Lock Timeouts and Heap Space Exhaustion

I'm having some trouble figuring out the best way to handle resource constraints in my application. Generally speaking, the application works well after starting for about a day or so, but inevitably starts generating "Lock timeout" messages and eventually runs out of heap space.
Here is the main entity class:
http://github.com/justindthomas/flower_as/blob/master/src/java/name/justinthomas/flower/analysis/statistics/StatisticalInterval.java
Here is a supporting, persistent class:
http://github.com/justindthomas/flower_as/blob/master/src/java/name/justinthomas/flower/analysis/statistics/StatisticalFlow.java
This is the data accessor:
http://github.com/justindthomas/flower_as/blob/master/src/java/name/justinthomas/flower/analysis/statistics/StatisticsAccessor.java
And here is the class that controls the insertion and retrieval of data:
http://github.com/justindthomas/flower_as/blob/master/src/java/name/justinthomas/flower/analysis/statistics/StatisticsManager.java
The general flow is that a netflow packet is received from a sensor and the StatisticsManager normalizes the flow as it is inserted into the database. The normalization converts the summarized flow into several "resolutions." For example, one resolution might be 5000 ms. So the StatisticsManager takes the flow's end time/5000 - start time/5000 and divides the volume by the result and inserts that data into the database. It sounds kind of confusing, but results in a dataset that allows me to query for netflow activity for any time frame.
It also means that the database is queried as it is written to; existing data is updated more frequently than new data is written.
Regardless, Sleepycat seems to be holding on to more data than it needs to. Once an interval has passed (maybe 5 minutes or so), it is unlikely to be accessed again until queried to create charts. However, the memory usage grows out of control despite the lack of necessity for keeping all but recently entered entries in cache.
This is how the trouble generally starts (note that I've increased the timeout to 15000 ms to try to accommodate for longer wait times, but that just seems to delay the onset of the issue by a day or so):
[#|2010-10-23T13:46:00.854-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=64;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 30264205 -1_pool-6-thread-8_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:32426808 node=17057517 type=READ grant=WAIT_NEW timeoutMillis=15000 startTime=1287866745448 endTime=1287866760795
Owners: [<LockInfo locker="29616818 -1_pool-6-thread-5_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="7246740 -1_pool-6-thread-6_ThreadLocker" type="READ"/>, <LockInfo locker="26940477 -1_pool-6-thread-2_ThreadLocker" type="WRITE"/>, <LockInfo locker="5099094 -1_pool-6-thread-4_ThreadLocker" type="READ"/>]
|#]
[#|2010-10-23T15:00:41.343-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=65;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 14184769 -1_pool-6-thread-1_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:32730917 node=17057517 type=READ grant=WAIT_NEW timeoutMillis=15000 startTime=1287871223679 endTime=1287871241341
Owners: [<LockInfo locker="23975039 -1_pool-6-thread-8_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="19650664 -1_pool-6-thread-6_ThreadLocker" type="READ"/>]
|#]
[#|2010-10-23T15:32:13.090-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=66;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 17937364 -1_pool-6-thread-7_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:20265315 node=17057517 type=WRITE grant=WAIT_NEW timeoutMillis=15000 startTime=1287873113904 endTime=1287873133089
Owners: [<LockInfo locker="3251671 -1_pool-6-thread-1_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="32174859 -1_pool-6-thread-8_ThreadLocker" type="READ"/>, <LockInfo locker="33186148 -1_pool-6-thread-4_ThreadLocker" type="WRITE"/>, <LockInfo locker="17825718 -1_pool-6-thread-2_ThreadLocker" type="READ"/>]
|#]
[#|2010-10-23T15:32:13.096-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=64;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 32174859 -1_pool-6-thread-8_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:20265315 node=17057517 type=READ grant=WAIT_NEW timeoutMillis=15000 startTime=1287873118064 endTime=1287873133092
Owners: [<LockInfo locker="3251671 -1_pool-6-thread-1_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="33186148 -1_pool-6-thread-4_ThreadLocker" type="WRITE"/>, <LockInfo locker="17825718 -1_pool-6-thread-2_ThreadLocker" type="READ"/>]
|#]
[#|2010-10-23T15:32:13.367-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=67;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 33186148 -1_pool-6-thread-4_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:20265315 node=17057517 type=WRITE grant=WAIT_NEW timeoutMillis=15000 startTime=1287873118366 endTime=1287873133366
Owners: [<LockInfo locker="3251671 -1_pool-6-thread-1_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="17825718 -1_pool-6-thread-2_ThreadLocker" type="READ"/>, <LockInfo locker="25145711 -1_pool-6-thread-6_ThreadLocker" type="READ"/>, <LockInfo locker="5544029 -1_pool-6-thread-5_ThreadLocker" type="READ"/>]
|#]
[#|2010-10-23T15:33:14.030-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=68;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 31602565 -1_pool-6-thread-5_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:11219992 node=17057517 type=WRITE grant=WAIT_NEW timeoutMillis=15000 startTime=1287873175916 endTime=1287873194019
Owners: [<LockInfo locker="27649147 -1_pool-6-thread-2_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="3895581 -1_pool-6-thread-7_ThreadLocker" type="WRITE"/>, <LockInfo locker="8345933 -1_pool-6-thread-8_ThreadLocker" type="WRITE"/>, <LockInfo locker="12576013 -1_pool-6-thread-6_ThreadLocker" type="WRITE"/>, <LockInfo locker="5695501 -1_pool-6-thread-1_ThreadLocker" type="WRITE"/>]
|#]
[#|2010-10-23T15:33:23.334-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=64;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 8345933 -1_pool-6-thread-8_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:11219992 node=17057517 type=WRITE grant=WAIT_NEW timeoutMillis=15000 startTime=1287873184851 endTime=1287873203333
Owners: [<LockInfo locker="3895581 -1_pool-6-thread-7_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="12576013 -1_pool-6-thread-6_ThreadLocker" type="WRITE"/>, <LockInfo locker="5695501 -1_pool-6-thread-1_ThreadLocker" type="WRITE"/>, <LockInfo locker="13327115 -1_pool-6-thread-4_ThreadLocker" type="READ"/>, <LockInfo locker="11939897 -1_pool-6-thread-5_ThreadLocker" type="READ"/>]
|#]
[#|2010-10-23T15:33:23.344-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=69;_ThreadName=Thread-1;|addStatisticalSeconds Failed: (JE 4.0.104) Lock expired. Locker 12576013 -1_pool-6-thread-6_ThreadLocker: waited for lock on database=persist#Statistics#name.justinthomas.flower.analysis.statistics.StatisticalInterval LockAddr:11219992 node=17057517 type=WRITE grant=WAIT_NEW timeoutMillis=15000 startTime=1287873184893 endTime=1287873203343
Owners: [<LockInfo locker="3895581 -1_pool-6-thread-7_ThreadLocker" type="WRITE"/>]
Waiters: [<LockInfo locker="5695501 -1_pool-6-thread-1_ThreadLocker" type="WRITE"/>, <LockInfo locker="13327115 -1_pool-6-thread-4_ThreadLocker" type="READ"/>, <LockInfo locker="11939897 -1_pool-6-thread-5_ThreadLocker" type="READ"/>]
|#]
Those errors go on and on and on, until I eventually see this:
[#|2010-10-23T17:37:29.876-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=71;_ThreadName=Thread-1;|Exception in thread "ContainerBackgroundProcessor[StandardEngine[com.sun.appserv]]" |#]
[#|2010-10-23T17:37:34.915-0700|INFO|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=23;_ThreadName=Thread-1;|In main loop, we have serious trouble: java.lang.OutOfMemoryError: Java heap space|#]
[#|2010-10-23T17:37:56.516-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=66;_ThreadName=Thread-1;|Exception in thread "pool-6-thread-7" |#]
[#|2010-10-23T17:39:11.060-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=23;_ThreadName=Thread-1;|Exception in thread "{felix.fileinstall.poll=5000, felix.fileinstall.bundles.new.start=true, service.pid=org.apache.felix.fileinstall.fd8877ce-71aa-41d2-8ddc-15ce996cde1b, felix.fileinstall.dir=/opt/glassfishv3/glassfish/domains/domain1/autodeploy/bundles/, felix.fileinstall.filename=org.apache.felix.fileinstall-autodeploy-bundles.cfg, service.factorypid=org.apache.felix.fileinstall, felix.fileinstall.debug=1}" |#]
[#|2010-10-23T17:39:11.070-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=66;_ThreadName=Thread-1;|java.lang.OutOfMemoryError: Java heap space
     at java.util.IdentityHashMap.init(IdentityHashMap.java:261)
     at java.util.IdentityHashMap.<init>(IdentityHashMap.java:207)
     at com.sleepycat.je.utilint.IdentityHashMap.<init>(IdentityHashMap.java:25)
     at com.sleepycat.je.cleaner.LocalUtilizationTracker.<init>(LocalUtilizationTracker.java:39)
     at com.sleepycat.je.recovery.Checkpointer.flushDirtyNodes(Checkpointer.java:665)
     at com.sleepycat.je.recovery.Checkpointer.syncDatabase(Checkpointer.java:604)
     at com.sleepycat.je.dbi.DatabaseImpl.sync(DatabaseImpl.java:977)
     at com.sleepycat.je.dbi.DatabaseImpl.handleClosed(DatabaseImpl.java:863)
     at com.sleepycat.je.Database.closeInternal(Database.java:458)
     at com.sleepycat.je.Database.close(Database.java:314)
     at com.sleepycat.je.SecondaryDatabase.close(SecondaryDatabase.java:331)
     at com.sleepycat.persist.impl.Store.closeDb(Store.java:1454)
     at com.sleepycat.persist.impl.Store.close(Store.java:1059)
     at com.sleepycat.persist.EntityStore.close(EntityStore.java:630)
     at name.justinthomas.flower.analysis.persistence.FlowReceiver.addFlow(FlowReceiver.java:94)
     at name.justinthomas.flower.analysis.persistence.FlowReceiver.addFlow(FlowReceiver.java:65)
     at name.justinthomas.flower.collector.FlowWorker.parseData(FlowWorker.java:382)
     at name.justinthomas.flower.collector.FlowWorker.v9(FlowWorker.java:111)
     at name.justinthomas.flower.collector.FlowWorker.run(FlowWorker.java:61)
     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
     at java.lang.Thread.run(Thread.java:636)
|#]
[#|2010-10-23T17:39:11.124-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=23;_ThreadName=Thread-1;|java.lang.OutOfMemoryError: Java heap space
|#]
[#|2010-10-23T17:39:11.141-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=72;_ThreadName=Thread-1;|Exception in thread "pool-6-thread-3" |#]
[#|2010-10-23T17:39:11.144-0700|SEVERE|glassfish3.0.1|javax.enterprise.system.std.com.sun.enterprise.v3.services.impl|_ThreadID=72;_ThreadName=Thread-1;|java.lang.OutOfMemoryError: Java heap space
|#]
It's very frustrating, because things run so well at first and then just deteriorate into a resource nightmare. Any suggestions would be welcome. The application is running with 3 CPU cores and 2GB RAM.
Edited by: justindthomas on Oct 23, 2010 7:19 PM: I initially tried to use the forum's "URL" mechanism, but that doesn't seem to work worth anything, so I un-did it.

I've disabled that thread for now. While debugging that, I ran into a SecondaryIntegrityException and I read that I shouldn't use secondary indexes without also using transactions. I enabled transactional processing, but the locking issues grew far worse. I opted to find ways to not use secondary indexes instead.You're right that with secondaries it is important to use txns. But I'm not sure why you're having such severe locking problems with txns. Were you using a txn with a cursor, to perform a scan? If so, I can probably suggest ways of doing that without the txn, if you can describe what you're doing and/or point me to your source code. Or, perhaps you've decided not to use secondaries, and this isn't an issue anymore?
--mark                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       

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    Copyright 2001-2009 Paul Davis, Stephane Letz, Jack O'Quinn, Torben Hohn and others.
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    Hi!
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    adm disk lp wheel http network video audio optical storage power users polkitd vboxusers wireshark kismet
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    Last edited by iamgabo (2012-12-15 02:21:08)

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    Java Threads: ( => current thread )
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    0x02a65000 JavaThread "Swing-Shell" daemon [_thread_blocked, id=3708]
    0x03066c00 JavaThread "Image Fetcher 3" daemon [_thread_blocked, id=4052]
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    0x02b3a000 JavaThread "AWT-Windows" daemon [_thread_in_native, id=2400]
    0x02b38c00 JavaThread "AWT-Shutdown" [_thread_blocked, id=3240]
    0x02b38000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=2016]
    0x02a6d400 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=4244]
    0x02a68c00 JavaThread "CompilerThread0" daemon [_thread_blocked, id=4104]
    0x02a67800 JavaThread "Attach Listener" daemon [_thread_blocked, id=2128]
    0x02a66800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=4468]
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    def new generation total 4544K, used 4085K [0x1a900000, 0x1ade0000, 0x1b2d0000)
    eden space 4096K, 99% used [0x1a900000, 0x1acfd640, 0x1ad00000)
    from space 448K, 0% used [0x1ad00000, 0x1ad00000, 0x1ad70000)
    to space 448K, 0% used [0x1ad70000, 0x1ad70000, 0x1ade0000)
    tenured generation total 60544K, used 0K [0x1b2d0000, 0x1edf0000, 0x22900000)
    the space 60544K, 0% used [0x1b2d0000, 0x1b2d0000, 0x1b2d0200, 0x1edf0000)
    compacting perm gen total 12288K, used 1189K [0x22900000, 0x23500000, 0x2a900000)
    the space 12288K, 9% used [0x22900000, 0x22a295c8, 0x22a29600, 0x23500000)
    ro space 8192K, 66% used [0x2a900000, 0x2ae4d978, 0x2ae4da00, 0x2b100000)
    rw space 12288K, 52% used [0x2b100000, 0x2b749cb8, 0x2b749e00, 0x2bd00000)
    Dynamic libraries:
    0x00400000 - 0x00423000      C:\java\jdk1.6.0_02\bin\javaw.exe
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    0x77e10000 - 0x77e6f000      C:\WINNT\system32\USER32.dll
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    System # 01 is an Older Gateway Computer 838GM (Media Center) Pentium 4 - 630 HT Processor 3.0 GHz/2MB Cache, 1.536 GB of RAM (1.49GB Recognized) PC3200 with 800 MHz FSB and 200 GB Hard Drive running Windows XP Media Center 2002 SP2 with all latest updates (Actually I was told it is XP Professional plus additional programs for media) and a GMA900 on-board Video outputting to a Gateway EV700 CTR Monitor using a Linksys Cable Modem Model: BEFCMU10 Version 4.0 and Comcast Broadband ISP for Internet Connection.
    System # 02 is a Newer Gateway Computer GM5457E (Media Center) Core 2 Duo Processor E6320 1.86 GHz per CPU Core @ 1066 MHz FSB/4MB Cache, 4.096 GB of RAM (3.405216GB Available to Windows) PC5400 with Intel 945G Chip Set, a SATA II 500 GB Hard Drive running Windows Vista Home Premium V 6.0 (Build 6000) and an NVIDIA GE Force 7500LE Video Card outputting DVI to a new Acer AL2223W HDLCD 22" Monitor using a Linksys Cable Modem Model: BEFCMU10 Version 4.0 and Comcast Broadband ISP for Internet Connection.
    I am a high volume quick trading new "day trader" (actually a "minute" trader) and I have been having an "EXTREEME" problem over the past 10 months, maybe longer, with my older and my newer computer SYSTEMS of locking up (looping, I think, nothing using JAVA seems to work, totally locked) when running JAVA based TD Ameritrade�s "Command Center 2.0". During early very FAST trading minutes (usually 9:30 AM to 10:00 AM) with all functions (limited to 6 each functions each by TD Ameritrade), maybe 20-28 windows working at the same time. I use "Charts, Last Sales, Level II, Watch Lists, Trade Tickets, Actives", as a "DAY-TRADER". The JAVA plug-in providing "streaming" data to my older computer was unreliable, always locking-up. I bought a totally new computer system after I was told by TD Ameritrade TECHNICAL that "IT COULD BE MY OLDER COMPUTER". I bought a new computer, and the same problem, lock-up on this computer with CPU usage between 52% and 59%. I have spent over 12 hours with many different TD Ameritrade technicians trying to help me. I have tried both foxfire and IE and problem is on both. I place a buy order trade and then I need to sell it in less than a minute some times. I can not afford for JAVA to lock up on me for any number of SECONDS while I am trading, and JAVA has done that to me so many times I can�t count. By the time that I "End Task" and then re-open my account I can be down (LOST) several thousand dollars. This only happens when the market is trading furiously and JAVA can�t keep up, at least on my computer. I have tried all modification fixes that TD Ameritrade technicians have given me, and some on your blog http://forum.java.sun.com/profile.jspa?userID=523605), and some fixes from other sites that have been recommended, but I still fear that the problem is "not fixed". I have set -Xmx to "-Xmx100m" and Temp Internet Files to 100 MB. This has worked so far for me all day today but the stock market was not TOO busy and I did not have my second trading account up as I usually do. I think the problem is amplified when the "Market Volume" is very high, meaning that the data is constantly streaming so fast that either JAVA or my computer cannot keep up. I also noticed that there is a totally new version of JAVA (http://www.java.net/download/jdk6/6u10/promoted/b11/binaries/jre-6u10-ea-bin-b11-windows-i586-p-24_jan_2008.exe), do you think I should try this version?? , I had version 6 I think rev.4 a while ago and it failed too. Is this version 6 newer than a month or so ago ??? I am now running 1.6.0 (build 1.6.0_03-b05)
    I have not tried all solutions on you list of "ALL" but this fix seems to work so far, that is I set parameters to -Xmx100m works for me so far, just one day. I will let you know of new failures or continuing good operation,
    Thanks Russ Bower [email protected] I NEED THIS JAVA program TO WORK RELIABLY. Also it seems to be a problem on SCOTT Trade also from a blog I visited, several people claiming it is a JAVA bug.

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