I came across exactly the same error.
Just by following the tutorial http://opennmt.net/OpenNMT-py/quickstart.html 91 , when typing
python train.py -data data/demo -save_model demo-model

it gives me the same warning.
/OpenNMT-py/onmt/modules/GlobalAttention.py:177: UserWarning: Implicit dimension choice for softmax has been deprecated. Change the call to include dim=X as an argument.

Can anyone please help as to how can this be resolved?