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Problem cancelling loading huge session #115

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olegs opened this issue Apr 21, 2020 · 2 comments
Open

Problem cancelling loading huge session #115

olegs opened this issue Apr 21, 2020 · 2 comments
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bug Something isn't working

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@olegs
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olegs commented Apr 21, 2020 •
edited
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Original report by Roman Chernyatchik

  1. Load big session
  2. Press Cancel
  3. Menus actions are disabled (AWT thread still working)
020-04-21 21:38:39,765 INFO [AWT-EventQueue-0] o.j.b.b.f.Session [Session.kt:172] Navigate: 1:138655775-154233939
2020-04-21 21:38:39,765 INFO [ForkJoinPool-9-worker-13] o.j.b.b.GenomeBrowser [LoggerExtensions.kt:35] Preprocessing track 'repeats_hg19_LINE.bed': [CANCELED] after 15.18 s
2020-04-21 21:38:39,766 INFO [AWT-EventQueue-0] o.j.b.b.f.Session [Session.kt:222] Session /Users/romeo/work/aging-wgbs/_playground/_wgbs_dmrs/_sessions_/y2020_rrbs_paper_vs_pipeline.yaml loaded
2020-04-21 21:38:39,766 INFO [ForkJoinPool-9-worker-7] o.j.b.b.GenomeBrowser [LoggerExtensions.kt:35] Preprocessing track 'repeats_hg19_SINE.bed': [CANCELED] after 14.81 s
2020-04-21 21:38:39,767 INFO [Thread-7] o.j.b.b.GenomeBrowser [ProgressDialog.kt:175] [CANCELED] Opening session: y2020_rrbs_paper_vs_pipeline.yaml

jstack utility shows that AWT thread is processing dialog, looks like cancellation failed and JBR tries to load all tracks in background on AWT

AWT-EventQueue-0" #18 prio=6 os_prio=31 cpu=125330.93ms elapsed=161.87s tid=0x00007ffb9f318000 nid=0x10b03 runnable  [0x00007000105f7000]
   java.lang.Thread.State: RUNNABLE
	at java.lang.String.regionMatches([email protected]/Unknown Source)
	at kotlin.text.StringsKt__StringsJVMKt.regionMatches(StringsJVM.kt:533)
	at kotlin.text.StringsKt__StringsKt.findAnyOf$StringsKt__StringsKt(Strings.kt:905)
	at kotlin.text.StringsKt__StringsKt.access$findAnyOf(Strings.kt:1)
	at kotlin.text.StringsKt__StringsKt$rangesDelimitedBy$4.invoke(Strings.kt:1167)
	at kotlin.text.StringsKt__StringsKt$rangesDelimitedBy$4.invoke(Strings.kt)
	at kotlin.text.DelimitedRangesSequence$iterator$1.calcNext(Strings.kt:1095)
	at kotlin.text.DelimitedRangesSequence$iterator$1.hasNext(Strings.kt:1124)
	at kotlin.sequences.TransformingSequence$iterator$1.hasNext(Sequences.kt:176)
	at kotlin.sequences.SequencesKt___SequencesKt.toCollection(_Sequences.kt:702)
	at kotlin.sequences.SequencesKt___SequencesKt.toMutableList(_Sequences.kt:732)
	at kotlin.sequences.SequencesKt___SequencesKt.toList(_Sequences.kt:723)
	at kotlin.text.StringsKt__StringsKt.lines(Strings.kt:1287)
	at org.jetbrains.bio.browser.desktop.dialogs.ProgressDialog$1$append$1.run(ProgressDialog.kt:61)
	at java.awt.event.InvocationEvent.dispatch([email protected]/Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl([email protected]/Unknown Source)
	at java.awt.EventQueue$4.run([email protected]/Unknown Source)
	at java.awt.EventQueue$4.run([email protected]/Unknown Source)
	at java.security.AccessController.doPrivileged([email protected]/Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege([email protected]/Unknown Source)
	at java.awt.EventQueue.dispatchEvent([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.run([email protected]/Unknown Source)
@olegs olegs added the bug Something isn't working label Apr 21, 2020
@iromeo
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iromeo commented Apr 21, 2020

In my case noticeable ui freeze noticed on 2-nd attempt to open large session, 1st seems to be ok and UI was responsive.

@iromeo
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iromeo commented Apr 21, 2020

full trace

2020-04-21 21:40:30
Full thread dump OpenJDK 64-Bit Server VM (11.0.6+10-LTS mixed mode):

Threads class SMR info:
_java_thread_list=0x0000600003633e80, length=18, elements={
0x00007ffb9f808800, 0x00007ffba080c000, 0x00007ffba081b800, 0x00007ffba081c800,
0x00007ffb9e007800, 0x00007ffb9e01a800, 0x00007ffb9f018800, 0x00007ffb9f019000,
0x00007ffba096c000, 0x00007ffba0969000, 0x00007ffb9e19f800, 0x00007ffb9f2fd000,
0x00007ffb9f318000, 0x00007ffba0e15000, 0x00007ffba0a03000, 0x00007ffb9f128800,
0x00007ffb9f93d000, 0x00007ffba700d000
}

"Reference Handler" #2 daemon prio=10 os_prio=31 cpu=2262.34ms elapsed=163.00s tid=0x00007ffb9f808800 nid=0x3e03 waiting on condition  [0x000070000eeab000]
   java.lang.Thread.State: RUNNABLE
	at java.lang.ref.Reference.waitForReferencePendingList([email protected]/Native Method)
	at java.lang.ref.Reference.processPendingReferences([email protected]/Unknown Source)
	at java.lang.ref.Reference$ReferenceHandler.run([email protected]/Unknown Source)

"Finalizer" #3 daemon prio=8 os_prio=31 cpu=4.36ms elapsed=163.00s tid=0x00007ffba080c000 nid=0x4003 in Object.wait()  [0x000070000efae000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait([email protected]/Native Method)
	- waiting on <no object reference available>
	at java.lang.ref.ReferenceQueue.remove([email protected]/Unknown Source)
	- waiting to re-lock in wait() <0x0000000783d0ad80> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove([email protected]/Unknown Source)
	at java.lang.ref.Finalizer$FinalizerThread.run([email protected]/Unknown Source)

"Signal Dispatcher" #4 daemon prio=9 os_prio=31 cpu=0.34ms elapsed=162.99s tid=0x00007ffba081b800 nid=0x5603 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" #5 daemon prio=9 os_prio=31 cpu=12913.74ms elapsed=162.99s tid=0x00007ffba081c800 nid=0xa503 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   No compile task

"C1 CompilerThread0" #8 daemon prio=9 os_prio=31 cpu=2714.15ms elapsed=162.99s tid=0x00007ffb9e007800 nid=0xa303 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE
   No compile task

"Sweeper thread" #9 daemon prio=9 os_prio=31 cpu=80.06ms elapsed=162.99s tid=0x00007ffb9e01a800 nid=0xa003 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Service Thread" #10 daemon prio=9 os_prio=31 cpu=0.05ms elapsed=162.96s tid=0x00007ffb9f018800 nid=0x9e03 runnable  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Common-Cleaner" #11 daemon prio=8 os_prio=31 cpu=8.38ms elapsed=162.95s tid=0x00007ffb9f019000 nid=0x9a03 in Object.wait()  [0x000070000f6c3000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait([email protected]/Native Method)
	- waiting on <no object reference available>
	at java.lang.ref.ReferenceQueue.remove([email protected]/Unknown Source)
	- waiting to re-lock in wait() <0x0000000783d0d110> (a java.lang.ref.ReferenceQueue$Lock)
	at jdk.internal.ref.CleanerImpl.run([email protected]/Unknown Source)
	at java.lang.Thread.run([email protected]/Unknown Source)
	at jdk.internal.misc.InnocuousThread.run([email protected]/Unknown Source)

"AppKit Thread" #12 daemon prio=5 os_prio=31 cpu=5319.58ms elapsed=162.62s tid=0x00007ffba096c000 nid=0x307 runnable  [0x00007ffee4009000]
   java.lang.Thread.State: RUNNABLE
	at sun.lwawt.macosx.LWCToolkit.doAWTRunLoopImpl([email protected]/Native Method)
	at sun.lwawt.macosx.LWCToolkit.doAWTRunLoop([email protected]/Unknown Source)
	at sun.lwawt.macosx.LWCToolkit.invokeAndWait([email protected]/Unknown Source)
	at com.apple.laf.ScreenMenu.invokeOpenLater([email protected]/Unknown Source)

"AWT-Shutdown" #13 prio=5 os_prio=31 cpu=2.18ms elapsed=162.57s tid=0x00007ffba0969000 nid=0x6a03 in Object.wait()  [0x000070000fad2000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait([email protected]/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait([email protected]/Unknown Source)
	at sun.awt.AWTAutoShutdown.run([email protected]/Unknown Source)
	- waiting to re-lock in wait() <0x0000000783d0b098> (a java.lang.Object)
	at java.lang.Thread.run([email protected]/Unknown Source)

"Java2D Queue Flusher" #15 daemon prio=10 os_prio=31 cpu=207.14ms elapsed=162.15s tid=0x00007ffb9e19f800 nid=0xda07 in Object.wait()  [0x000070000fde1000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait([email protected]/Native Method)
	- waiting on <no object reference available>
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run([email protected]/Unknown Source)
	- waiting to re-lock in wait() <0x0000000783d0b640> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)
	at java.lang.Thread.run([email protected]/Unknown Source)

"Java2D Disposer" #16 daemon prio=10 os_prio=31 cpu=121.87ms elapsed=162.09s tid=0x00007ffb9f2fd000 nid=0xe90b in Object.wait()  [0x000070000fee4000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait([email protected]/Native Method)
	- waiting on <no object reference available>
	at java.lang.ref.ReferenceQueue.remove([email protected]/Unknown Source)
	- waiting to re-lock in wait() <0x0000000783d0d3f0> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove([email protected]/Unknown Source)
	at sun.java2d.Disposer.run([email protected]/Unknown Source)
	at java.lang.Thread.run([email protected]/Unknown Source)

"AWT-EventQueue-0" #18 prio=6 os_prio=31 cpu=125330.93ms elapsed=161.87s tid=0x00007ffb9f318000 nid=0x10b03 runnable  [0x00007000105f7000]
   java.lang.Thread.State: RUNNABLE
	at java.lang.String.regionMatches([email protected]/Unknown Source)
	at kotlin.text.StringsKt__StringsJVMKt.regionMatches(StringsJVM.kt:533)
	at kotlin.text.StringsKt__StringsKt.findAnyOf$StringsKt__StringsKt(Strings.kt:905)
	at kotlin.text.StringsKt__StringsKt.access$findAnyOf(Strings.kt:1)
	at kotlin.text.StringsKt__StringsKt$rangesDelimitedBy$4.invoke(Strings.kt:1167)
	at kotlin.text.StringsKt__StringsKt$rangesDelimitedBy$4.invoke(Strings.kt)
	at kotlin.text.DelimitedRangesSequence$iterator$1.calcNext(Strings.kt:1095)
	at kotlin.text.DelimitedRangesSequence$iterator$1.hasNext(Strings.kt:1124)
	at kotlin.sequences.TransformingSequence$iterator$1.hasNext(Sequences.kt:176)
	at kotlin.sequences.SequencesKt___SequencesKt.toCollection(_Sequences.kt:702)
	at kotlin.sequences.SequencesKt___SequencesKt.toMutableList(_Sequences.kt:732)
	at kotlin.sequences.SequencesKt___SequencesKt.toList(_Sequences.kt:723)
	at kotlin.text.StringsKt__StringsKt.lines(Strings.kt:1287)
	at org.jetbrains.bio.browser.desktop.dialogs.ProgressDialog$1$append$1.run(ProgressDialog.kt:61)
	at java.awt.event.InvocationEvent.dispatch([email protected]/Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl([email protected]/Unknown Source)
	at java.awt.EventQueue$4.run([email protected]/Unknown Source)
	at java.awt.EventQueue$4.run([email protected]/Unknown Source)
	at java.security.AccessController.doPrivileged([email protected]/Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege([email protected]/Unknown Source)
	at java.awt.EventQueue.dispatchEvent([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents([email protected]/Unknown Source)
	at java.awt.EventDispatchThread.run([email protected]/Unknown Source)

"Timer-0" #20 daemon prio=5 os_prio=31 cpu=2.56ms elapsed=159.38s tid=0x00007ffba0e15000 nid=0xff1b in Object.wait()  [0x0000700010a05000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait([email protected]/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait([email protected]/Unknown Source)
	at java.util.TimerThread.mainLoop([email protected]/Unknown Source)
	- waiting to re-lock in wait() <0x000000078563a4b0> (a java.util.TaskQueue)
	at java.util.TimerThread.run([email protected]/Unknown Source)

"TimerQueue" #32 daemon prio=5 os_prio=31 cpu=3.85ms elapsed=156.75s tid=0x00007ffba0a03000 nid=0x1ee07 waiting on condition  [0x000070001121d000]
   java.lang.Thread.State: WAITING (parking)
	at jdk.internal.misc.Unsafe.park([email protected]/Native Method)
	- parking to wait for  <0x0000000791663f78> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park([email protected]/Unknown Source)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await([email protected]/Unknown Source)
	at java.util.concurrent.DelayQueue.take([email protected]/Unknown Source)
	at javax.swing.TimerQueue.run([email protected]/Unknown Source)
	at java.lang.Thread.run([email protected]/Unknown Source)

"ForkJoinPool-3-worker-3" #33 daemon prio=6 os_prio=31 cpu=464.28ms elapsed=156.75s tid=0x00007ffb9f128800 nid=0x1ed03 waiting on condition  [0x0000700011320000]
   java.lang.Thread.State: WAITING (parking)
	at jdk.internal.misc.Unsafe.park([email protected]/Native Method)
	- parking to wait for  <0x000000079169bb58> (a java.util.concurrent.ForkJoinPool)
	at java.util.concurrent.locks.LockSupport.park([email protected]/Unknown Source)
	at java.util.concurrent.ForkJoinPool.runWorker([email protected]/Unknown Source)
	at java.util.concurrent.ForkJoinWorkerThread.run([email protected]/Unknown Source)

"DestroyJavaVM" #34 prio=5 os_prio=31 cpu=3258.71ms elapsed=156.67s tid=0x00007ffb9f93d000 nid=0x2e03 waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Attach Listener" #90 daemon prio=9 os_prio=31 cpu=0.69ms elapsed=0.20s tid=0x00007ffba700d000 nid=0xfb0f waiting on condition  [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"VM Thread" os_prio=31 cpu=198.14ms elapsed=163.01s tid=0x00007ffb9f01a800 nid=0x4303 runnable

"GC Thread#0" os_prio=31 cpu=2998.33ms elapsed=163.03s tid=0x00007ffba101e800 nid=0x3503 runnable

"GC Thread#1" os_prio=31 cpu=2995.36ms elapsed=161.98s tid=0x00007ffba0a84000 nid=0xec17 runnable

"GC Thread#2" os_prio=31 cpu=3044.18ms elapsed=161.98s tid=0x00007ffba0a90800 nid=0xed03 runnable

"GC Thread#3" os_prio=31 cpu=3011.46ms elapsed=161.98s tid=0x00007ffb9f302000 nid=0x11203 runnable

"GC Thread#4" os_prio=31 cpu=3014.28ms elapsed=161.98s tid=0x00007ffb9f302800 nid=0x11103 runnable

"GC Thread#5" os_prio=31 cpu=2994.01ms elapsed=161.98s tid=0x00007ffb9f304800 nid=0xf003 runnable

"GC Thread#6" os_prio=31 cpu=2841.74ms elapsed=157.21s tid=0x00007ffb9f3da000 nid=0x1fa07 runnable

"GC Thread#7" os_prio=31 cpu=2787.07ms elapsed=150.39s tid=0x00007ffba2057000 nid=0x17c0b runnable

"G1 Main Marker" os_prio=31 cpu=5.68ms elapsed=163.03s tid=0x00007ffba103e800 nid=0x3603 runnable

"G1 Conc#0" os_prio=31 cpu=26771.28ms elapsed=163.03s tid=0x00007ffba103f800 nid=0x3903 runnable

"G1 Conc#1" os_prio=31 cpu=26803.47ms elapsed=159.52s tid=0x00007ffba09de800 nid=0xfe3f runnable

"G1 Refine#0" os_prio=31 cpu=373.68ms elapsed=163.02s tid=0x00007ffba10e0000 nid=0x3a03 runnable

"G1 Refine#1" os_prio=31 cpu=108.98ms elapsed=157.82s tid=0x00007ffba1287800 nid=0x1f80b runnable

"G1 Refine#2" os_prio=31 cpu=60.70ms elapsed=157.80s tid=0x00007ffba0946000 nid=0x16007 runnable

"G1 Refine#3" os_prio=31 cpu=36.01ms elapsed=157.80s tid=0x00007ffb9e851800 nid=0x16607 runnable

"G1 Refine#4" os_prio=31 cpu=25.29ms elapsed=157.80s tid=0x00007ffb9e384000 nid=0x1f307 runnable

"G1 Refine#5" os_prio=31 cpu=10.56ms elapsed=157.80s tid=0x00007ffb9f478000 nid=0x16507 runnable

"G1 Refine#6" os_prio=31 cpu=1.89ms elapsed=157.80s tid=0x00007ffba21e7800 nid=0x15c07 runnable

"G1 Young RemSet Sampling" os_prio=31 cpu=81.68ms elapsed=163.02s tid=0x00007ffba10e1000 nid=0x3b03 runnable
"VM Periodic Task Thread" os_prio=31 cpu=75.55ms elapsed=162.96s tid=0x00007ffba10ff000 nid=0x9d03 waiting on condition

JNI global refs: 225, weak refs: 165

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@iromeo @olegs