMAREngine.unmarshalUB1(T4CMAREngine.java:1104)
at oracle.jdbc.driver.T4CMAREngine.unmarshalSB1(T4CMAREngine.java:1075)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:480)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:216)
at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:966)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1170)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3339)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3423)
- locked <0xa887d2d0> (a oracle.jdbc.driver.T4CPreparedStatement)
- locked <0xa8853dd0> (a oracle.jdbc.driver.T4CConnection)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2319)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2234)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:83)
"Low Memory Detector" daemon prio=10 tid=0x09472c00 nid=0xd99 runnable [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread1" daemon prio=10 tid=0x09470c00 nid=0xd98 waiting on condition [0x00000000..0xa3bfe3f8]
java.lang.Thread.State: RUNNABLE
"CompilerThread0" daemon prio=10 tid=0x0946f000 nid=0xd97 waiting on condition [0x00000000..0xa3dec378]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0x0946dc00 nid=0xd96 waiting on condition [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0x09455c00 nid=0xd95 in Object.wait() [0xa408e000..0xa408efb0]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0xa863ad60> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
- locked <0xa863ad60> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
"Reference Handler" daemon prio=10 tid=0x09451800 nid=0xd94 in Object.wait() [0xa40df000..0xa40e0130]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0xa86a8c20> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked <0xa86a8c20> (a java.lang.ref.Reference$Lock)
"main" prio=10 tid=0x093ac400 nid=0xd8e waiting on condition [0xb7f8f000..0xb7f90208]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at chemaxon.jchem.db.Regenerator.run(Regenerator.java:309)
at chemaxon.jchem.db.UpdateHandler.recalculateTable(UpdateHandler.java:3112)
at chemaxon.jchem.Command.regenerateTable(Command.java:1109)
at chemaxon.jchem.Command.regenerateTable(Command.java:1090)
at chemaxon.jchem.Command.run(Command.java:602)
at chemaxon.jchem.Command.main(Command.java:201)
"VM Thread" prio=10 tid=0x0944e800 nid=0xd93 runnable
"GC task thread#0 (ParallelGC)" prio=10 tid=0x093b3000 nid=0xd8f runnable
"GC task thread#1 (ParallelGC)" prio=10 tid=0x093b4000 nid=0xd90 runnable
"GC task thread#2 (ParallelGC)" prio=10 tid=0x093b5400 nid=0xd91 runnable
"GC task thread#3 (ParallelGC)" prio=10 tid=0x093b6400 nid=0xd92 runnable
"VM Periodic Task Thread" prio=10 tid=0x09474400 nid=0xd9a waiting on condition
JNI global references: 1152
Heap
PSYoungGen total 21312K, used 17554K [0xb37f0000, 0xb4e00000, 0xb4e20000)
eden space 19968K, 83% used [0xb37f0000,0xb4850a30,0xb4b70000)
from space 1344K, 58% used [0xb4b70000,0xb4c34000,0xb4cc0000)
to space 1280K, 0% used [0xb4cc0000,0xb4cc0000,0xb4e00000)
PSOldGen total 9536K, used 3410K [0xa8620000, 0xa8f70000, 0xb37f0000)
object space 9536K, 35% used [0xa8620000,0xa8974ac0,0xa8f70000)
PSPermGen total 20736K, used 10390K [0xa4620000, 0xa5a60000, 0xa8620000)
object space 20736K, 50% used [0xa4620000,0xa5045960,0xa5a60000)
ChemAxon 60ee1f1328
08-07-2008 13:03:20
GUI hangs at same cd_id as above and then jcman needs to be killed (will not close normally)
ChemAxon aa7c50abf8
08-07-2008 14:07:10
Thank you, Daniel, for the detailed info. We're looking into it.
Thanks
Peter
ChemAxon 60ee1f1328
08-07-2008 14:11:26
Hi Peter,
I did a select * from dba_locks before kicking off the process and no blocking locks apparent. KIcked off jcman from cmd line and checked dba_locks again - blocking locks now apparent - looks like this process is causing the locks and not any other?
More output from process below...does seem to be same record...shall I post the data record?
Daniel.
Regenerating moleculesv3baro ... Error at molecule with cd_id: 562
java.sql.SQLException: ORA-00060: deadlock detected while waiting for resource
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:112)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:331)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:288)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:745)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:216)
at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:966)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1170)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3339)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3423)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2319)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2234)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:83)
2008-07-08 14:18:53
Full thread dump Java HotSpot(TM) Server VM (10.0-b19 mixed mode):
"Thread-3" prio=10 tid=0xa36f0400 nid=0xef4 runnable [0xa375c000..0xa375ce30]
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:129)
at oracle.net.ns.Packet.receive(Unknown Source)
at oracle.net.ns.DataPacket.receive(Unknown Source)
at oracle.net.ns.NetInputStream.getNextPacket(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.jdbc.driver.T4CMAREngine.unmarshalUB1(T4CMAREngine.java:1104)
at oracle.jdbc.driver.T4CMAREngine.unmarshalSB1(T4CMAREngine.java:1075)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:480)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:216)
at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:966)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1170)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3339)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3423)
- locked <0xa87e7298> (a oracle.jdbc.driver.T4CPreparedStatement)
- locked <0xa8637c78> (a oracle.jdbc.driver.T4CConnection)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2319)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2234)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:83)
"Thread-2" prio=10 tid=0xa3677400 nid=0xef3 waiting for monitor entry [0xa37ad000..0xa37addb0]
java.lang.Thread.State: BLOCKED (on object monitor)
at oracle.jdbc.driver.PhysicalConnection.needLineUnchecked(PhysicalConnection.java:2405)
- waiting to lock <0xa86356d8> (a oracle.jdbc.driver.T4CConnection)
at oracle.jdbc.driver.PhysicalConnection.needLine(PhysicalConnection.java:2399)
at oracle.jdbc.driver.OracleResultSetImpl.internal_close(OracleResultSetImpl.java:1883)
at oracle.jdbc.driver.OracleResultSetImpl.close(OracleResultSetImpl.java:86)
- locked <0xb3c30870> (a oracle.jdbc.driver.OracleResultSetImpl)
at chemaxon.jchem.db.Regenerator.getNextMolData(Regenerator.java:137)
- locked <0xa8641510> (a chemaxon.jchem.db.Regenerator)
at chemaxon.jchem.db.Regenerator.access$100(Regenerator.java:25)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:78)
"Thread-1" prio=10 tid=0xa354a800 nid=0xef2 waiting for monitor entry [0xa398d000..0xa398df30]
java.lang.Thread.State: BLOCKED (on object monitor)
at chemaxon.jchem.db.Regenerator.getNextMolData(Regenerator.java:121)
- waiting to lock <0xa8641510> (a chemaxon.jchem.db.Regenerator)
at chemaxon.jchem.db.Regenerator.access$100(Regenerator.java:25)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:78)
"Thread-0" prio=10 tid=0xa3560800 nid=0xef1 runnable [0xa39de000..0xa39deeb0]
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:129)
at oracle.net.ns.Packet.receive(Unknown Source)
at oracle.net.ns.DataPacket.receive(Unknown Source)
at oracle.net.ns.NetInputStream.getNextPacket(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.net.ns.NetInputStream.read(Unknown Source)
at oracle.jdbc.driver.T4CMAREngine.unmarshalUB1(T4CMAREngine.java:1104)
at oracle.jdbc.driver.T4CMAREngine.unmarshalSB1(T4CMAREngine.java:1075)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:480)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:216)
at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:966)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1170)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3339)
at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3423)
- locked <0xa8840b38> (a oracle.jdbc.driver.T4CPreparedStatement)
- locked <0xa86356d8> (a oracle.jdbc.driver.T4CConnection)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2319)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2234)
at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:83)
"Low Memory Detector" daemon prio=10 tid=0xa41b7800 nid=0xee5 runnable [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"CompilerThread1" daemon prio=10 tid=0xa41b6000 nid=0xee4 waiting on condition [0x00000000..0xa3bd05f8]
java.lang.Thread.State: RUNNABLE
"CompilerThread0" daemon prio=10 tid=0xa41b4c00 nid=0xee3 waiting on condition [0x00000000..0xa3c51578]
java.lang.Thread.State: RUNNABLE
"Signal Dispatcher" daemon prio=10 tid=0xa41b3800 nid=0xee2 waiting on condition [0x00000000..0x00000000]
java.lang.Thread.State: RUNNABLE
"Finalizer" daemon prio=10 tid=0xa419bc00 nid=0xee1 in Object.wait() [0xa427a000..0xa427adb0]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0xa85e6740> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
- locked <0xa85e6740> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
"Reference Handler" daemon prio=10 tid=0xa419a800 nid=0xee0 in Object.wait() [0xa3ef3000..0xa3ef3f30]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0xa85d0d08> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked <0xa85d0d08> (a java.lang.ref.Reference$Lock)
"main" prio=10 tid=0x0941e400 nid=0xeda sleeping[0xb7f1d000..0xb7f1e208]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at chemaxon.jchem.db.Regenerator.run(Regenerator.java:309)
at chemaxon.jchem.db.UpdateHandler.recalculateTable(UpdateHandler.java:3112)
at chemaxon.jchem.Command.regenerateTable(Command.java:1109)
at chemaxon.jchem.Command.regenerateTable(Command.java:1090)
at chemaxon.jchem.Command.run(Command.java:602)
at chemaxon.jchem.Command.main(Command.java:201)
"VM Thread" prio=10 tid=0xa4197800 nid=0xedf runnable
"GC task thread#0 (ParallelGC)" prio=10 tid=0x09425000 nid=0xedb runnable
"GC task thread#1 (ParallelGC)" prio=10 tid=0x09426000 nid=0xedc runnable
"GC task thread#2 (ParallelGC)" prio=10 tid=0x09427400 nid=0xedd runnable
"GC task thread#3 (ParallelGC)" prio=10 tid=0x09428400 nid=0xede runnable
"VM Periodic Task Thread" prio=10 tid=0xa41b9400 nid=0xee6 waiting on condition
JNI global references: 1244
Heap
PSYoungGen total 21376K, used 6097K [0xb3780000, 0xb4db0000, 0xb4db0000)
eden space 20160K, 27% used [0xb3780000,0xb3ce8588,0xb4b30000)
from space 1216K, 46% used [0xb4b30000,0xb4bbc000,0xb4c60000)
to space 1216K, 0% used [0xb4c80000,0xb4c80000,0xb4db0000)
PSOldGen total 10176K, used 3655K [0xa85b0000, 0xa8fa0000, 0xb3780000)
object space 10176K, 35% used [0xa85b0000,0xa8941f18,0xa8fa0000)
PSPermGen total 20224K, used 10476K [0xa45b0000, 0xa5970000, 0xa85b0000)
object space 20224K, 51% used [0xa45b0000,0xa4feb2a0,0xa5970000)
ChemAxon aa7c50abf8
08-07-2008 14:22:25
| Quote: |
| looks like this process is causing the locks and not any other |
Yes, it pretty much looks like this is a bug in regeneration. I don't think we need more diagnostics data for the moment.
Thanks
Peter
ChemAxon 9c0afc9aaf
08-07-2008 18:02:41
Hi Daniel,
JChem 5.0.6.1 has been released specifically to fix this problem.
Please try it and let us know if it solves your problem.
Best regards,
Szilard
ChemAxon 60ee1f1328
08-07-2008 18:05:35
I will do so first thing tomorrow morning...
ATB,
Daniel.
ChemAxon 60ee1f1328
09-07-2008 09:38:18
that looks like it is working now...the regeneration has certainly gone way beyond the point of breaking yesterday...