Support layer parallelism in transformer application (#2420)

This PR adds the capability to support layer parallelism in transformers, variable-length version of The Pile pretokenized dataset, updates to the LBANN graph visualizer script, and some minor tweaks to weights layer.

Author: tbennun

Diff for: applications/nlp/transformer/datasets/pretokenize/varlen/pretokenize-validation.py

@@ -0,0 +1,34 @@
+from tqdm import trange
+from multiprocessing import Pool
+import numpy as np
+import pickle
+
+
+class Processor:
+
+    def __init__(self, total_threads: int):
+        self.threads = total_threads
+
+    def __call__(self, tid: int):
+        import thepile as dataset
+        num_samples = dataset.num_val_samples()
+        filename = f'/p/vast1/data/datasets/the-pile-huggingface/pretokenized-varlen/val.bin'
+        len_filename = f'/p/vast1/data/datasets/the-pile-huggingface/pretokenized-varlen/val-seqlen.bin'
+
+        with open(filename, 'ab') as fp:
+            with open(len_filename, 'ab') as slfp:
+                for i in trange(num_samples):
+                    text = dataset.dataset_val[i]['text']
+                    tokenized = dataset.tokenize(text)
+                    sample = np.array(tokenized, dtype=np.uint16)
+                    sample_len = np.array([len(sample)], dtype=np.uint32)
+                    sample.tofile(fp)
+                    sample_len.tofile(slfp)
+
+        print('Done')
+
+
+if __name__ == '__main__':
+    threads = 1
+    with Pool(threads) as pool:
+        pool.map(Processor(threads), range(threads))

Diff for: applications/nlp/transformer/datasets/pretokenize/varlen/pretokenize.py

@@ -0,0 +1,78 @@
+from tqdm import trange
+from multiprocessing import Pool
+import numpy as np
+import os
+import argparse
+from pathlib import Path
+
+
+class Processor:
+
+    def __init__(self, total_threads: int):
+        self.threads = total_threads
+
+    def __call__(self, tid: int):
+        import thepile as dataset
+        num_samples = dataset.num_train_samples()
+        np.random.seed(20231023)
+        indices = np.random.permutation(num_samples)
+        local_samples = num_samples // self.threads
+        offset = tid * local_samples
+        # Add remainder
+        if tid == self.threads - 1:
+            local_samples += num_samples % self.threads
+        section = indices[offset:offset + local_samples]
+        filename = f'/p/vast1/data/datasets/the-pile-huggingface/pretokenized-varlen/train-pretokenized-{tid:02d}-of-{self.threads}.bin'
+        len_filename = f'/p/vast1/data/datasets/the-pile-huggingface/pretokenized-varlen/train-seqlen-{tid:02d}-of-{self.threads}.bin'
+
+        # Create file
+        if not os.path.isfile(filename):
+            Path(filename).touch()
+        if not os.path.isfile(len_filename):
+            Path(len_filename).touch()
+
+        sz = os.path.getsize(len_filename)
+        assert sz % 4 == 0
+        sequences_processed = sz // 4
+        print(tid, ': Size in bytes:', sz, '. Sequences processed:',
+              sequences_processed)
+
+        with open(filename, 'ab') as fp:
+            with open(len_filename, 'ab') as slfp:
+                for i in trange(sequences_processed,
+                                section.shape[0],
+                                desc=f'Thread {tid}'):
+                    text = dataset.dataset_train[int(section[i])]['text']
+                    sample = dataset.tokenize(text)
+                    sample = np.array(sample, dtype=np.uint16)
+                    sample.tofile(fp)
+                    sample_len = np.array([len(sample)], dtype=np.uint32)
+                    sample_len.tofile(slfp)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('-j',
+                        action='store',
+                        default=0,
+                        type=int,
+                        help='Threads (default 0 = number of cores)')
+    parser.add_argument('-t',
+                        action='store',
+                        default=0,
+                        type=int,
+                        help='Total Chunks (default 0 = number of threads)')
+    parser.add_argument('-o',
+                        action='store',
+                        default=0,
+                        type=int,
+                        help='Chunk offset (default 0)')
+    args = parser.parse_args()
+
+    threads = args.j or os.cpu_count()
+    total_chunks = args.t or threads
+    offset = args.o
+    assert offset + threads <= total_chunks
+    with Pool(threads) as pool:
+        pool.map(Processor(total_chunks), range(offset, offset + threads))

Diff for: applications/nlp/transformer/datasets/thepile.py

@@ -91,7 +91,7 @@ def get_train_sample(index):
 
 def get_val_sample(index):
     """Token indices for a data sample from the validation set."""
-    text = dataset_train[index]['text']
+    text = dataset_val[index]['text']
     tokenized = tokenize(text)
 
     # Trim long sequences, left-pad short sequences
@@ -120,3 +120,12 @@ def sample_dims():
 
 def vocab_size():
     return tokenizer.get_vocab_size()
+
+
+if __name__ == '__main__':
+    print('Training samples:', num_train_samples())
+    print('Validation samples:', num_val_samples())
+    print('Training sample 101:')
+    print(tokenizer.decode(get_train_sample(101)))
+    print('Validation sample 233:')
+    print(tokenizer.decode(get_val_sample(233)))

Diff for: applications/nlp/transformer/datasets/thepile_pretokenized.py

@@ -1,5 +1,5 @@
 """
-The Pile dataset, stored as pre-tokenized binary files for optimized processing.
+The Pile dataset, stored as pre-tokenized, pre-packed binary files for optimized processing.
 """
 import os
 import os.path
@@ -10,7 +10,9 @@
 # Options
 # ----------------------------------------------
 
-sequence_length = int(os.getenv('THE_PILE_SEQUENCE_LENGTH', default='512'))
+# Sequence length is hardcoded to 512 in the pre-packed binary dataset.
+# To use other sequence lengths, see ``thepile_pretokenized_varlen.py``
+sequence_length = 512
 
 # ----------------------------------------------
 # Setup

Diff for: applications/nlp/transformer/datasets/thepile_pretokenized_varlen.py

@@ -0,0 +1,105 @@
+"""
+The Pile dataset, stored as pre-tokenized binary files for optimized processing.
+"""
+import os
+import os.path
+
+import numpy as np
+# ----------------------------------------------
+# Options
+# ----------------------------------------------
+
+sequence_length = int(os.getenv('THE_PILE_SEQUENCE_LENGTH', default='512'))
+
+# ----------------------------------------------
+# Setup
+# ----------------------------------------------
+
+# Load the datasets
+data_dir = os.getenv('THE_PILE_DATA_DIR',
+                     '/p/vast1/data/datasets/the-pile-pretokenized')
+dataset_train = np.memmap(os.path.join(data_dir, 'train.bin'),
+                          dtype=np.uint16,
+                          mode='r')
+sample_lengths_train = np.fromfile(os.path.join(data_dir, 'train-seqlen.bin'),
+                                   dtype=np.uint32).astype(np.uint64)
+sample_offsets_train = np.zeros_like(sample_lengths_train)
+sample_offsets_train[1:] = np.cumsum(sample_lengths_train)[:-1]
+dataset_val = np.memmap(os.path.join(data_dir, 'val.bin'),
+                        dtype=np.uint16,
+                        mode='r')
+sample_lengths_val = np.fromfile(os.path.join(data_dir, 'val-seqlen.bin'),
+                                 dtype=np.uint32).astype(np.uint64)
+sample_offsets_val = np.zeros_like(sample_lengths_val)
+sample_offsets_val[1:] = np.cumsum(sample_lengths_val)[:-1]
+
+# Uses the definition from the GPT-NeoX-20B tokenizer
+pad_index = 1  # '<|padding|>'
+_vocab_size = 50277
+
+# ----------------------------------------------
+# Sample access functions
+# ----------------------------------------------
+
+
+def trim_and_pad(sample, random: bool):
+    # Trim long sequences
+    if len(sample) > sequence_length:
+        if random:
+            pos = np.random.rand()
+            offset = (len(sample) - sequence_length + 1) * pos
+            offset = int(np.floor(offset))
+            sample = sample[offset:offset + sequence_length]
+        else:
+            sample = sample[0:sequence_length]
+
+    # Left-pad short sequences
+    if len(sample) < sequence_length:
+        sample_pad = np.full(sequence_length, pad_index, dtype=np.int32)
+        if len(sample) > 0:
+            sample_pad[-len(sample):] = sample
+        return sample_pad
+
+    return sample
+
+
+def get_train_sample(index: int):
+    sample = np.copy(
+        dataset_train[sample_offsets_train[index]:sample_offsets_train[index] +
+                      sample_lengths_train[index]]).astype(np.int32)
+    return trim_and_pad(sample, True)
+
+
+def get_val_sample(index):
+    sample = np.copy(
+        dataset_val[sample_offsets_val[index]:sample_offsets_val[index] +
+                    sample_lengths_val[index]]).astype(np.int32)
+    return trim_and_pad(sample, False)
+
+
+def num_train_samples():
+    return sample_lengths_train.shape[0]
+
+
+def num_val_samples():
+    return sample_lengths_val.shape[0]
+
+
+def sample_dims():
+    return (sequence_length, )
+
+
+def vocab_size():
+    return _vocab_size
+
+
+if __name__ == '__main__':
+    print('Training samples:', num_train_samples())
+    print('Validation samples:', num_val_samples())
+    from tokenizers import Tokenizer
+    tokenizer = Tokenizer.from_file(
+        os.path.join(data_dir, '20B_tokenizer.json'))
+    print('Training sample 101:')
+    print(tokenizer.decode(get_train_sample(101)))
+    print('Validation sample 233:')
+    print(tokenizer.decode(get_val_sample(233)))

Diff for: applications/nlp/transformer/modeling.py

@@ -87,6 +87,7 @@ def create_encoder_decoder_transformer(dataset, args: argparse.Namespace):
         transformer, args)
     parallelism.apply_ffn_model_parallelism(transformer, args)
     parallelism.apply_fsdp_mlp(transformer, [embedding_weights], args)
+    parallelism.apply_layer_parallelism(transformer, args)
 
     # Run through transformer
     result = transformer(encoder_input, decoder_input, sequence_length - 1)
@@ -124,6 +125,7 @@ def create_encoder_decoder_transformer(dataset, args: argparse.Namespace):
     )
 
     parallelism.apply_fsdp_allweights(result, args)
+    parallelism.apply_layer_parallelism_postamble(result, args)
     return result
 
 
@@ -186,6 +188,7 @@ def create_causal_lm_decoder_transformer(dataset, embed_dim: int,
         transformer, args)
     parallelism.apply_ffn_model_parallelism(transformer, args)
     parallelism.apply_fsdp_mlp(transformer, [embedding_weights], args)
+    parallelism.apply_layer_parallelism(transformer, args)
 
     # Run through transformer with the same sequence
     result = transformer(decoder_input, decoder_input, sequence_length)
@@ -227,6 +230,7 @@ def create_causal_lm_decoder_transformer(dataset, embed_dim: int,
     )
 
     parallelism.apply_fsdp_allweights(result, args)
+    parallelism.apply_layer_parallelism_postamble(result, args)
     return result