Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-4217

2.11.3 develop build hanging in tests..

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Reopened
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.3.0
    • Component/s: Dev and Dep
    • Labels:

      Description

      We have lurking sync/wait issues in the test suite still, causing Jalview Builds to hang..

      Stack trace from today:
      2023-06-30 12:30:11
      Full thread dump OpenJDK 64-Bit Server VM (11.0.15+10 mixed mode):

      Threads class SMR info:
      _java_thread_list=0x00007f8dd4106360, length=156, elements={
      0x00007f8e20029800, 0x00007f8e2013e800, 0x00007f8e20142800, 0x00007f8e20157800,
      0x00007f8e20159800, 0x00007f8e2015c000, 0x00007f8e2015e000, 0x00007f8e20160000,
      0x00007f8e20214800, 0x00007f8e20866800, 0x00007f8e20886000, 0x00007f8e208b0000,
      0x00007f8e21401800, 0x00007f8e2148c800, 0x00007f8e2148e000, 0x00007f8d7401a800,
      0x00007f8e229d1800, 0x00007f8e229d3000, 0x00007f8e229d4000, 0x00007f8e229d8000,
      0x00007f8e229dc000, 0x00007f8e22a06000, 0x00007f8e22a0b000, 0x00007f8e21877800,
      0x00007f8e2259c000, 0x00007f8e2251b000, 0x00007f8e20e30800, 0x00007f8e229ed800,
      0x00007f8e20e2b800, 0x00007f8e20e3d000, 0x00007f8e20e3e800, 0x00007f8e211bf000,
      0x00007f8e20e2e800, 0x00007f8e211c0000, 0x00007f8e214c9000, 0x00007f8e200de800,
      0x00007f8e20ddf000, 0x00007f8e20e43000, 0x00007f8e214cf000, 0x00007f8e20dda000,
      0x00007f8e2045c800, 0x00007f8e20e70800, 0x00007f8e20ddd800, 0x00007f8e20e71800,
      0x00007f8e20e73800, 0x00007f8e2045e800, 0x00007f8e2045a800, 0x00007f8e21228800,
      0x00007f8e20459800, 0x00007f8e21226000, 0x00007f8e2045b800, 0x00007f8e20fa9800,
      0x00007f8e20e75800, 0x00007f8e20fa8000, 0x00007f8e20f1b800, 0x00007f8e20f1e000,
      0x00007f8e2122b800, 0x00007f8e20f1c800, 0x00007f8e21216000, 0x00007f8e2122a800,
      0x00007f8e21217800, 0x00007f8e21221800, 0x00007f8e20982000, 0x00007f8e20f20000,
      0x00007f8e21224800, 0x00007f8e2122c000, 0x00007f8e20960800, 0x00007f8e20ec0000,
      0x00007f8e20ec1000, 0x00007f8e20e01000, 0x00007f8e20e02800, 0x00007f8e20ec4800,
      0x00007f8e20ec2800, 0x00007f8e20ec3800, 0x00007f8e20e03800, 0x00007f8e20ec5800,
      0x00007f8e2017f000, 0x00007f8e2017e000, 0x00007f8e20ec6800, 0x00007f8e20e07000,
      0x00007f8e20183800, 0x00007f8e21114000, 0x00007f8e20184800, 0x00007f8e21112800,
      0x00007f8e20181800, 0x00007f8e20180000, 0x00007f8e20b79000, 0x00007f8e20b7b800,
      0x00007f8e20e05800, 0x00007f8e20fa4000, 0x00007f8e20b7d800, 0x00007f8e2099b000,
      0x00007f8e2099a000, 0x00007f8e21114800, 0x00007f8e21117800, 0x00007f8e210f4800,
      0x00007f8e210f8800, 0x00007f8e210fa800, 0x00007f8e20b7a000, 0x00007f8e210f7800,
      0x00007f8e2099c000, 0x00007f8e20c43800, 0x00007f8e210f9800, 0x00007f8e20c45800,
      0x00007f8e20c46800, 0x00007f8e210c0800, 0x00007f8e210c3800, 0x00007f8e210c6000,
      0x00007f8e21089000, 0x00007f8e210c5000, 0x00007f8e2099e000, 0x00007f8e21116000,
      0x00007f8e210bf800, 0x00007f8e20c44000, 0x00007f8e20ee6800, 0x00007f8e2108e800,
      0x00007f8e2108f800, 0x00007f8e20d92800, 0x00007f8e20fe6800, 0x00007f8e20fe5000,
      0x00007f8e2108b000, 0x00007f8e20fe1000, 0x00007f8e20fe1800, 0x00007f8e20c41800,
      0x00007f8e20d93800, 0x00007f8e2127e000, 0x00007f8e21281800, 0x00007f8e21285000,
      0x00007f8e21280800, 0x00007f8e20fe3000, 0x00007f8e21283000, 0x00007f8e2108c800,
      0x00007f8e21284000, 0x00007f8e21282000, 0x00007f8e20d8f000, 0x00007f8e20c26800,
      0x00007f8e20c29000, 0x00007f8e20c2a000, 0x00007f8e20ca4800, 0x00007f8e20ca6800,
      0x00007f8e20d90000, 0x00007f8e20c28800, 0x00007f8e20cab000, 0x00007f8e20c27800,
      0x00007f8e20d94800, 0x00007f8e20980800, 0x00007f8e20c25800, 0x00007f8e2097f800,
      0x00007f8e20eec800, 0x00007f8e20eee800, 0x00007f8e214b5800, 0x00007f8e214b9000,
      0x00007f8deceb3800, 0x00007f8dc8019800, 0x00007f8dec183800, 0x00007f8dd4119000
      }

      "Test worker" #1 prio=5 os_prio=0 cpu=7106.86ms elapsed=2123.14s tid=0x00007f8e20029800 nid=0x7b72 in Object.wait() [0x00007f8e26e14000]
         java.lang.Thread.State: WAITING (on object monitor)
      at java.lang.Object.wait(java.base@11.0.15/Native Method)
      - waiting on <no object reference available>
      at java.lang.Object.wait(java.base@11.0.15/Object.java:328)
      at java.awt.EventQueue.invokeAndWait(java.desktop@11.0.15/EventQueue.java:1361)
      - waiting to re-lock in wait() <0x00000000ccaaa4a8> (a java.awt.EventQueue$1AWTInvocationLock)
      at java.awt.Window.doDispose(java.desktop@11.0.15/Window.java:1227)
      at java.awt.Window.dispose(java.desktop@11.0.15/Window.java:1164)
      at jalview.gui.Desktop.closeDesktop(Desktop.java:3626)
      at jalview.bin.CommandsTest.tearDown(CommandsTest.java:52)
      at jalview.bin.CommandsTest.__CLR4_4_1shrjyq41rv(CommandsTest.java:140)
      at jalview.bin.CommandsTest.structureImageOutputTest(CommandsTest.java:118)
      at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(java.base@11.0.15/Native Method)
      at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(java.base@11.0.15/NativeMethodAccessorImpl.java:62)
      at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(java.base@11.0.15/DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(java.base@11.0.15/Method.java:566)
      at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
      at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
      at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
      at org.testng.TestRunner.privateRun(TestRunner.java:771)
      at org.testng.TestRunner.run(TestRunner.java:621)
      at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
      at org.testng.SuiteRunner.run(SuiteRunner.java:259)
      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
      at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
      at org.testng.TestNG.run(TestNG.java:1009)
      at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141)
      at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90)
      at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
      at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(java.base@11.0.15/Native Method)
      at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(java.base@11.0.15/NativeMethodAccessorImpl.java:62)
      at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(java.base@11.0.15/DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(java.base@11.0.15/Method.java:566)
      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
      at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
      at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
      at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
      at com.sun.proxy.$Proxy2.stop(Unknown Source)
      at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
      at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
      at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
      at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
      at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
      at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:133)
      at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71)
      at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
      at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: