Incremental backup never closes connection

[dravenweston]

I am attempting to run an incremental backup against a small oplog and the process never completes. A jstack has the following in the output and I noticed that the "Finalizer" and "Reference Handler" are in a waiting state. Can you direct me to what it is waiting on and ultimately how to get it to close?

Full thread dump Java HotSpot(TM) 64-Bit Server VM (20.12-b01-434 mixed mode):

"Attach Listener" daemon prio=9 tid=7fdd211e7000 nid=0x11056c000 waiting on condition [00000000]
java.lang.Thread.State: RUNNABLE

"DestroyJavaVM" prio=5 tid=7fdd212f7800 nid=0x1065c8000 waiting on condition [00000000]
java.lang.Thread.State: RUNNABLE

"Thread-5" prio=5 tid=7fdd212f6800 nid=0x1102ce000 waiting on condition [1102cd000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at com.wordnik.system.mongodb.StopFileMonitor.run(StopFileMonitor.java:14)

"oplog" prio=5 tid=7fdd212f6000 nid=0x1101cb000 runnable [1101ca000]
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:129)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:258)
at java.io.BufferedInputStream.read(BufferedInputStream.java:317)
- locked <7bc4461c8> (a java.io.BufferedInputStream)
at org.bson.io.Bits.readFully(Bits.java:35)
at org.bson.io.Bits.readFully(Bits.java:28)
at com.mongodb.Response.(Response.java:39)
at com.mongodb.DBPort.go(DBPort.java:128)
- locked <7bc438ad8> (a com.mongodb.DBPort)
at com.mongodb.DBPort.call(DBPort.java:79)
at com.mongodb.DBTCPConnector.call(DBTCPConnector.java:218)
at com.mongodb.DBTCPConnector.call(DBTCPConnector.java:189)
at com.mongodb.DBApiLayer$Result._advance(DBApiLayer.java:452)
at com.mongodb.DBApiLayer$Result.hasNext(DBApiLayer.java:418)
at com.mongodb.DBCursor._hasNext(DBCursor.java:509)
at com.mongodb.DBCursor.hasNext(DBCursor.java:529)
at com.wordnik.system.mongodb.OplogTailThread.run(OplogTailThread.java:143)

"MongoCleaner1234403385" daemon prio=5 tid=7fdd212f3000 nid=0x1100c8000 waiting on condition [1100c7000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at com.mongodb.Mongo$DBCleanerThread.run(Mongo.java:681)

"ReplicaSetStatus:Updater" daemon prio=5 tid=7fdd212f2800 nid=0x10ffc5000 waiting on condition [10ffc4000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at com.mongodb.ReplicaSetStatus$Updater.run(ReplicaSetStatus.java:428)

"MongoCleaner1751161119" daemon prio=5 tid=7fdd26069800 nid=0x10fe84000 waiting on condition [10fe83000]
java.lang.Thread.State: TIMED_WAITING (sleeping)
at java.lang.Thread.sleep(Native Method)
at com.mongodb.Mongo$DBCleanerThread.run(Mongo.java:681)

"Low Memory Detector" daemon prio=5 tid=7fdd2501a800 nid=0x10f9e9000 runnable [00000000]
java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" daemon prio=9 tid=7fdd25019800 nid=0x10f8e6000 waiting on condition [00000000]
java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" daemon prio=9 tid=7fdd25019000 nid=0x10f7e3000 waiting on condition [00000000]
java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=9 tid=7fdd25018000 nid=0x10f6e0000 runnable [00000000]
java.lang.Thread.State: RUNNABLE

"Surrogate Locker Thread (Concurrent GC)" daemon prio=5 tid=7fdd25017000 nid=0x10f5dd000 waiting on condition [00000000]
java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=8 tid=7fdd211dd800 nid=0x10f3d3000 in Object.wait() [10f3d2000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <7bb401300> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
- locked <7bb401300> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=7fdd211dc800 nid=0x10f2d0000 in Object.wait() [10f2cf000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <7bb4011d8> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Object.java:485)
at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
- locked <7bb4011d8> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=9 tid=7fdd211d8000 nid=0x10f1cd000 runnable

"Gang worker#0 (Parallel GC Threads)" prio=9 tid=7fdd21001800 nid=0x1099cb000 runnable

"Gang worker#1 (Parallel GC Threads)" prio=9 tid=7fdd21002000 nid=0x109ace000 runnable

"Gang worker#2 (Parallel GC Threads)" prio=9 tid=7fdd21002800 nid=0x109bd1000 runnable

"Gang worker#3 (Parallel GC Threads)" prio=9 tid=7fdd21003000 nid=0x109cd4000 runnable

"Gang worker#4 (Parallel GC Threads)" prio=9 tid=7fdd21004000 nid=0x109dd7000 runnable

"Gang worker#5 (Parallel GC Threads)" prio=9 tid=7fdd21004800 nid=0x109eda000 runnable

"Gang worker#6 (Parallel GC Threads)" prio=9 tid=7fdd21005000 nid=0x109fdd000 runnable

"Gang worker#7 (Parallel GC Threads)" prio=9 tid=7fdd21005800 nid=0x10a0e0000 runnable

"Concurrent Mark-Sweep GC Thread" prio=9 tid=7fdd210e3000 nid=0x10ee1f000 runnable
"Gang worker#0 (Parallel CMS Threads)" prio=9 tid=7fdd210e2000 nid=0x10e419000 runnable

"Gang worker#1 (Parallel CMS Threads)" prio=9 tid=7fdd210e2800 nid=0x10e51c000 runnable

"VM Periodic Task Thread" prio=10 tid=7fdd211ef000 nid=0x10faec000 waiting on condition

"Exception Catcher Thread" prio=10 tid=7fdd24001800 nid=0x1067f3000 runnable
JNI global references: 1091

[fehguy]

Howdy, the incremental backup is waiting for the next event to come over the oplog--it will never complete by design until it finds a stop file (./stop.txt). That is the nature of the incremental backup, it's supposed to continually write records.