Add sdpa for BioGpt (#33592)

* Add sdpa for BioGpt

* Updates

* Add the docs

* [run_slow] biogpt

* Use the copy mechanism to ensure consistency

* [run_slow] biogpt

docs/source/en/model_doc/biogpt.md

@@ -32,6 +32,51 @@ This model was contributed by [kamalkraj](https://huggingface.co/kamalkraj). The
 - BioGPT was trained with a causal language modeling (CLM) objective and is therefore powerful at predicting the next token in a sequence. Leveraging this feature allows BioGPT to generate syntactically coherent text as it can be observed in the run_generation.py example script.
 - The model can take the `past_key_values` (for PyTorch) as input, which is the previously computed key/value attention pairs. Using this (past_key_values or past) value prevents the model from re-computing pre-computed values in the context of text generation. For PyTorch, see past_key_values argument of the BioGptForCausalLM.forward() method for more information on its usage.
 
+### Using Scaled Dot Product Attention (SDPA)
+
+PyTorch includes a native scaled dot-product attention (SDPA) operator as part of `torch.nn.functional`. This function 
+encompasses several implementations that can be applied depending on the inputs and the hardware in use. See the 
+[official documentation](https://pytorch.org/docs/stable/generated/torch.nn.functional.scaled_dot_product_attention.html) 
+or the [GPU Inference](https://huggingface.co/docs/transformers/main/en/perf_infer_gpu_one#pytorch-scaled-dot-product-attention)
+page for more information.
+
+SDPA is used by default for `torch>=2.1.1` when an implementation is available, but you may also set 
+`attn_implementation="sdpa"` in `from_pretrained()` to explicitly request SDPA to be used.
+
+```
+from transformers import BioGptForCausalLM
+model = BioGptForCausalLM.from_pretrained("microsoft/biogpt", attn_implementation="sdpa", torch_dtype=torch.float16)
+```
+
+On a local benchmark (NVIDIA GeForce RTX 2060-8GB, PyTorch 2.3.1, OS Ubuntu 20.04) with `float16` and `microsoft/biogpt` model with a CausalLM head,
+we saw the following speedups during training.
+
+For the best speedups, we recommend loading the model in half-precision (e.g. `torch.float16` or `torch.bfloat16`).
+
+| num_training_steps | batch_size | seq_len | is cuda | Time per batch (eager - s) | Time per batch (sdpa - s) | Speedup (%) | Eager peak mem (MB) | sdpa peak mem (MB) | Mem saving (%) |
+|--------------------|------------|---------|---------|----------------------------|---------------------------|-------------|---------------------|--------------------|----------------|
+| 100                | 1          | 128     | False   | 0.038                      | 0.031                     | 21.301      | 1601.862            | 1601.497           | 0.023          |
+| 100                | 1          | 256     | False   | 0.039                      | 0.034                     | 15.084      | 1624.944            | 1625.296           | -0.022         |
+| 100                | 2          | 128     | False   | 0.039                      | 0.033                     | 16.820      | 1624.567            | 1625.296           | -0.045         |
+| 100                | 2          | 256     | False   | 0.065                      | 0.059                     | 10.255      | 1672.164            | 1672.164           | 0.000          |
+| 100                | 4          | 128     | False   | 0.062                      | 0.058                     | 6.998       | 1671.435            | 1672.164           | -0.044         |
+| 100                | 4          | 256     | False   | 0.113                      | 0.100                     | 13.316      | 2350.179            | 1848.435           | 27.144         |
+| 100                | 8          | 128     | False   | 0.107                      | 0.098                     | 9.883       | 2098.521            | 1848.435           | 13.530         |
+| 100                | 8          | 256     | False   | 0.222                      | 0.196                     | 13.413      | 3989.980            | 2986.492           | 33.601         |
+
+On a local benchmark (NVIDIA GeForce RTX 2060-8GB, PyTorch 2.3.1, OS Ubuntu 20.04) with `float16` and `microsoft/biogpt` model with a simple AutoModel head,
+we saw the following speedups during inference.
+
+| num_batches | batch_size | seq_len | is cuda | is half | use mask | Per token latency eager (ms) | Per token latency SDPA (ms) | Speedup (%) | Mem eager (MB) | Mem BT (MB) | Mem saved (%) |
+|-------------|------------|---------|---------|---------|----------|------------------------------|-----------------------------|-------------|----------------|--------------|---------------|
+| 50          | 1          | 64      | True    | True    | True     | 0.115                        | 0.098                       | 17.392      | 716.998        | 716.998      | 0.000         |
+| 50          | 1          | 128     | True    | True    | True     | 0.115                        | 0.093                       | 24.640      | 730.916        | 730.916      | 0.000         |
+| 50          | 2          | 64      | True    | True    | True     | 0.114                        | 0.096                       | 19.204      | 730.900        | 730.900      | 0.000         |
+| 50          | 2          | 128     | True    | True    | True     | 0.117                        | 0.095                       | 23.529      | 759.262        | 759.262      | 0.000         |
+| 50          | 4          | 64      | True    | True    | True     | 0.113                        | 0.096                       | 18.325      | 759.229        | 759.229      | 0.000         |
+| 50          | 4          | 128     | True    | True    | True     | 0.186                        | 0.178                       | 4.289       | 816.478        | 816.478      | 0.000         |
+
+
 ## Resources
 
 - [Causal language modeling task guide](../tasks/language_modeling)

docs/source/en/perf_infer_gpu_one.md

@@ -208,6 +208,7 @@ For now, Transformers supports SDPA inference and training for the following arc
 * [Audio Spectrogram Transformer](https://huggingface.co/docs/transformers/model_doc/audio-spectrogram-transformer#transformers.ASTModel)
 * [Bart](https://huggingface.co/docs/transformers/model_doc/bart#transformers.BartModel)
 * [Bert](https://huggingface.co/docs/transformers/model_doc/bert#transformers.BertModel)
+* [BioGpt](https://huggingface.co/docs/transformers/model_doc/biogpt#transformers.BioGptModel)
 * [CamemBERT](https://huggingface.co/docs/transformers/model_doc/camembert#transformers.CamembertModel)
 * [Chameleon](https://huggingface.co/docs/transformers/model_doc/chameleon#transformers.Chameleon)
 * [CLIP](https://huggingface.co/docs/transformers/model_doc/clip#transformers.CLIPModel)

src/transformers/models/biogpt/modeling_biogpt.py

@@ -23,7 +23,7 @@ from torch import nn
 from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
 
 from ...activations import ACT2FN
-from ...modeling_attn_mask_utils import _prepare_4d_causal_attention_mask
+from ...modeling_attn_mask_utils import _prepare_4d_causal_attention_mask, _prepare_4d_causal_attention_mask_for_sdpa
 from ...modeling_outputs import (
     BaseModelOutputWithPastAndCrossAttentions,
     CausalLMOutputWithCrossAttentions,
@@ -244,16 +244,130 @@ class BioGptAttention(nn.Module):
         return attn_output, attn_weights_reshaped, past_key_value
 
 
+# Copied from transformers.models.bart.modeling_bart.BartSdpaAttention with Bart->BioGpt
+class BioGptSdpaAttention(BioGptAttention):
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        key_value_states: Optional[torch.Tensor] = None,
+        past_key_value: Optional[Tuple[torch.Tensor]] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        layer_head_mask: Optional[torch.Tensor] = None,
+        output_attentions: bool = False,
+    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
+        """Input shape: Batch x Time x Channel"""
+        if output_attentions or layer_head_mask is not None:
+            # TODO: Improve this warning with e.g. `model.config._attn_implementation = "manual"` once this is implemented.
+            logger.warning_once(
+                "BioGptModel is using BioGptSdpaAttention, but `torch.nn.functional.scaled_dot_product_attention` does not support `output_attentions=True` or `layer_head_mask` not None. Falling back to the manual attention"
+                ' implementation, but specifying the manual implementation will be required from Transformers version v5.0.0 onwards. This warning can be removed using the argument `attn_implementation="eager"` when loading the model.'
+            )
+            return super().forward(
+                hidden_states,
+                key_value_states=key_value_states,
+                past_key_value=past_key_value,
+                attention_mask=attention_mask,
+                layer_head_mask=layer_head_mask,
+                output_attentions=output_attentions,
+            )
+
+        # if key_value_states are provided this layer is used as a cross-attention layer
+        # for the decoder
+        is_cross_attention = key_value_states is not None
+
+        bsz, tgt_len, _ = hidden_states.size()
+
+        # get query proj
+        query_states = self.q_proj(hidden_states)
+        # get key, value proj
+        # `past_key_value[0].shape[2] == key_value_states.shape[1]`
+        # is checking that the `sequence_length` of the `past_key_value` is the same as
+        # the provided `key_value_states` to support prefix tuning
+        if (
+            is_cross_attention
+            and past_key_value is not None
+            and past_key_value[0].shape[2] == key_value_states.shape[1]
+        ):
+            # reuse k,v, cross_attentions
+            key_states = past_key_value[0]
+            value_states = past_key_value[1]
+        elif is_cross_attention:
+            # cross_attentions
+            key_states = self._shape(self.k_proj(key_value_states), -1, bsz)
+            value_states = self._shape(self.v_proj(key_value_states), -1, bsz)
+        elif past_key_value is not None:
+            # reuse k, v, self_attention
+            key_states = self._shape(self.k_proj(hidden_states), -1, bsz)
+            value_states = self._shape(self.v_proj(hidden_states), -1, bsz)
+            key_states = torch.cat([past_key_value[0], key_states], dim=2)
+            value_states = torch.cat([past_key_value[1], value_states], dim=2)
+        else:
+            # self_attention
+            key_states = self._shape(self.k_proj(hidden_states), -1, bsz)
+            value_states = self._shape(self.v_proj(hidden_states), -1, bsz)
+
+        if self.is_decoder:
+            # if cross_attention save Tuple(torch.Tensor, torch.Tensor) of all cross attention key/value_states.
+            # Further calls to cross_attention layer can then reuse all cross-attention
+            # key/value_states (first "if" case)
+            # if uni-directional self-attention (decoder) save Tuple(torch.Tensor, torch.Tensor) of
+            # all previous decoder key/value_states. Further calls to uni-directional self-attention
+            # can concat previous decoder key/value_states to current projected key/value_states (third "elif" case)
+            # if encoder bi-directional self-attention `past_key_value` is always `None`
+            past_key_value = (key_states, value_states)
+
+        query_states = self._shape(query_states, tgt_len, bsz)
+
+        # We dispatch to SDPA's Flash Attention or Efficient kernels via this `is_causal` if statement instead of an inline conditional assignment
+        # in SDPA to support both torch.compile's dynamic shapes and full graph options. An inline conditional prevents dynamic shapes from compiling.
+        # The tgt_len > 1 is necessary to match with AttentionMaskConverter.to_causal_4d that does not create a causal mask in case tgt_len == 1.
+        is_causal = True if self.is_causal and attention_mask is None and tgt_len > 1 else False
+
+        # NOTE: SDPA with memory-efficient backend is currently (torch==2.1.2) bugged when using non-contiguous inputs and a custom attn_mask,
+        # but we are fine here as `_shape` do call `.contiguous()`. Reference: https://github.com/pytorch/pytorch/issues/112577
+        attn_output = torch.nn.functional.scaled_dot_product_attention(
+            query_states,
+            key_states,
+            value_states,
+            attn_mask=attention_mask,
+            dropout_p=self.dropout if self.training else 0.0,
+            is_causal=is_causal,
+        )
+
+        if attn_output.size() != (bsz, self.num_heads, tgt_len, self.head_dim):
+            raise ValueError(
+                f"`attn_output` should be of size {(bsz, self.num_heads, tgt_len, self.head_dim)}, but is"
+                f" {attn_output.size()}"
+            )
+
+        attn_output = attn_output.transpose(1, 2)
+
+        # Use the `embed_dim` from the config (stored in the class) rather than `hidden_state` because `attn_output` can be
+        # partitioned across GPUs when using tensor-parallelism.
+        attn_output = attn_output.reshape(bsz, tgt_len, self.embed_dim)
+
+        attn_output = self.out_proj(attn_output)
+
+        return attn_output, None, past_key_value
+
+
+BIOGPT_ATTENTION_CLASSES = {
+    "eager": BioGptAttention,
+    "sdpa": BioGptSdpaAttention,
+}
+
+
 class BioGptDecoderLayer(nn.Module):
     def __init__(self, config: BioGptConfig):
         super().__init__()
         self.embed_dim = config.hidden_size
 
-        self.self_attn = BioGptAttention(
+        self.self_attn = BIOGPT_ATTENTION_CLASSES[config._attn_implementation](
             embed_dim=self.embed_dim,
             num_heads=config.num_attention_heads,
             dropout=config.attention_probs_dropout_prob,
             is_decoder=True,
+            is_causal=True,
         )
         self.dropout = config.hidden_dropout_prob
         self.activation_fn = ACT2FN[config.hidden_act]
@@ -337,6 +451,7 @@ class BioGptPreTrainedModel(PreTrainedModel):
     config_class = BioGptConfig
     base_model_prefix = "biogpt"
     supports_gradient_checkpointing = True
+    _supports_sdpa = True
 
     def _init_weights(self, module):
         """Initialize the weights"""
@@ -444,6 +559,7 @@ class BioGptModel(BioGptPreTrainedModel):
         self.layer_norm = nn.LayerNorm(self.embed_dim)
 
         self.gradient_checkpointing = False
+        self._use_sdpa = config._attn_implementation == "sdpa"
         # Initialize weights and apply final processing
         self.post_init()
 
@@ -511,9 +627,16 @@ class BioGptModel(BioGptPreTrainedModel):
         # embed positions
         positions = self.embed_positions(attention_mask, past_key_values_length)
 
-        attention_mask = _prepare_4d_causal_attention_mask(
+        if self._use_sdpa and not output_attentions and head_mask is None:
-            attention_mask, input_shape, inputs_embeds, past_key_values_length
+            # output_attentions=True & head_mask can not be supported when using SDPA, fall back to
-        )
+            # the manual implementation that requires a 4D causal mask in all cases.
+            attention_mask = _prepare_4d_causal_attention_mask_for_sdpa(
+                attention_mask, input_shape, inputs_embeds, past_key_values_length
+            )
+        else:
+            attention_mask = _prepare_4d_causal_attention_mask(
+                attention_mask, input_shape, inputs_embeds, past_key_values_length
+            )
 
         hidden_states = inputs_embeds + positions