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I have hit counter running on Java. It works 24 hours and hits pass at about 100 times per second. During the day GC processing time slowly rises from 20-60 ms till 10000-60000 ms and then drops to 20-60 ms. Such pattern is repeated from time to time. From GC logs I found that mostly all time GC spend for processing Reference objects (Ref Proc). So what's the causes of such long GC time could be? Server: Amazon EC2 m1.small OS: Ubuntu 10.04.3 LTS Java: Oracle 1.7.0_07 Example of GC logs: 2012-09-13T16:51:20.091+0400: 167239.936: [GC pause (young), 62.58395400 secs] ... [Other: 62489.7 ms] [Choose CSet: 0.0 ms] [Ref Proc: 62433.9 ms] [Ref Enq: 0.0 ms] [Free CSet: 0.7 ms] [Eden: 200M(200M)->0B(199M) Survivors: 4096K->5120K Heap: 578M(1024M)->380M(1024M)] Time - "Ref Proc" graph: 09:37:59 - 242.4 ms 09:38:50 - 226.0 ms 09:39:00 - 83.6 ms ... 11:45:22 - 451.8 ms 11:46:04 - 489.3 ms 11:46:46 - 505.6 ms ... 14:05:40 - 1027.3 ms 14:06:01 - 796.6 ms 14:06:35 - 1064.0 ms ... 15:44:32 - 1920.4 ms 15:45:04 - 2116.7 ms 15:45:39 - 2196.8 ms ... 16:19:07 - 3983.3 ms 16:19:43 - 4494.9 ms 16:20:16 - 4065.2 ms ... 16:33:11 - 7690.1 ms 16:33:50 - 8501.4 ms 16:34:28 - 8059.3 ms ... 16:47:14 - 51378.6 ms 16:49:11 - 57529.2 ms 16:51:20 - 62433.9 ms 16:53:00 - 46.1 ms 16:53:30 - 45.5 ms 16:54:03 - 45.0 ms ... 16:54:38 - 57.0 ms 16:55:09 - 20.9 ms 16:55:43 - 21.3 ms ... 16:09:45 - 134.3 ms 16:10:21 - 142.1 ms 16:10:58 - 147.5 ms ... 17:18:51 - 177.3 ms 17:19:27 - 135.8 ms 17:20:03 - 179.6 ms I found in java sources parameter PrintReferenceGC. GC log showed next [SoftReference, 0 refs, 0.0000050 secs] [WeakReference, 6 refs, 0.0000030 secs] [FinalReference, 113 refs, 0.0011180 secs] [PhantomReference, 0 refs, 0.0000020 secs] [JNI Weak Reference, 3.9010450 secs] This is some problem of JNI Weak Reference.

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