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Runaway thread creation if used in BigStitcher-Spark #2

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kgabor opened this issue Jan 4, 2023 · 3 comments · Fixed by #3
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Runaway thread creation if used in BigStitcher-Spark #2

kgabor opened this issue Jan 4, 2023 · 3 comments · Fixed by #3
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kgabor commented Jan 4, 2023 •
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If the zarr reader is used in BigStitcher-Spark AffineFusion, it creates new reader thread for each job chunk and fails to destroy them.

jupyter@7262e9376515:~/fusion_test_2022-12-01$ java -cp $(cat cp.txt) -Dspark.master=local 
net.preibisch.bigstitcher.spark.AffineFusion -x /home/jupyter/exaSPIM_609281_2022-11-03_proc_2022-11-22/affine_ip_alignment.xml -o /home/jupyter/test-spark1201 
--bdv 0,0 --storage N5 --xmlout=/home/jupyter/fusion_test_2022-12-01/dataset.xml

01:28:47.138 [Executor task launch worker for task 7] ERROR org.apache.spark.util.SparkUncaughtExceptionHandler - Uncaught exception in thread Thread[Executor task launch worker for task 7,5,main]
java.lang.OutOfMemoryError: unable to create new native thread
        at java.lang.Thread.start0(Native Method)
        at java.lang.Thread.start(Thread.java:719)
        at net.imglib2.cache.queue.FetcherThreads.<init>(FetcherThreads.java:92)
        at net.imglib2.cache.queue.FetcherThreads.<init>(FetcherThreads.java:70)
        at bdv.util.volatiles.SharedQueue.<init>(SharedQueue.java:49)
        at bdv.util.volatiles.VolatileViews.wrapCachedCellImg(VolatileViews.java:178)
        at bdv.util.volatiles.VolatileViews.wrapAsVolatileViewData(VolatileViews.java:124)
        at bdv.util.volatiles.VolatileViews.wrapAsVolatile(VolatileViews.java:86)
        at bdv.util.volatiles.VolatileViews.wrapAsVolatile(VolatileViews.java:70)
        at bdv.img.omezarr.MultiscaleImage.init(MultiscaleImage.java:151)
        at bdv.img.omezarr.MultiscaleImage.getType(MultiscaleImage.java:246)
        at bdv.img.omezarr.ZarrImageLoader$SetupImgLoader.<init>(ZarrImageLoader.java:128)
        at bdv.img.omezarr.ZarrImageLoader.createSetupImgLoader(ZarrImageLoader.java:88)
        at bdv.img.omezarr.ZarrImageLoader.openZarr(ZarrImageLoader.java:62)
        at bdv.img.omezarr.ZarrImageLoader.getSetupImgLoader(ZarrImageLoader.java:345)
        at bdv.img.omezarr.ZarrImageLoader.getSetupImgLoader(ZarrImageLoader.java:37)
        at net.preibisch.bigstitcher.spark.util.ViewUtil.getTransformedBoundingBox(ViewUtil.java:32)
        at net.preibisch.bigstitcher.spark.AffineFusion.lambda$call$6156960b$1(AffineFusion.java:342)
        at org.apache.spark.api.java.JavaRDDLike$$anonfun$foreach$1.apply(JavaRDDLike.scala:351)
        at org.apache.spark.api.java.JavaRDDLike$$anonfun$foreach$1.apply(JavaRDDLike.scala:351)
        at scala.collection.Iterator$class.foreach(Iterator.scala:891)
        at org.apache.spark.InterruptibleIterator.foreach(InterruptibleIterator.scala:28)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1$$anonfun$apply$27.apply(RDD.scala:972)
        at org.apache.spark.rdd.RDD$$anonfun$foreach$1$$anonfun$apply$27.apply(RDD.scala:972)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
        at org.apache.spark.scheduler.Task.run(Task.scala:123)
        at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
        at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:750)

Debug hint by @tpietzsch:setNumFetcherThreads(0) that is used by BigStitcher-Spark is not respected rather default thread creation is performed.
@kgabor kgabor added the bug Something isn't working label Jan 4, 2023
@kgabor kgabor linked a pull request Mar 9, 2023 that will close this issue
2 runaway thread #3
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@kgabor kgabor self-assigned this Mar 10, 2023
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kgabor commented Mar 25, 2023

It seems that this bug is still around, this is a phase correlation run on 64 CPU with the development branch that supposed to respect setNumFetcherThreads
hs_err_pid717.log
.

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Could you try to hardcode private int requestedNumFetcherThreads = 0; and see whether that fixes the problem?
(I suspect maybe openZarr() is called before setNumFetcherThreads(). If so, we should find a way to avoid that.)

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kgabor commented Apr 26, 2023

Could you try to hardcode private int requestedNumFetcherThreads = 0; and see whether that fixes the problem? (I suspect maybe openZarr() is called before setNumFetcherThreads(). If so, we should find a way to avoid that.)

The culprit was a missing isOpen=true in openZarr().

@kgabor kgabor closed this as completed in #3 Apr 26, 2023
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2 runaway thread bigdataviewer/bigdataviewer-omezarr
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@tpietzsch @kgabor