add unpad_input_for_concatenated_sequences (#499)

* add unpad_input_for_concatenated_sequences

* modify docstring

flash_attn/bert_padding.py

@@ -122,6 +122,78 @@ def unpad_input(hidden_states, attention_mask):
     )
 
 
+def unpad_input_for_concatenated_sequences(hidden_states, attention_mask_in_length):
+    """
+    Supports concatenating short samples in one sequence. The attention_mask_in_length is utilized to mask other short samples. It helps efficient training of variant lengths-based samples (e.g., the supervised fine-tuning task in large language model).
+    The motivation for this function is explained [here](https://github.com/Dao-AILab/flash-attention/issues/432#issuecomment-1668822286).
+    
+    For example, if batch = 3 and seqlen = 6, the attention_mask_in_length is:
+        ```
+        [
+          [2, 3, 0, 0, 0, 0],
+          [3, 2, 0, 0, 0, 0],
+          [6, 0, 0, 0, 0, 0]
+        ]
+        ```
+    , which refers to the 3D-attention mask:
+        ```
+        [
+          [
+            [1, 0, 0, 0, 0, 0],
+            [1, 1, 0, 0, 0, 0],
+            [0, 0, 1, 0, 0, 0],
+            [0, 0, 1, 1, 0, 0],
+            [0, 0, 1, 1, 1, 0],
+            [0, 0, 0, 0, 0, 1]
+          ],
+          [
+            [1, 0, 0, 0, 0, 0],
+            [1, 1, 0, 0, 0, 0],
+            [1, 1, 1, 0, 0, 0],
+            [0, 0, 0, 1, 0, 0],
+            [0, 0, 0, 1, 1, 0],
+            [0, 0, 0, 0, 0, 1]
+          ],
+          [
+            [1, 0, 0, 0, 0, 0],
+            [1, 1, 0, 0, 0, 0],
+            [1, 1, 1, 0, 0, 0],
+            [1, 1, 1, 1, 0, 0],
+            [1, 1, 1, 1, 1, 0],
+            [1, 1, 1, 1, 1, 1]
+          ]
+        ]
+        ```.
+
+    Arguments:
+        hidden_states: (batch, seqlen, ...)
+        attention_mask_in_length: (batch, seqlen), int, a nonzero number (e.g., 1, 2, 3, etc.) means length of concatenated sequence in b-th batch, and 0 means none.
+    Return:
+        hidden_states: (total_nnz, ...), where total_nnz = number of tokens in selected in attention_mask.
+        cu_seqlens: (batch + 1), the cumulative sequence lengths, used to index into hidden_states.
+        max_seqlen_in_batch: int
+    """
+    length = attention_mask_in_length.sum(dim=-1)
+    seqlen = attention_mask_in_length.size(-1)
+    attention_mask_2d = torch.arange(seqlen, device=length.device, dtype=length.dtype).expand(len(length), seqlen) < length.unsqueeze(1)
+    real_indices_idx = torch.nonzero(attention_mask_in_length.flatten(), as_tuple=False).flatten()
+    seqlens_in_batch = attention_mask_in_length.flatten()[real_indices_idx]
+    indices = torch.nonzero(attention_mask_2d.flatten(), as_tuple=False).flatten()
+    max_seqlen_in_batch = seqlens_in_batch.max().item()
+    cu_seqlens = F.pad(torch.cumsum(seqlens_in_batch, dim=0, dtype=torch.torch.int32), (1, 0))
+    # TD [2022-03-04] We don't want to index with a bool mask, because Pytorch will expand the
+    # bool mask, then call nonzero to get the indices, then index with those. The indices is @dim
+    # times larger than it needs to be, wasting memory. It's faster and more memory-efficient to
+    # index with integer indices. Moreover, torch's index is a bit slower than it needs to be,
+    # so we write custom forward and backward to make it a bit faster.
+    return (
+        index_first_axis(rearrange(hidden_states, "b s ... -> (b s) ..."), indices),
+        indices,
+        cu_seqlens,
+        max_seqlen_in_batch,
+    )
+
+
 def pad_input(hidden_states, indices, batch, seqlen):
     """
     Arguments: