Ticket #6693: cellsens-stack.txt

File cellsens-stack.txt, 15.0 KB (added by saloynton, 8 years ago)
Line 
12011-09-07 12:06:42
2Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.1-b02-384 mixed mode):
3
4"Attach Listener" daemon prio=9 tid=103bb0000 nid=0x123f8d000 waiting on condition [00000000]
5   java.lang.Thread.State: RUNNABLE
6
7"pool-2-thread-1" prio=5 tid=103e94000 nid=0x11fb06000 runnable [11fb04000]
8   java.lang.Thread.State: RUNNABLE
9        at sun.nio.ch.FileDispatcher.pread0(Native Method)
10        at sun.nio.ch.FileDispatcher.pread(FileDispatcher.java:31)
11        at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:199)
12        at sun.nio.ch.IOUtil.read(IOUtil.java:175)
13        at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:612)
14        at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:120)
15        at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:105)
16        at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:510)
17        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:108)
18        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:116)
19        at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:125)
20        at loci.common.Location.getHandle(Location.java:284)
21        at loci.common.Location.getHandle(Location.java:255)
22        at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:80)
23        at loci.formats.in.CellSensReader.decodeTile(CellSensReader.java:406)
24        at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:218)
25        at loci.formats.ImageReader.openBytes(ImageReader.java:396)
26        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:183)
27        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:175)
28        at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:180)
29        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
30        at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
31        at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:873)
32        at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:798)
33        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:575)
34        at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:216)
35        at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
36        at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
37        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
38        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
39        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
40        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
41        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:206)
42        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
43        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
44        at java.lang.Thread.run(Thread.java:680)
45
46"pool-1-thread-1" prio=5 tid=103d80800 nid=0x120ead000 waiting on condition [120eac000]
47   java.lang.Thread.State: WAITING (parking)
48        at sun.misc.Unsafe.park(Native Method)
49        - parking to wait for  <7dd7f3870> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
50        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
51        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
52        at java.util.concurrent.DelayQueue.take(DelayQueue.java:160)
53        at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:609)
54        at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:602)
55        at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
56        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
57        at java.lang.Thread.run(Thread.java:680)
58
59"pool-3-thread-1" prio=5 tid=104bf0000 nid=0x123b1c000 waiting on condition [123b1b000]
60   java.lang.Thread.State: TIMED_WAITING (parking)
61        at sun.misc.Unsafe.park(Native Method)
62        - parking to wait for  <7de1a0a30> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
63        at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:198)
64        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2025)
65        at java.util.concurrent.DelayQueue.take(DelayQueue.java:164)
66        at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:609)
67        at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:602)
68        at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
69        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
70        at java.lang.Thread.run(Thread.java:680)
71
72"Ice.Timer" prio=6 tid=103907000 nid=0x123a19000 in Object.wait() [123a18000]
73   java.lang.Thread.State: WAITING (on object monitor)
74        at java.lang.Object.wait(Native Method)
75        - waiting on <7dde174b0> (a IceInternal.Timer)
76        at java.lang.Object.wait(Object.java:485)
77        at IceInternal.Timer.run(Timer.java:177)
78        - locked <7dde174b0> (a IceInternal.Timer)
79
80"Ice.SelectorThread" prio=6 tid=1039f6800 nid=0x123916000 runnable [123915000]
81   java.lang.Thread.State: RUNNABLE
82        at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
83        at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:136)
84        at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:69)
85        at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69)
86        - locked <7ddff96a0> (a sun.nio.ch.Util$2)
87        - locked <7ddff9688> (a java.util.Collections$UnmodifiableSet)
88        - locked <7ddf4d090> (a sun.nio.ch.KQueueSelectorImpl)
89        at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80)
90        at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84)
91        at IceInternal.Selector.select(Selector.java:139)
92        at IceInternal.SelectorThread.run(SelectorThread.java:120)
93        at IceInternal.SelectorThread$HelperThread.run(SelectorThread.java:273)
94
95"Ice.ThreadPool.Client-0" prio=6 tid=103979000 nid=0x123813000 runnable [123812000]
96   java.lang.Thread.State: RUNNABLE
97        at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
98        at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:136)
99        at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:69)
100        at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69)
101        - locked <7ddfc03e0> (a sun.nio.ch.Util$2)
102        - locked <7ddfc03c8> (a java.util.Collections$UnmodifiableSet)
103        - locked <7ddf4d0d8> (a sun.nio.ch.KQueueSelectorImpl)
104        at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80)
105        at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84)
106        at IceInternal.Selector.select(Selector.java:139)
107        at IceInternal.ThreadPool.run(ThreadPool.java:335)
108        at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
109        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
110
111"Ice.EndpointHostResolverThread" prio=6 tid=103d10000 nid=0x123710000 in Object.wait() [12370f000]
112   java.lang.Thread.State: WAITING (on object monitor)
113        at java.lang.Object.wait(Native Method)
114        - waiting on <7de017b78> (a IceInternal.EndpointHostResolver)
115        at java.lang.Object.wait(Object.java:485)
116        at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:77)
117        - locked <7de017b78> (a IceInternal.EndpointHostResolver)
118        at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:146)
119
120"omero.ClientCallback.ThreadPool-4" prio=6 tid=103d0d000 nid=0x12360d000 in Object.wait() [12360c000]
121   java.lang.Thread.State: WAITING (on object monitor)
122        at java.lang.Object.wait(Native Method)
123        - waiting on <7de00f988> (a IceInternal.ThreadPool)
124        at java.lang.Object.wait(Object.java:485)
125        at IceInternal.ThreadPool.run(ThreadPool.java:315)
126        - locked <7de00f988> (a IceInternal.ThreadPool)
127        at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
128        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
129
130"omero.ClientCallback.ThreadPool-3" prio=6 tid=103d0c800 nid=0x12350a000 in Object.wait() [123509000]
131   java.lang.Thread.State: WAITING (on object monitor)
132        at java.lang.Object.wait(Native Method)
133        - waiting on <7de00f988> (a IceInternal.ThreadPool)
134        at java.lang.Object.wait(Object.java:485)
135        at IceInternal.ThreadPool.run(ThreadPool.java:315)
136        - locked <7de00f988> (a IceInternal.ThreadPool)
137        at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
138        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
139
140"omero.ClientCallback.ThreadPool-2" prio=6 tid=103be8800 nid=0x123407000 in Object.wait() [123406000]
141   java.lang.Thread.State: WAITING (on object monitor)
142        at java.lang.Object.wait(Native Method)
143        - waiting on <7de00f988> (a IceInternal.ThreadPool)
144        at java.lang.Object.wait(Object.java:485)
145        at IceInternal.ThreadPool.run(ThreadPool.java:315)
146        - locked <7de00f988> (a IceInternal.ThreadPool)
147        at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
148        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
149
150"omero.ClientCallback.ThreadPool-1" prio=6 tid=103ed2000 nid=0x123304000 in Object.wait() [123303000]
151   java.lang.Thread.State: WAITING (on object monitor)
152        at java.lang.Object.wait(Native Method)
153        - waiting on <7de00f988> (a IceInternal.ThreadPool)
154        at java.lang.Object.wait(Object.java:485)
155        at IceInternal.ThreadPool.run(ThreadPool.java:315)
156        - locked <7de00f988> (a IceInternal.ThreadPool)
157        at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
158        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
159
160"omero.ClientCallback.ThreadPool-0" prio=6 tid=103f2a800 nid=0x123201000 runnable [123200000]
161   java.lang.Thread.State: RUNNABLE
162        at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
163        at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:136)
164        at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:69)
165        at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:69)
166        - locked <7ddfd8d68> (a sun.nio.ch.Util$2)
167        - locked <7ddfd8db0> (a java.util.Collections$UnmodifiableSet)
168        - locked <7ddfd0140> (a sun.nio.ch.KQueueSelectorImpl)
169        at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:80)
170        at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:84)
171        at IceInternal.Selector.select(Selector.java:139)
172        at IceInternal.ThreadPool.run(ThreadPool.java:335)
173        at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
174        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
175
176"Poller SunPKCS11-Darwin" daemon prio=1 tid=103c49000 nid=0x120fb0000 waiting on condition [120faf000]
177   java.lang.Thread.State: TIMED_WAITING (sleeping)
178        at java.lang.Thread.sleep(Native Method)
179        at sun.security.pkcs11.SunPKCS11$TokenPoller.run(SunPKCS11.java:692)
180        at java.lang.Thread.run(Thread.java:680)
181
182"DestroyJavaVM" prio=5 tid=104a1c000 nid=0x103001000 waiting on condition [00000000]
183   java.lang.Thread.State: RUNNABLE
184
185"TimerQueue" daemon prio=5 tid=1038c2000 nid=0x11f842000 in Object.wait() [11f841000]
186   java.lang.Thread.State: WAITING (on object monitor)
187        at java.lang.Object.wait(Native Method)
188        at javax.swing.TimerQueue.run(TimerQueue.java:232)
189        - locked <7dd7b1090> (a javax.swing.TimerQueue)
190        at java.lang.Thread.run(Thread.java:680)
191
192"AWT-EventQueue-0" prio=6 tid=103b52000 nid=0x11f73f000 in Object.wait() [11f73e000]
193   java.lang.Thread.State: WAITING (on object monitor)
194        at java.lang.Object.wait(Native Method)
195        at java.lang.Object.wait(Object.java:485)
196        at java.awt.EventQueue.getNextEvent(EventQueue.java:520)
197        - locked <7dd7b7fe0> (a java.awt.EventQueue)
198        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:263)
199        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
200        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
201        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
202        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
203        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
204
205"AWT-Shutdown" prio=5 tid=104aba800 nid=0x11f63c000 in Object.wait() [11f63b000]
206   java.lang.Thread.State: WAITING (on object monitor)
207        at java.lang.Object.wait(Native Method)
208        at java.lang.Object.wait(Object.java:485)
209        at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
210        - locked <7dd8edaa0> (a java.lang.Object)
211        at java.lang.Thread.run(Thread.java:680)
212
213"Java2D Disposer" daemon prio=10 tid=103b45000 nid=0x11f411000 in Object.wait() [11f410000]
214   java.lang.Thread.State: WAITING (on object monitor)
215        at java.lang.Object.wait(Native Method)
216        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
217        - locked <7dd7f7fd8> (a java.lang.ref.ReferenceQueue$Lock)
218        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
219        at sun.java2d.Disposer.run(Disposer.java:127)
220        at java.lang.Thread.run(Thread.java:680)
221
222"Timer-0" daemon prio=5 tid=1038bf800 nid=0x11e1fa000 in Object.wait() [11e1f9000]
223   java.lang.Thread.State: WAITING (on object monitor)
224        at java.lang.Object.wait(Native Method)
225        - waiting on <7dd901ba0> (a java.util.TaskQueue)
226        at java.lang.Object.wait(Object.java:485)
227        at java.util.TimerThread.mainLoop(Timer.java:483)
228        - locked <7dd901ba0> (a java.util.TaskQueue)
229        at java.util.TimerThread.run(Timer.java:462)
230
231"AWT-AppKit" daemon prio=5 tid=104997800 nid=0x7fff7119aca0 runnable [00000000]
232   java.lang.Thread.State: RUNNABLE
233
234"Low Memory Detector" daemon prio=5 tid=104895000 nid=0x10be99000 runnable [00000000]
235   java.lang.Thread.State: RUNNABLE
236
237"C2 CompilerThread1" daemon prio=9 tid=104894000 nid=0x10bd96000 waiting on condition [00000000]
238   java.lang.Thread.State: RUNNABLE
239
240"C2 CompilerThread0" daemon prio=9 tid=104893800 nid=0x10bc93000 waiting on condition [00000000]
241   java.lang.Thread.State: RUNNABLE
242
243"Signal Dispatcher" daemon prio=9 tid=104892800 nid=0x10bb90000 runnable [00000000]
244   java.lang.Thread.State: RUNNABLE
245
246"Surrogate Locker Thread (Concurrent GC)" daemon prio=5 tid=104891800 nid=0x10ba8d000 waiting on condition [00000000]
247   java.lang.Thread.State: RUNNABLE
248
249"Finalizer" daemon prio=8 tid=103823000 nid=0x10b98a000 in Object.wait() [10b989000]
250   java.lang.Thread.State: WAITING (on object monitor)
251        at java.lang.Object.wait(Native Method)
252        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
253        - locked <7dd901c90> (a java.lang.ref.ReferenceQueue$Lock)
254        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
255        at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
256
257"Reference Handler" daemon prio=10 tid=103822800 nid=0x10b887000 in Object.wait() [10b886000]
258   java.lang.Thread.State: WAITING (on object monitor)
259        at java.lang.Object.wait(Native Method)
260        at java.lang.Object.wait(Object.java:485)
261        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
262        - locked <7dd7b1078> (a java.lang.ref.Reference$Lock)
263
264"VM Thread" prio=9 tid=10381e000 nid=0x10b784000 runnable
265
266"Gang worker#0 (Parallel GC Threads)" prio=9 tid=104800800 nid=0x104304000 runnable
267
268"Gang worker#1 (Parallel GC Threads)" prio=9 tid=104801000 nid=0x104407000 runnable
269
270"Concurrent Mark-Sweep GC Thread" prio=9 tid=10484c000 nid=0x10b490000 runnable
271"VM Periodic Task Thread" prio=10 tid=1048a6800 nid=0x10bf9c000 waiting on condition
272
273"Exception Catcher Thread" prio=10 tid=103801800 nid=0x104201000 runnable
274JNI global references: 36883
275

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