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Test TestPullImagePlus fail at build on MacOS #68

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StRigaud opened this issue Sep 28, 2024 · 6 comments
Open

Test TestPullImagePlus fail at build on MacOS #68

StRigaud opened this issue Sep 28, 2024 · 6 comments

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@StRigaud
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I have to use -DskipTests when calling maven for the build to pass, other wise getting the following error:

[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.155 s -- in TestPullImagePlus
[DEBUG] #
[DEBUG] # A fatal error has been detected by the Java Runtime Environment:
[DEBUG] #
[DEBUG] #  SIGSEGV (0xb) at pc=0x000000011b821134, pid=39304, tid=28675
[DEBUG] #
[DEBUG] # JRE version: OpenJDK Runtime Environment Zulu21.34+19-CA (21.0.3+9) (build 21.0.3+9-LTS)
[DEBUG] # Java VM: OpenJDK 64-Bit Server VM Zulu21.34+19-CA (21.0.3+9-LTS, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, bsd-aarch64)
[DEBUG] # Problematic frame:
[DEBUG] # C  [libJCLIc.dylib+0x21134]  cle::Array::~Array()+0xe0
[DEBUG] #
[DEBUG] # No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
[DEBUG] #
[DEBUG] # An error report file with more information is saved as:
[DEBUG] # /Users/strigaud/Documents/github/clesperanto/clesperantoj_prototype/hs_err_pid39304.log
[DEBUG] #
[DEBUG] # If you would like to submit a bug report, please visit:
[DEBUG] #   http://www.azul.com/support/
[DEBUG] # The crash happened outside the Java Virtual Machine in native code.
/bin/sh: line 1: 39304 Abort trap: 6           '/Library/Java/JavaVirtualMachines/zulu-21.jdk/Contents/Home/bin/java' '-Xmx1024m' '-jar' '/Users/strigaud/Documents/github/clesperanto/clesperantoj_prototype/target/surefire/surefirebooter-20240928161223913_18.jar' '/Users/strigaud/Documents/github/clesperanto/clesperantoj_prototype/target/surefire' '2024-09-28T16-12-23_803-jvmRun1' 'surefire-20240928161223913_16tmp' 'surefire_5-20240928161223913_17tmp'
@StRigaud StRigaud mentioned this issue Sep 28, 2024
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@StRigaud
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TestPullImagePlus issue seems related to a missing in = null; at the end of tests. But that does not really fix the build issue I have:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:3.2.5:test (default-test) on project clesperantoj: 
[ERROR] 
[ERROR] Please refer to /Users/strigaud/Documents/github/clesperanto/clesperantoj_prototype/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream.
[ERROR] ExecutionException Error occurred in starting fork, check output in log
[ERROR] org.apache.maven.surefire.booter.SurefireBooterForkException: ExecutionException Error occurred in starting fork, check output in log
[ERROR]         at org.apache.maven.plugin.surefire.booterclient.ForkStarter.awaitResultsDone(ForkStarter.java:456)
[ERROR]         at org.apache.maven.plugin.surefire.booterclient.ForkStarter.runSuitesForkPerTestSet(ForkStarter.java:418)
[ERROR]         at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:297)
[ERROR]         at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:250)
[ERROR]         at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeProvider(AbstractSurefireMojo.java:1241)
[ERROR]         at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:1090)
[ERROR]         at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:910)
[ERROR]         at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:126)
[ERROR]         at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute2(MojoExecutor.java:328)
[ERROR]         at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute(MojoExecutor.java:316)
[ERROR]         at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
[ERROR]         at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:174)
[ERROR]         at org.apache.maven.lifecycle.internal.MojoExecutor.access$000(MojoExecutor.java:75)
[ERROR]         at org.apache.maven.lifecycle.internal.MojoExecutor$1.run(MojoExecutor.java:162)
[ERROR]         at org.apache.maven.plugin.DefaultMojosExecutionStrategy.execute(DefaultMojosExecutionStrategy.java:39)
[ERROR]         at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:159)
[ERROR]         at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:105)
[ERROR]         at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:73)
[ERROR]         at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:53)
[ERROR]         at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:118)
[ERROR]         at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:261)
[ERROR]         at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:173)
[ERROR]         at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:101)
[ERROR]         at org.apache.maven.cli.MavenCli.execute(MavenCli.java:906)
[ERROR]         at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:283)
[ERROR]         at org.apache.maven.cli.MavenCli.main(MavenCli.java:206)
[ERROR]         at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
[ERROR]         at java.base/java.lang.reflect.Method.invoke(Method.java:580)
[ERROR]         at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:283)
[ERROR]         at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:226)
[ERROR]         at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:407)
[ERROR]         at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:348)
[ERROR] Caused by: org.apache.maven.surefire.booter.SurefireBooterForkException: Error occurred in starting fork, check output in log
[ERROR]         at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:577)
[ERROR]         at org.apache.maven.plugin.surefire.booterclient.ForkStarter.lambda$null$7(ForkStarter.java:401)
[ERROR]         at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
[ERROR]         at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
[ERROR]         at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
[ERROR]         at java.base/java.lang.Thread.run(Thread.java:1583)
[ERROR] 
[ERROR] -> [Help 1]

and a dump log:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0000000000000000, pid=71213, tid=27911
#
# JRE version: OpenJDK Runtime Environment Zulu21.34+19-CA (21.0.3+9) (build 21.0.3+9-LTS)
# Java VM: OpenJDK 64-Bit Server VM Zulu21.34+19-CA (21.0.3+9-LTS, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, bsd-aarch64)
# Problematic frame:
# C  0x0000000000000000
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   http://www.azul.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  S U M M A R Y ------------

Command Line: -Xmx1024m /Users/strigaud/Documents/github/clesperanto/clesperantoj_prototype/target/surefire/surefirebooter-20240928175514716_6.jar /Users/strigaud/Documents/github/clesperanto/clesperantoj_prototype/target/surefire 2024-09-28T17-55-14_589-jvmRun1 surefire-20240928175514716_4tmp surefire_1-20240928175514716_5tmp

Host: "Mac14,5" arm64, 12 cores, 32G, Darwin 23.6.0, macOS 14.6.1 (23G93)
Time: Sat Sep 28 17:55:15 2024 EEST elapsed time: 0.353070 seconds (0d 0h 0m 0s)

---------------  T H R E A D  ---------------

Current thread (0x00000001262a9e00):  JavaThread "JavaCPP Deallocator" daemon [_thread_in_native, id=27911, stack(0x0000000170414000,0x0000000170617000) (2060K)]

Stack: [0x0000000170414000,0x0000000170617000],  sp=0x0000000170616830,  free space=2058k
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  org.bytedeco.javacpp.Pointer$NativeDeallocator.deallocate(JJ)V+0
j  org.bytedeco.javacpp.Pointer$NativeDeallocator.deallocate()V+27
j  org.bytedeco.javacpp.Pointer$DeallocatorReference.clear()V+46
j  org.bytedeco.javacpp.Pointer$DeallocatorThread.run()V+11
v  ~StubRoutines::call_stub 0x000000011a6d8140

...

This still seems related to memory release or something like that.

However, this does not seems to make any of the local run nor CLIJ3 build and test fail ...

@StRigaud StRigaud mentioned this issue Sep 28, 2024
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@StRigaud
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I silence the tests that fail into a side branch / PR. The issue is related to ImagePlus.

@carlosuc3m
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HAving a look at it right now! If not silencing the fail can work as a patch for now!
Is it failing on mac intel or max M? @StRigaud

@StRigaud
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Mine is M2, don't know if it plays or not. Don't have access to my Unix right now.

@carlosuc3m
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okk, just asking so i can replicate it with the github action!

@StRigaud
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FYI, It does not fail on my Linux ubuntu ...

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macos-error clEsperanto/clesperantoj_prototype
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@StRigaud @carlosuc3m