Well, actually, this problem was found because of the brnn stucking problem.
I found that if continue a training from checkpoint model twice (different checkpoint model). The epoch would not end up even the number of iteration was exceed.
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[09/27/17 13:34:02 INFO] Epoch 3 ; Iteration 76400/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 6994 ; Perplexity 23.82
[09/27/17 13:34:12 INFO] Epoch 3 ; Iteration 76450/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7004 ; Perplexity 22.87
[09/27/17 13:34:24 INFO] Epoch 3 ; Iteration 76500/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7046 ; Perplexity 26.03
[09/27/17 13:34:35 INFO] Epoch 3 ; Iteration 76550/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7053 ; Perplexity 24.08
[09/27/17 13:34:47 INFO] Epoch 3 ; Iteration 76600/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7044 ; Perplexity 23.67
[09/27/17 13:34:57 INFO] Epoch 3 ; Iteration 76650/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 6786 ; Perplexity 22.38
[09/27/17 13:35:09 INFO] Epoch 3 ; Iteration 76700/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 6762 ; Perplexity 24.63
[09/27/17 13:35:21 INFO] Epoch 3 ; Iteration 76750/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7448 ; Perplexity 26.97
[09/27/17 13:35:32 INFO] Epoch 3 ; Iteration 76800/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 6960 ; Perplexity 23.75
[09/27/17 13:35:43 INFO] Epoch 3 ; Iteration 76850/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7113 ; Perplexity 23.02
[09/27/17 13:35:55 INFO] Epoch 3 ; Iteration 76900/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7298 ; Perplexity 27.34
[09/27/17 13:36:07 INFO] Epoch 3 ; Iteration 76950/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7105 ; Perplexity 26.38
[09/27/17 13:36:19 INFO] Epoch 3 ; Iteration 77000/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7458 ; Perplexity 25.72
[09/27/17 13:36:30 INFO] Epoch 3 ; Iteration 77050/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 6877 ; Perplexity 24.18
[09/27/17 13:36:43 INFO] Epoch 3 ; Iteration 77100/76803 ; Optim SGD LR 1.000000 ; Source tokens/s 7407 ; Perplexity 27.12
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