When initializing the GRU layer, Fairseq enforced the dropout from https://github.com/pytorch/fairseq/blob/master/fairseq/models/lstm.py#L180 3 
        self.lstm = LSTM(
            input_size=embed_dim,
            hidden_size=hidden_size,
            num_layers=num_layers,
            dropout=self.dropout_out if num_layers > 1 else 0.,
            bidirectional=bidirectional,
        )

But why does it drop out again after the GRU?
From https://github.com/pytorch/fairseq/blob/master/fairseq/models/lstm.py#L227 4, it looks like after applying the GRU and unpacking the sequence it dropouts again:

    def forward(self, src_tokens, src_lengths):
        if self.left_pad:
            # convert left-padding to right-padding
            src_tokens = utils.convert_padding_direction(
                src_tokens,
                self.padding_idx,
                left_to_right=True,
            )

        bsz, seqlen = src_tokens.size()

        # embed tokens
        x = self.embed_tokens(src_tokens)
        x = F.dropout(x, p=self.dropout_in, training=self.training)

        # B x T x C -> T x B x C
        x = x.transpose(0, 1)

        # pack embedded source tokens into a PackedSequence
        packed_x = nn.utils.rnn.pack_padded_sequence(x, src_lengths.data.tolist())

        # apply LSTM
        if self.bidirectional:
            state_size = 2 * self.num_layers, bsz, self.hidden_size
        else:
            state_size = self.num_layers, bsz, self.hidden_size
        h0 = x.data.new(*state_size).zero_()
        c0 = x.data.new(*state_size).zero_()
        packed_outs, (final_hiddens, final_cells) = self.lstm(packed_x, (h0, c0))

        # unpack outputs and apply dropout
        x, _ = nn.utils.rnn.pad_packed_sequence(packed_outs, padding_value=self.padding_value)
        x = F.dropout(x, p=self.dropout_out, training=self.training)
        assert list(x.size()) == [seqlen, bsz, self.output_units]