Replace regular filesystem calls with fsspec + add s3 support (#18)

Summary:

For compatibility with either local/nfs or S3 datasets, swap to fsspec.

Add a tool to compare local and remote filesystems

Test Plan:

- Ran regular train script
- Ran with config with data in S3

.gitignore

@@ -165,4 +165,4 @@ cython_debug/
 figures/
 .vscode/
 .DS_Store
-
+internal/

bytelatent/args.py

@@ -46,8 +46,11 @@ def distribute_data_to_rank(
     arrow_batch_size: int,
     rank: int,
     world_size: int,
+    s3_profile: str | None = None,
 ) -> ArrowFileIterator:
-    dataset_chunks = find_and_sanitize_chunks(dataset_path, world_size)
+    dataset_chunks = find_and_sanitize_chunks(
+        dataset_path, world_size, s3_profile=s3_profile
+    )
     n_workers_per_chunk = world_size // len(dataset_chunks)
     rank_to_arrow_iterator_params = []
     for chunk_path in dataset_chunks:
@@ -61,6 +64,7 @@ def distribute_data_to_rank(
                     dataset_files=None,
                     entropy_model_name=entropy_model_name,
                     arrow_batch_size=arrow_batch_size,
+                    s3_profile=s3_profile,
                 )
             )
     return rank_to_arrow_iterator_params[rank]
@@ -68,6 +72,7 @@ def distribute_data_to_rank(
 
 class DataloaderArgs(BaseModel):
     model_config = ConfigDict(extra="forbid")
+    s3_profile: str | None = None
     root_dir: str | None = None
     sources: dict[str, float] = {}
     batch_size: int = 2
@@ -107,6 +112,7 @@ class DataloaderArgs(BaseModel):
                 arrow_batch_size=self.arrow_batch_size,
                 rank=rank,
                 world_size=world_size,
+                s3_profile=self.s3_profile,
             )
             looping_iterator = LoopingIterator(arrow_iterator)
             preprocess_iterator = PreprocessIterator(

bytelatent/data/file_util.py

@@ -0,0 +1,117 @@
+import os
+
+import fsspec
+import pyarrow as pa
+
+# pyarrow needs the initialization from this import
+import pyarrow.dataset  # pyright: ignore
+import typer
+from pyarrow.lib import ArrowInvalid
+from rich.progress import track
+
+
+def is_valid_arrow_file(path: str):
+    try:
+        dataset = pa.dataset.dataset(path, format="arrow")
+        return True
+    except ArrowInvalid:
+        return False
+
+
+app = typer.Typer()
+
+S3_PREFIX = "s3://"
+
+
+def get_fs(path: str, s3_profile: str | None = None) -> fsspec.AbstractFileSystem:
+    if path.startswith("s3://"):
+        if s3_profile is None:
+            return fsspec.filesystem("s3")
+        else:
+            return fsspec.filesystem("s3", profile=s3_profile)
+    else:
+        return fsspec.filesystem("file")
+
+
+@app.command()
+def print_local_to_delete(
+    blob_dir: str, local_dirs: list[str], s3_profile: str = "blt"
+):
+    for s in local_dirs:
+        assert s.endswith("/"), "Dirs must end with /"
+    assert blob_dir.endswith("/"), "Dirs must end with /"
+    blob_fs = fsspec.filesystem("s3", profile=s3_profile)
+    blob_files = blob_fs.find(blob_dir)
+    for f in track(blob_files):
+        size = blob_fs.info(f)["Size"]
+        if not f.lower().endswith(".complete"):
+            assert size != 0, f"Size was invalidly zero for {f}"
+
+    blob_relative_paths = {f[len(blob_dir) - len(S3_PREFIX) :] for f in blob_files}
+    local_fs = fsspec.filesystem("file")
+
+    files_to_delete = []
+    for local_dir in local_dirs:
+        local_files = local_fs.find(local_dir)
+        for f in local_files:
+            relative_path = f[len(local_dir) :]
+            if relative_path in blob_relative_paths and not os.path.islink(f):
+                files_to_delete.append(f)
+    print(len(files_to_delete))
+    with open("/tmp/files_to_delete.txt", "w") as f:
+        for file in files_to_delete:
+            f.write(f"{file}\n")
+
+
+@app.command()
+def compare_local_to_blob(
+    source_dirs: list[str], dst_dir: str, s3_profile: str = "blt"
+):
+    for s in source_dirs:
+        assert s.endswith("/"), "Dirs must end with /"
+    assert dst_dir.endswith("/"), "Dirs must end with /"
+    assert len(source_dirs) != 0
+    assert dst_dir.startswith("s3://")
+    local_fs = fsspec.filesystem("file")
+    dst_fs = fsspec.filesystem("s3", profile=s3_profile)
+    source_to_files = {}
+    all_local_files = set()
+    for s in source_dirs:
+        skipped = []
+        if s not in source_to_files:
+            source_to_files[s] = []
+        for f in local_fs.find(s):
+            if os.path.islink(f):
+                continue
+            if f.endswith(".COMPLETE") or f.endswith(".complete"):
+                is_complete_file = True
+                assert os.path.getsize(f) == 0, ".COMPLETE files should be empty"
+            else:
+                is_complete_file = False
+
+            if not is_complete_file and os.path.getsize(f) == 0:
+                skipped.append(f)
+                continue
+            if f.endswith(".arrow"):
+                if not is_valid_arrow_file(f):
+                    skipped.append(f)
+                    continue
+
+            source_to_files[s].append(f)
+            all_local_files.add(f[len(s) :])
+        print(s, len(source_to_files[s]), "skipped", len(skipped), skipped[:10])
+
+    dst_files = dst_fs.find(dst_dir)
+    print(dst_dir, len(dst_files))
+
+    dst_file_set = {f[len(dst_dir) - len(S3_PREFIX) :] for f in dst_files}
+    diff = all_local_files.symmetric_difference(dst_file_set)
+    print("Local files", len(all_local_files))
+    print("DST Files", len(dst_file_set))
+    print("Symmetric difference", len(diff))
+    dst_only_files = dst_file_set - all_local_files
+    print("DST only", len(dst_only_files), list(dst_only_files)[:10])
+
+
+if __name__ == "__main__":
+    app()

bytelatent/data/iterators/arrow_iterator.py

@@ -1,17 +1,20 @@
 # Copyright (c) Meta Platforms, Inc. and affiliates.
+import os
 import re
 from logging import getLogger
-from pathlib import Path
 from typing import Any, Generator
 
+import fsspec
 import pyarrow as pa
 
 # pyarrow needs the initialization from this import
 import pyarrow.dataset  # pyright: ignore
+import s3fs
 from pydantic import BaseModel, ConfigDict
 
 from bytelatent import ByteLatentError
 from bytelatent.data.data_types import BltExample
+from bytelatent.data.file_util import get_fs
 from bytelatent.data.iterators.abstract_iterator import IteratorState, StatefulIterator
 
 logger = getLogger(__name__)
@@ -27,6 +30,8 @@ class ArrowFileIteratorState(BaseModel, IteratorState):
     dataset_files: list[str] | None
     entropy_model_name: str | None
     arrow_batch_size: int = 100
+    s3_profile: str | None
+    filesystem_type: str | None = None
 
     def build(self) -> "ArrowFileIterator":
         arrow_file = ArrowFileIterator(
@@ -37,14 +42,17 @@ class ArrowFileIteratorState(BaseModel, IteratorState):
             entropy_model_name=self.entropy_model_name,
             arrow_batch_size=self.arrow_batch_size,
             dataset_files=self.dataset_files,
+            s3_profile=self.s3_profile,
+            filesystem_type=self.filesystem_type,
         )
         if self.row_num != 0:
             arrow_file._set_row_num(self.row_num)
         return arrow_file
 
 
-def shard_sort_key(file: str | Path):
-    match = re.search(r".+\.shard_([0-9]+)\.arrow", str(file))
+def shard_sort_key(file: str):
+    assert isinstance(file, str)
+    match = re.search(r".+\.shard_([0-9]+)\.arrow", file)
     shard_number = int(match.group(1))
     return shard_number
 
@@ -60,6 +68,8 @@ class ArrowFileIterator(StatefulIterator):
         entropy_model_name: str | None,
         arrow_batch_size: int,
         dataset_files: list[str] | None = None,
+        s3_profile: str | None = None,
+        filesystem_type: str | None = None,
     ):
         assert 0 <= worker_id < num_workers, (worker_id, num_workers)
         if file_path is None and dataset_files is None:
@@ -75,16 +85,41 @@ class ArrowFileIterator(StatefulIterator):
         self.preprocess_dir = preprocess_dir
         self.entropy_model_name = entropy_model_name
         self.arrow_batch_size = arrow_batch_size
+        self.s3_profile = s3_profile
+        self.filesystem_type = filesystem_type
+        self.fs = None
+        if self.filesystem_type is not None:
+            if self.filesystem_type == "file":
+                self.fs = fsspec.filesystem("file")
+            elif self.filesystem_type == "s3":
+                self.fs = fsspec.filesystem("s3", profile=s3_profile)
+
         if dataset_files is None:
             # Prepare arrow shards
-            jsonl_file = Path(file_path)
-            parts = re.match(r"(.+)\.chunk\.[0-9]+\.jsonl", jsonl_file.name)
+            jsonl_file = file_path
+            parts = re.match(
+                r"(.+)\.chunk\.[0-9]+\.jsonl", os.path.basename(jsonl_file)
+            )
             assert parts is not None
             dataset = parts.group(1)
-            data_dir = Path(preprocess_dir) / dataset / entropy_model_name
-            shard_files = list(data_dir.glob(f"{jsonl_file.name}.shard_*.arrow"))
+            data_dir = os.path.join(preprocess_dir, dataset, entropy_model_name)
+            data_dir_with_glob = os.path.join(
+                data_dir, f"{os.path.basename(jsonl_file)}.shard_*.arrow"
+            )
+            if self.fs is None:
+                self.fs = get_fs(data_dir_with_glob, s3_profile=s3_profile)
+                if isinstance(self.fs, s3fs.S3FileSystem):
+                    self.filesystem_type = "s3"
+                else:
+                    self.filesystem_type = "file"
+            shard_files = self.fs.glob(data_dir_with_glob)
+
             for s in shard_files:
-                if not (data_dir / f"{s.name}.complete").exists():
+                complete_file = os.path.join(
+                    data_dir, f"{os.path.basename(s)}.complete"
+                )
+
+                if not self.fs.exists(complete_file):
                     raise ValueError(f"Missing .complete for input file: {s}")
 
             shard_files = sorted(shard_files, key=shard_sort_key)
@@ -92,10 +127,19 @@ class ArrowFileIterator(StatefulIterator):
                 raise ByteLatentError(
                     f"Zero shard_files found corresponding to: {file_path} using preprocess_dir={preprocess_dir} and entropy_model_name={entropy_model_name}, so the search path is data_dir={data_dir} for matches to {jsonl_file.name}.shard_*.arrow"
                 )
-            self.dataset_files = [str(f) for f in shard_files]
+            self.dataset_files = [f for f in shard_files]
         else:
             self.preprocess_dir = None
             self.dataset_files = dataset_files
+            if dataset_files[0].startswith("s3://"):
+                for f in dataset_files:
+                    assert f.startswith("s3://")
+            if self.fs is None:
+                self.fs = get_fs(dataset_files[0], s3_profile=s3_profile)
+                if isinstance(self.fs, s3fs.S3FileSystem):
+                    self.filesystem_type = "s3"
+                else:
+                    self.filesystem_type = "file"
 
     def get_state(self) -> ArrowFileIteratorState:
         return ArrowFileIteratorState(
@@ -107,13 +151,21 @@ class ArrowFileIterator(StatefulIterator):
             entropy_model_name=self.entropy_model_name,
             arrow_batch_size=self.arrow_batch_size,
             dataset_files=self.dataset_files,
+            s3_profile=self.s3_profile,
+            filesystem_type=self.filesystem_type,
         )
 
     def create_iter(
         self,
     ) -> Generator[BltExample, Any, None]:
         if self.dataset is None:
-            self.dataset = pa.dataset.dataset(self.dataset_files, format="arrow")
+            if isinstance(self.fs, s3fs.core.S3FileSystem):
+                filesystem = self.fs
+            else:
+                filesystem = None
+            self.dataset = pa.dataset.dataset(
+                self.dataset_files, format="arrow", filesystem=filesystem
+            )
             self.batch_iterator = self.dataset.to_batches(
                 batch_size=self.arrow_batch_size
             )
@@ -165,7 +217,13 @@ class ArrowFileIterator(StatefulIterator):
             self.batch_iterator = None
             self.batch_to_consume = None
         else:
-            self.dataset = pa.dataset.dataset(self.dataset_files, format="arrow")
+            if isinstance(self.fs, s3fs.core.S3FileSystem):
+                filesystem = self.fs
+            else:
+                filesystem = None
+            self.dataset = pa.dataset.dataset(
+                self.dataset_files, format="arrow", filesystem=filesystem
+            )
             self.batch_iterator = self.dataset.to_batches(
                 batch_size=self.arrow_batch_size
             )
@@ -198,9 +256,14 @@ TRAIN_DATA_FILE_PATTERN = "*.chunk.*.jsonl"
 
 
 def find_and_sanitize_chunks(
-    dataset_path: str, world_size: int, file_pattern: str = TRAIN_DATA_FILE_PATTERN
+    dataset_path: str,
+    world_size: int,
+    file_pattern: str = TRAIN_DATA_FILE_PATTERN,
+    s3_profile: str | None = None,
 ):
-    dataset_chunks = [str(p) for p in Path(dataset_path).glob(file_pattern)]
+    fs = get_fs(dataset_path, s3_profile=s3_profile)
+    path_with_glob = os.path.join(dataset_path, file_pattern)
+    dataset_chunks = fs.glob(path_with_glob)
     n_chunks = len(dataset_chunks)
 
     if n_chunks > world_size:

bytelatent/logger.py

@@ -91,7 +91,7 @@ def init_logger(
     log_file: str | None = None,
     *,
     name: str | None = None,
-    level: str = "NOTSET",
+    level: str = "INFO",
 ):
     """
     Setup logging.

requirements.txt

@@ -20,3 +20,4 @@ altair
 submitit
 typer
 rich
+fsspec[full]

setup/download_prepare_hf_data.py

@@ -5,6 +5,7 @@ import os
 import subprocess
 import time
 
+import fsspec
 import requests
 from huggingface_hub import snapshot_download
 
@@ -38,11 +39,21 @@ def download_dataset(repo_id, local_dir, allow_patterns):
     print(f"Dataset downloaded to {local_dir}")
 
 
-def parquet_to_jsonl(dataset, work_dir, src_dir, tgt_dir, ntasks=64):
+def parquet_to_jsonl(
+    dataset, work_dir, src_dir, tgt_dir, ntasks=64, s3_profile: str | None = None
+):
     from datatrove.executor import LocalPipelineExecutor
     from datatrove.pipeline.readers import ParquetReader
     from datatrove.pipeline.writers import JsonlWriter
 
+    if tgt_dir.startswith("s3//"):
+        if s3_profile is None:
+            out_spec = tgt_dir
+        else:
+            out_spec = (tgt_dir, fsspec.filesystem("s3", profile=s3_profile))
+    else:
+        out_spec = tgt_dir
+
     pipeline_exec = LocalPipelineExecutor(
         pipeline=[
             ParquetReader(
@@ -52,7 +63,7 @@ def parquet_to_jsonl(dataset, work_dir, src_dir, tgt_dir, ntasks=64):
                 glob_pattern="**/*.parquet",
             ),
             JsonlWriter(
-                tgt_dir,
+                out_spec,
                 output_filename=dataset + ".chunk.${rank}.jsonl",
                 compression=None,
             ),
@@ -77,7 +88,7 @@ def setup_terashuf(work_dir):
     return terashuf_dir
 
 
-def main(dataset, memory, data_dir, seed=42, nchunks=32):
+def main(dataset, memory, data_dir, seed=42, nchunks=32, s3_profile: str | None = None):
     # Configuration
     repo_id = {
         "fineweb_edu": "HuggingFaceFW/fineweb-edu",