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A DSL for data-driven computational pipelines
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Nextflow not terminating after all tasks completed #2693

Open mebbert opened 2 years ago

mebbert commented 2 years ago

Bug report

Hello, I submitted a Nextflow workflow to our cluster (SLURM scheduler), but Nextflow did not terminate after all tasks were completed. It eventually timed out because of the SLURM time constraint. Steve on bioinformatics.stackexchange.com thinks it may be related to the errorStrategy 'ignore' I added to all of the tasks.

Expected behavior and actual behavior

I expected Nextflow to terminate on its own after completing all tasks.

Steps to reproduce the problem

This is all based on code in my GitHub repository to test .bam sorting algorithms: Samtools_sort_optimization_test. It seems to be reproducible in my environment.

Program output

The .nextflow.log (attached) ends with hundreds of No more task to compute -- Execution may be stalled statements

nextflow.log.de_identified.txt

Environment

bentsherman commented 2 years ago

I have had this problem as well, and I also think it had something to do with the fact that I was using errorStrategy = 'ignore'. My theory is that when some tasks fail and there are downstream processes, the failed tasks get ignored and the downstream processes get left hanging somehow.

Lehmann-Fabian commented 2 years ago

I think this problem was related to my PR (https://github.com/nextflow-io/nextflow/pull/2787) and should be fixed in the newest Nextflow version.

chasemc commented 2 years ago

Not sure if it's the same but I've started suddenly having this as well (Everything finishes succesfully but then the process hangs on completion)

The last bit of the log file:

Sep-06 11:01:12.261 [main] DEBUG nextflow.Session - Session await > all process finished
Sep-06 11:01:12.262 [main] DEBUG nextflow.Session - Session await > all barriers passed
Sep-06 11:03:21.172 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT
Sep-06 11:03:21.181 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active:
  [operator] buffer

Sep-06 11:03:21.195 [main] INFO  nextflow.Nextflow - -[socialgene/sgnf] Pipeline completed with errors-
Sep-06 11:03:21.195 [main] INFO  nextflow.Nextflow - -[socialgene/sgnf] Pipeline completed with errors-
Sep-06 11:03:21.197 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=60; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=9m 12s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=23; peakCpus=24; peakMemory=204.8 MB; ]
Sep-06 11:03:21.198 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Sep-06 11:03:21.198 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Sep-06 11:03:21.250 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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Sep-06 11:03:21.639 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Sep-06 11:03:21.723 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Sep-06 11:03:21.730 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
pditommaso commented 2 years ago

What version are you using?

chasemc commented 2 years ago

Sorry, 22.04.0.

It's a DSL2 workflow and pretty large so I've been working to whittle it down to the source and it does appear to a .buffer() from a DSL2 subworkflow output

chasemc commented 2 years ago

I lost a lot of time on that so I just reverted some commits back on my pipeline and something fixed it though I'm still not sure what (Fortunately/Unfortunately). If the issue comes back I'll let you know, otherwise I am unable to reproduce the error at this time.

DriesSchaumont commented 2 years ago

I managed to reproduce the error when pushing a null value in the output from toList() and using view: N E X T F L O W ~ version 21.10.6

nextflow.enable.dsl=2
workflow {
  Channel.fromList(["foo"])
    | toList()
    | map { bar -> null }
    | view()
}
chasemc commented 2 years ago

That fits what I believe was happening in my case

stale[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

mes5k commented 1 year ago

I managed to reproduce the error when pushing a null value in the output from toList() and using view: N E X T F L O W ~ version 21.10.6

nextflow.enable.dsl=2
workflow {
  Channel.fromList(["foo"])
    | toList()
    | map { bar -> null }
    | view()
}

@DriesSchaumont while this does hang I don't see the "DEBUG n.processor.TaskPollingMonitor - No more task to compute -- Execution may be stalled" log messages, so I'm not sure it's the same problem. Also using 21.10.6.

pditommaso commented 1 year ago

I think this is somehow "expected". What happens is that the null is considered as lack of value by the underlying dataflow library and therefore the view event is never triggered.

If the null is meant to skip some value you should consider the use of filter, eg. 

  Channel.fromList(["foo"])
    | toList()
    | filter { bar -> bar!='foo' }
    | view()