[kepler-dev] [Bug 5399] New: "./kepler.sh -runwf -nogui -nocache" command will not quit if some parameters are set.

Wed May 11 16:39:14 PDT 2011

http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5399

           Summary: "./kepler.sh -runwf -nogui -nocache" command will not
                    quit if some parameters are set.
           Product: Kepler
           Version: 2.1.0
          Platform: Other
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: core
        AssignedTo: david.v.welker at gmail.com
        ReportedBy: jianwu at sdsc.edu
         QAContact: kepler-dev at kepler-project.org
   Estimated Hours: 0.0

When parameters are set, such as "./kepler.sh -runwf -nogui -nocache -Para
newValue workflow.xml", the whole workflow execution will finish correctly. But
the process will not quit unless using "Ctrl C". It is because LSIDGenerator
try to update database for the parameter value change, which cause HSQL data
base server keep running even after the workflow execution is done. 

The trace stack for HSQL accessing is (I got it by deleting
hsqldb-1.8.0.10.jar).

    at
org.kepler.util.sql.DatabaseType._connectInitialize(DatabaseType.java:885)
    at org.kepler.util.sql.DatabaseType.connect(DatabaseType.java:88)
    at
org.kepler.util.sql.DatabaseFactory.getConnectedDatabaseType(DatabaseFactory.java:269)
    at
org.kepler.util.sql.DatabaseFactory.getConnectedDatabaseType(DatabaseFactory.java:146)
    at
org.kepler.objectmanager.lsid.LSIDGenerator.openDatabase(LSIDGenerator.java:289)
    at
org.kepler.objectmanager.lsid.LSIDGenerator.<init>(LSIDGenerator.java:103)
    at
org.kepler.objectmanager.lsid.LSIDGenerator.getInstance(LSIDGenerator.java:126)
    at org.kepler.moml.NamedObjId.updateRevision(NamedObjId.java:740)
    at org.kepler.moml.NamedObjId.handleMoMLChangeRequest(NamedObjId.java:540)
    at org.kepler.moml.NamedObjId.changeExecuted(NamedObjId.java:686)
    at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:202)
    at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:735)
    at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1775)
    at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1921)
    at
ptolemy.moml.MoMLCommandLineApplication.<init>(MoMLCommandLineApplication.java:162)
    at
ptolemy.moml.MoMLCommandLineApplication.main(MoMLCommandLineApplication.java:214)

The content I got after workflow execution using 'Ctrl \':

     [null] 28 ms. Memory: 83008K Free: 70679K (85%)
^\2011-05-11 16:35:22
Full thread dump Java HotSpot(TM) 64-Bit Server VM (19.1-b02-334 mixed mode):

"Thread-4" daemon prio=5 tid=1019a5800 nid=0x10d758000 runnable [10d757000]
   java.lang.Thread.State: RUNNABLE
    at java.io.FileInputStream.readBytes(Native Method)
    at java.io.FileInputStream.read(FileInputStream.java:177)
    at
java.lang.UNIXProcess$DeferredCloseInputStream.read(UNIXProcess.java:218)
    at org.apache.tools.ant.taskdefs.StreamPumper.run(StreamPumper.java:92)
    at java.lang.Thread.run(Thread.java:680)

"Thread-3" daemon prio=5 tid=1019a5000 nid=0x10d655000 runnable [10d654000]
   java.lang.Thread.State: RUNNABLE
    at java.io.FileInputStream.readBytes(Native Method)
    at java.io.FileInputStream.read(FileInputStream.java:199)
    at
java.lang.UNIXProcess$DeferredCloseInputStream.read(UNIXProcess.java:227)
    at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
    at java.io.BufferedInputStream.read1(BufferedInputStream.java:258)
    at java.io.BufferedInputStream.read(BufferedInputStream.java:317)
    - locked <7f33af418> (a java.io.BufferedInputStream)
    at java.io.FilterInputStream.read(FilterInputStream.java:90)
    at org.apache.tools.ant.taskdefs.StreamPumper.run(StreamPumper.java:92)
    at java.lang.Thread.run(Thread.java:680)

"process reaper" daemon prio=5 tid=10395a000 nid=0x10d1e9000 runnable
[10d1e8000]
   java.lang.Thread.State: RUNNABLE
    at java.lang.UNIXProcess.waitForProcessExit(Native Method)
    at java.lang.UNIXProcess.access$900(UNIXProcess.java:17)
    at java.lang.UNIXProcess$2$1.run(UNIXProcess.java:86)

"Low Memory Detector" daemon prio=5 tid=103817800 nid=0x10c204000 runnable
[00000000]
   java.lang.Thread.State: RUNNABLE

"CompilerThread1" daemon prio=9 tid=103817000 nid=0x10c101000 waiting on
condition [00000000]
   java.lang.Thread.State: RUNNABLE

"CompilerThread0" daemon prio=9 tid=103816000 nid=0x10b707000 waiting on
condition [00000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=9 tid=103815800 nid=0x10b604000 waiting on
condition [00000000]
   java.lang.Thread.State: RUNNABLE

"Surrogate Locker Thread (CMS)" daemon prio=5 tid=103814800 nid=0x10b501000
waiting on condition [00000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=8 tid=1028b9800 nid=0x10b0ea000 in Object.wait()
[10b0e9000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <7f44e0848> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
    - locked <7f44e0848> (a java.lang.ref.ReferenceQueue$Lock)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=1028b8800 nid=0x10afe7000 in
Object.wait() [10afe6000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <7f44e3ec0> (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 <7f44e3ec0> (a java.lang.ref.Reference$Lock)

"main" prio=5 tid=103800800 nid=0x100501000 in Object.wait() [100500000]
   java.lang.Thread.State: WAITING (on object monitor)
    at java.lang.Object.wait(Native Method)
    - waiting on <7f33ad080> (a java.lang.UNIXProcess)
    at java.lang.Object.wait(Object.java:485)
    at java.lang.UNIXProcess.waitFor(UNIXProcess.java:115)
    - locked <7f33ad080> (a java.lang.UNIXProcess)
    at org.apache.tools.ant.taskdefs.Execute.waitFor(Execute.java:551)
    at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:482)
    at org.apache.tools.ant.taskdefs.Java.fork(Java.java:784)
    at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:211)
    at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:132)
    at org.apache.tools.ant.taskdefs.Java.execute(Java.java:105)
    at org.kepler.build.Run.runSuite(Run.java:309)
    at org.kepler.build.Run.run(Run.java:213)
    at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102)
    at org.kepler.build.runner.Kepler.run(Kepler.java:158)
    at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:102)
    at org.kepler.build.runner.Kepler.main(Kepler.java:89)

"VM Thread" prio=9 tid=10380c000 nid=0x10aee4000 runnable 

"Gang worker#0 (Parallel GC Threads)" prio=9 tid=103802000 nid=0x102401000
runnable 

"Gang worker#1 (Parallel GC Threads)" prio=9 tid=103802800 nid=0x102504000
runnable 

"Gang worker#2 (Parallel GC Threads)" prio=9 tid=103803000 nid=0x102607000
runnable 

"Gang worker#3 (Parallel GC Threads)" prio=9 tid=103804000 nid=0x10270a000
runnable 

"Concurrent Mark-Sweep GC Thread" prio=9 tid=10287b000 nid=0x10abf0000 runnable 
"VM Periodic Task Thread" prio=10 tid=103829800 nid=0x10c307000 waiting on
condition 

"Exception Catcher Thread" prio=10 tid=103801800 nid=0x10176a000 runnable 
JNI global references: 1330

Heap
 par new generation   total 19136K, used 5592K [7f3000000, 7f44c0000,
7f44c0000)
  eden     [null] 2011-05-11 16:35:22
     [null] Full thread dump Java HotSpot(TM) 64-Bit Server VM (19.1-b02-334
mixed mode):
     [null] 
     [null] "DestroyJavaVM" prio=5 tid=102427000 nid=0x101b6a000 waiting on
condition [00000000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null] 
     [null] "HSQLDB Connection @1a3526cf" prio=5 tid=107436800 nid=0x126101000
runnable [126100000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null]     at java.net.SocketInputStream.socketRead0(Native Method)
 space 17024K,  30% used [7f3000000, 7f351dff0, 7f40a0000)
  from space 2112K,  16% used [7f42b0000, 7f43083b8, 7f44c0000)
  to   space 2112K,   0% used [7f40a0000, 7f40a0000, 7f42b0000)
 concurrent mark-sweep generation total 63872K, used 1065K [7f44c0000,
7f8320000, 7fae00000)
 concurrent-mark-sweep perm gen total 21248K, used 6995K [7fae00000, 7fc2c0000,
800000000)

     [null]     at java.net.SocketInputStream.read(SocketInputStream.java:129)
     [null]     at java.net.SocketInputStream.read(SocketInputStream.java:182)
     [null]     at java.io.DataInputStream.readInt(DataInputStream.java:370)
     [null]     at org.hsqldb.Result.read(Unknown Source)
     [null]     at org.hsqldb.ServerConnection.run(Unknown Source)
     [null]     at java.lang.Thread.run(Thread.java:680)
     [null] 
     [null] "HSQLDB Timer @702eef15" daemon prio=5 tid=110312800
nid=0x113e61000 in Object.wait() [113e60000]
     [null]    java.lang.Thread.State: TIMED_WAITING (on object monitor)
     [null]     at java.lang.Object.wait(Native Method)
     [null]     - waiting on <7df4dd660> (a org.hsqldb.lib.HsqlTimer$TaskQueue)
     [null]     at org.hsqldb.lib.HsqlTimer$TaskQueue.park(Unknown Source)
     [null]     - locked <7df4dd660> (a org.hsqldb.lib.HsqlTimer$TaskQueue)
     [null]     at org.hsqldb.lib.HsqlTimer.nextTask(Unknown Source)
     [null]     - locked <7df4dd660> (a org.hsqldb.lib.HsqlTimer$TaskQueue)
     [null]     at org.hsqldb.lib.HsqlTimer$TaskRunner.run(Unknown Source)
     [null]     at java.lang.Thread.run(Thread.java:680)
     [null] 
     [null] "HSQLDB Server @46dab859" prio=5 tid=1102bc000 nid=0x127600000
runnable [1275ff000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null]     at java.net.PlainSocketImpl.socketAccept(Native Method)
     [null]     at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:408)
     [null]     - locked <7df4e4828> (a java.net.SocksSocketImpl)
     [null]     at java.net.ServerSocket.implAccept(ServerSocket.java:462)
     [null]     at java.net.ServerSocket.accept(ServerSocket.java:430)
     [null]     at org.hsqldb.Server.run(Unknown Source)
     [null]     at org.hsqldb.Server.access$000(Unknown Source)
     [null]     at org.hsqldb.Server$ServerThread.run(Unknown Source)
     [null] 
     [null] "AWT-AppKit" daemon prio=5 tid=11049e000 nid=0x7fff70e84ca0
runnable [00000000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null] 
     [null] "Poller SunPKCS11-Darwin" daemon prio=1 tid=10289b800
nid=0x11395e000 waiting on condition [11395d000]
     [null]    java.lang.Thread.State: TIMED_WAITING (sleeping)
     [null]     at java.lang.Thread.sleep(Native Method)
     [null]     at
sun.security.pkcs11.SunPKCS11$TokenPoller.run(SunPKCS11.java:692)
     [null]     at java.lang.Thread.run(Thread.java:680)
     [null] 
     [null] "Low Memory Detector" daemon prio=5 tid=10200b800 nid=0x10f90d000
runnable [00000000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null] 
     [null] "CompilerThread1" daemon prio=9 tid=10200b000 nid=0x10f40a000
waiting on condition [00000000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null] 
     [null] "CompilerThread0" daemon prio=9 tid=10200a000 nid=0x10ef07000
waiting on condition [00000000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null] 
     [null] "Signal Dispatcher" daemon prio=9 tid=102009800 nid=0x10ea04000
waiting on condition [00000000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null] 
     [null] "Surrogate Locker Thread (CMS)" daemon prio=5 tid=102008800
nid=0x10e501000 waiting on condition [00000000]
     [null]    java.lang.Thread.State: RUNNABLE
     [null] 
     [null] "Finalizer" daemon prio=8 tid=1070ee800 nid=0x10dd01000 in
Object.wait() [10dd00000]
     [null]    java.lang.Thread.State: WAITING (on object monitor)
     [null]     at java.lang.Object.wait(Native Method)
     [null]     - waiting on <7dee47cf0> (a java.lang.ref.ReferenceQueue$Lock)
     [null]     at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
     [null]     - locked <7dee47cf0> (a java.lang.ref.ReferenceQueue$Lock)
     [null]     at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
     [null]     at
java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
     [null] 
     [null] "Reference Handler" daemon prio=10 tid=1070ed800 nid=0x10cf4d000 in
Object.wait() [10cf4c000]
     [null]    java.lang.Thread.State: WAITING (on object monitor)
     [null]     at java.lang.Object.wait(Native Method)
     [null]     - waiting on <7dee44a48> (a java.lang.ref.Reference$Lock)
     [null]     at java.lang.Object.wait(Object.java:485)
     [null]     at
java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
     [null]     - locked <7dee44a48> (a java.lang.ref.Reference$Lock)
     [null] 
     [null] "VM Thread" prio=9 tid=1070e9000 nid=0x10ca4a000 runnable 
     [null] 
     [null] "Gang worker#0 (Parallel GC Threads)" prio=9 tid=107000000
nid=0x107d01000 runnable 
     [null] 
     [null] "Gang worker#1 (Parallel GC Threads)" prio=9 tid=107001000
nid=0x108204000 runnable 
     [null] 
     [null] "Gang worker#2 (Parallel GC Threads)" prio=9 tid=107001800
nid=0x108707000 runnable 
     [null] 
     [null] "Gang worker#3 (Parallel GC Threads)" prio=9 tid=107002000
nid=0x108c0a000 runnable 
     [null] 
     [null] "Concurrent Mark-Sweep GC Thread" prio=9 tid=10707d000
nid=0x10c756000 runnable 
     [null] "VM Periodic Task Thread" prio=10 tid=102015000 nid=0x10fe10000
waiting on condition 
     [null] 
     [null] "Exception Catcher Thread" prio=10 tid=102801800 nid=0x103d01000
runnable 
     [null] JNI global references: 1077
     [null] 
     [null] Heap
     [null]  par new generation   total 19136K, used 5918K [7dae00000,
7dc2c0000, 7dee00000)
     [null]   eden space 17024K,  31% used [7dae00000, 7db349138, 7dbea0000)
     [null]   from space 2112K,  23% used [7dc0b0000, 7dc12e978, 7dc2c0000)
     [null]   to   space 2112K,   0% used [7dbea0000, 7dbea0000, 7dc0b0000)
     [null]  concurrent mark-sweep generation total 63872K, used 8167K
[7dee00000, 7e2c60000, 7fae00000)
     [null]  concurrent-mark-sweep perm gen total 34480K, used 21401K
[7fae00000, 7fcfac000, 800000000)
     [null]

-- 
Configure bugmail: http://bugzilla.ecoinformatics.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the QA contact for the bug.