RejectedExecutionException on successive Console executions

[chrstphdm]

Bug report

I have to launch nextflow console for each code execution as I'm encountering an execption after each second run.

Expected behavior and actual behavior

Nextflow console should be able to run many run attempts.

Program output

This is the nextflow console output after the second attempt :

groovy> test = Channel.fromPath('*.docx').map{ file -> tuple(file.baseName,file)} 
groovy> test.subscribe {  println "Got: $it"  } 
ERROR ~ Task java.util.concurrent.CompletableFuture$UniRun@2bea071c rejected from java.util.concurrent.ThreadPoolExecutor@22db22f5[Terminated, pool size = 0, active threads = 0, queued tasks = 0, completed tasks = 1]

 -- Check '.nextflow-console.log' file for details

This is the .nextflow-console.log :

oct.-24 18:27:34.333 [AWT-EventQueue-0] DEBUG nextflow.Session - Session uuid: f7fabd19-31af-4753-9402-faff88294793
oct.-24 18:27:34.337 [AWT-EventQueue-0] DEBUG nextflow.Session - Run name: angry_pauling
oct.-24 18:27:34.337 [AWT-EventQueue-0] DEBUG nextflow.Session - Executor pool size: 4
oct.-24 18:27:34.464 [AWT-EventQueue-0] DEBUG nextflow.Session - Work-dir: /mnt/isilon_data_cifs/BIO_INFO/Christophe/DOCUMENTS/work [smb2]
oct.-24 18:27:34.783 [Thread-4] DEBUG nextflow.Session - Session start invoked
oct.-24 18:27:34.792 [Thread-4] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
oct.-24 18:27:35.556 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: ./; pattern: *.docx; options: [:]
oct.-24 18:27:35.686 [Thread-4] DEBUG nextflow.Session - Session await
oct.-24 18:27:35.687 [Thread-4] DEBUG nextflow.Session - Session await > all process finished
oct.-24 18:27:35.687 [Thread-4] DEBUG nextflow.Session - Session await > all barriers passed
oct.-24 18:27:35.697 [Thread-4] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=0; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=
0ms]
oct.-24 18:27:35.721 [Thread-4] DEBUG nextflow.CacheDB - Closing CacheDB done
oct.-24 18:27:39.810 [AWT-EventQueue-0] DEBUG nextflow.Session - Session uuid: 0c5dfada-b256-4113-b71c-1680b406c765
oct.-24 18:27:39.811 [AWT-EventQueue-0] DEBUG nextflow.Session - Run name: grave_goodall
oct.-24 18:27:39.811 [AWT-EventQueue-0] DEBUG nextflow.Session - Executor pool size: 4
oct.-24 18:27:39.820 [AWT-EventQueue-0] DEBUG nextflow.Session - Work-dir: /mnt/isilon_data_cifs/BIO_INFO/Christophe/DOCUMENTS/work [smb2]
oct.-24 18:27:39.998 [Thread-5] DEBUG nextflow.Session - Session start invoked
oct.-24 18:27:39.999 [Thread-5] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
oct.-24 18:27:40.043 [Thread-5] ERROR nextflow.Channel - Task java.util.concurrent.CompletableFuture$UniRun@2bea071c rejected from java.util.concurrent.ThreadPoolExecutor@22db22f5[Terminated, pool size = 0, active threads 
= 0, queued tasks = 0, completed tasks = 1]
java.util.concurrent.RejectedExecutionException: Task java.util.concurrent.CompletableFuture$UniRun@2bea071c rejected from java.util.concurrent.ThreadPoolExecutor@22db22f5[Terminated, pool size = 0, active threads = 0, que
ued tasks = 0, completed tasks = 1]
        at java.util.concurrent.ThreadPoolExecutor$AbortPolicy.rejectedExecution(ThreadPoolExecutor.java:2063)
        at java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:830)
        at java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1379)
        at java.util.concurrent.CompletableFuture$UniCompletion.claim(CompletableFuture.java:529)
        at java.util.concurrent.CompletableFuture.uniRun(CompletableFuture.java:703)
        at java.util.concurrent.CompletableFuture$UniRun.tryFire(CompletableFuture.java:687)
        at java.util.concurrent.CompletableFuture.uniRunStage(CompletableFuture.java:720)
        at java.util.concurrent.CompletableFuture.thenRunAsync(CompletableFuture.java:2019)
        at nextflow.file.PathVisitor.applyAsync(PathVisitor.groovy:75)
        at nextflow.Channel.fromPath0(Channel.groovy:214)
        at nextflow.Channel.fromPath(Channel.groovy:202)
        at nextflow.Channel.fromPath(Channel.groovy)
        at nextflow.Channel$fromPath.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:127)
        at ConsoleScript1.run(ConsoleScript1:1)
        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:264)
        at groovy.lang.GroovyShell.run(GroovyShell.java:373)
        at groovy.lang.GroovyShell.run(GroovyShell.java:352)
        at groovy.lang.GroovyShell.run(GroovyShell.java:172)
        at groovy.lang.GroovyShell$run$0.call(Unknown Source)
        at groovy.ui.Console$_runScriptImpl_closure22.doCall(Console.groovy:1158)
        at groovy.ui.Console$_runScriptImpl_closure22.doCall(Console.groovy)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:104)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:326)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
        at groovy.lang.Closure.call(Closure.java:411)
        at groovy.lang.Closure.call(Closure.java:405)
        at groovy.lang.Closure.run(Closure.java:492)
        at java.lang.Thread.run(Thread.java:748)
oct.-24 18:27:40.051 [Thread-5] DEBUG nextflow.Session - Session aborted -- Cause: Task java.util.concurrent.CompletableFuture$UniRun@2bea071c rejected from java.util.concurrent.ThreadPoolExecutor@22db22f5[Terminated, pool size = 0, active threads = 0, queued tasks = 0, completed tasks = 1]
oct.-24 18:27:40.065 [Thread-5] DEBUG nextflow.Session - Session await
oct.-24 18:27:40.066 [Thread-5] DEBUG nextflow.Session - Session await > all process finished
oct.-24 18:27:40.066 [Thread-5] DEBUG nextflow.Session - Session await > all barriers passed
oct.-24 18:27:40.066 [Thread-5] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=0; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms]
oct.-24 18:27:40.076 [Thread-5] DEBUG nextflow.CacheDB - Closing CacheDB done

Steps to reproduce the problem

1. launch nextflow console
2. run any command as a first attempt
3. run the same command (or another one) as the second attempt

Environment

• Nextflow version: [18.10.1]
• Java version: [1.8.0_181]
• Operating system: [ubuntu 18.10]

[chadisaad]

same issue here !

ENV:

openjdk 10.0.2 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2)
OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.2, mixed mode)

LOG:

oct.-24 18:06:23.245 [Thread-2] DEBUG nextflow.Session - Session start invoked
oct.-24 18:06:23.245 [Thread-2] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
oct.-24 18:06:23.265 [Thread-2] ERROR nextflow.Channel - Task java.util.concurrent.CompletableFuture$UniRun@2d50dba8 rejected from java.util.concurrent
.ThreadPoolExecutor@3cb5d24[Terminated, pool size = 0, active threads = 0, queued tasks = 0, completed tasks = 1]
java.util.concurrent.RejectedExecutionException: Task java.util.concurrent.CompletableFuture$UniRun@2d50dba8 rejected from java.util.concurrent.ThreadP
oolExecutor@3cb5d24[Terminated, pool size = 0, active threads = 0, queued tasks = 0, completed tasks = 1]
        at java.base/java.util.concurrent.ThreadPoolExecutor$AbortPolicy.rejectedExecution(ThreadPoolExecutor.java:2080)
        at java.base/java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:832)
        at java.base/java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1365)
        at java.base/java.util.concurrent.CompletableFuture.uniRunNow(CompletableFuture.java:813)
        at java.base/java.util.concurrent.CompletableFuture.uniRunStage(CompletableFuture.java:799)
        at java.base/java.util.concurrent.CompletableFuture.thenRunAsync(CompletableFuture.java:2130)
        at nextflow.file.PathVisitor.applyAsync(PathVisitor.groovy:75)
        at nextflow.Channel.fromPath0(Channel.groovy:214)
        at nextflow.Channel.fromPath(Channel.groovy:202)
        at nextflow.Channel.fromPath(Channel.groovy)
        at nextflow.Channel$fromPath.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:127)
        at ConsoleScript1.run(ConsoleScript1:1)
        at groovy.lang.GroovyShell.runScriptOrMainOrTestOrRunnable(GroovyShell.java:264)
        at groovy.lang.GroovyShell.run(GroovyShell.java:373)
        at groovy.lang.GroovyShell.run(GroovyShell.java:352)
        at groovy.lang.GroovyShell.run(GroovyShell.java:172)
        at groovy.lang.GroovyShell$run$0.call(Unknown Source)
:

[pditommaso]

This will be included in next release.