Update for transformers 5.0 (#1436)

Currently blocked by
huggingface/transformers#43510

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

* **New Features**
  * Added checkpoint loading validation test.
* Enhanced distributed testing infrastructure with improved port
configuration.

* **Improvements**
* Removed upper-bound version constraints on the transformer library for
broader compatibility.
* Improved weight initialization and checkpoint state management for
TransformerEngine-optimized models.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Peter St. John <pstjohn@nvidia.com>

Author: pstjohn

.devcontainer/recipes/requirements.txt

@@ -1,4 +1,4 @@
-accelerate
+accelerate @ git+https://github.com/huggingface/accelerate.git  # Until huggingface/accelerate#3852 is released.
 datasets
 deepspeed
 hydra-core
@@ -12,7 +12,7 @@ torchdata
 torchmetrics
 tqdm
 transformer_engine
-transformers<5.0
+transformers
 typer
 wandb
 zstandard

bionemo-recipes/models/amplify/pyproject.toml

@@ -18,7 +18,7 @@ dependencies = [
     "pytest",
     "torch==2.6.0a0+ecf3bae40a.nv25.01",
     "transformer_engine[pytorch]",
-    "transformers<5.0",
+    "transformers<5.0",                  # TODO(BIO-143): update AMPLIFY to support Transformers v5
     "xformers",
 ]
 

bionemo-recipes/models/esm2/pyproject.toml

@@ -19,7 +19,7 @@ dependencies = [
     "torch",
     "torchao!=0.14.0",
     "transformer_engine[pytorch]",
-    "transformers<5.0",
+    "transformers",
 ]
 
 

bionemo-recipes/models/esm2/src/esm/convert.py

@@ -131,7 +131,7 @@ def convert_esm_te_to_hf(model_te: nn.Module, **config_kwargs) -> nn.Module:
         ],
     )
 
-    output_model.tie_weights()
+    output_model.post_init()
 
     # Note: contact_head parameters are not preserved in TE models
     # They are lost during HF -> TE conversion and cannot be recovered

bionemo-recipes/models/esm2/src/esm/modeling_esm_te.py

@@ -22,7 +22,7 @@
 Adapted from `modeling_esm.py` in huggingface/transformers.
 """
 
-from typing import Literal, Optional, Unpack
+from typing import ClassVar, Literal, Optional, Unpack
 
 # TODO: put import guard around transformer_engine here, with an informative error message around
 # installation and the nvidia docker container.
@@ -256,10 +256,34 @@ def init_empty_weights(self):
         # Meta-device init seems to break weight tying, so we re-tie the weights here.
         self.tie_weights()
 
-    @classmethod
-    def get_init_context(cls, is_quantized: bool, _is_ds_init_called: bool):
-        """Override the default get_init_context method to allow for fp8 model initialization."""
-        return []
+    def _init_weights(self, module):
+        """Initialize module weights.
+
+        We only use this method for standard pytorch modules, TE modules handle their own weight initialization through
+        `init_method` parameters and the `reset_parameters` method.
+        """
+        if module.__module__.startswith("transformer_engine.pytorch"):
+            # Notably, we need to avoid calling the parent method for TE modules, since the default _init_weights will
+            # assume any class with `LayerNorm` in the name should have weights initialized to 1.0; breaking
+            # `LayerNormLinear` and `LayerNormMLP` modules that use `weight` for the linear layer and
+            # `layer_norm_weight` for the layer norm. Instead, we call `reset_parameters` if the module has it and the
+            # weights are not in fp8. We still need to figure out why this raises an error if we're using
+            # `quantized_model_init`.
+            if hasattr(module, "reset_parameters") and not getattr(module, "primary_weights_in_fp8", False):
+                module.reset_parameters()
+            return
+
+        super()._init_weights(module)
+
+    def state_dict(self, *args, **kwargs):
+        """Override state_dict to filter out TransformerEngine's _extra_state keys.
+
+        TransformerEngine layers add _extra_state attributes that are not compatible with HuggingFace v5 model loading.
+        These are filtered out to ensure checkpoints can be loaded with from_pretrained().
+        """
+        state_dict = super().state_dict(*args, **kwargs)
+        # Filter out _extra_state keys which are TransformerEngine-specific and not loadable
+        return {k: v for k, v in state_dict.items() if not k.endswith("_extra_state")}
 
 
 class NVEsmModel(NVEsmPreTrainedModel):
@@ -367,7 +391,7 @@ def forward(
 class NVEsmForMaskedLM(NVEsmPreTrainedModel):
     """NVEsmForMaskedLM is a TransformerEngine-optimized ESM model for masked language modeling."""
 
-    _tied_weights_keys = ("lm_head.decoder.weight",)
+    _tied_weights_keys: ClassVar[dict[str, str]] = {"lm_head.decoder.weight": "esm.embeddings.word_embeddings.weight"}
 
     def __init__(self, config: NVEsmConfig):
         """Initialize a NVEsmForMaskedLM.
@@ -386,7 +410,6 @@ def __init__(self, config: NVEsmConfig):
         self.esm = NVEsmModel(config, add_pooling_layer=False)
         self.lm_head = NVEsmLMHead(config)
 
-        self.init_weights()
         self.post_init()
 
     def get_output_embeddings(self):
@@ -614,7 +637,6 @@ def __init__(self, config):
             init_method=lambda x: torch.nn.init.normal_(x, mean=0.0, std=config.initializer_range),
         )
 
-        self.init_weights()
         self.post_init()
 
     def forward(

bionemo-recipes/models/esm2/tests/conftest.py

@@ -15,6 +15,7 @@
 
 import importlib
 import os
+import socket
 
 import pytest
 import transformer_engine.pytorch
@@ -32,6 +33,16 @@
     os.environ["TRITON_LIBCUDA_PATH"] = "/usr/local/cuda/lib64"
 
 
+@pytest.fixture
+def unused_tcp_port():
+    """Find and return an unused TCP port for torchrun rendezvous."""
+    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+        s.bind(("", 0))
+        s.listen(1)
+        port = s.getsockname()[1]
+    return port
+
+
 @pytest.fixture(autouse=True)
 def use_te_debug(monkeypatch):
     monkeypatch.setenv("NVTE_DEBUG", "1")

bionemo-recipes/models/esm2/tests/test_convert.py

@@ -38,6 +38,12 @@ def test_convert_te_to_hf_roundtrip():
             torch.testing.assert_close(original_state_dict[key], converted_state_dict[key], atol=1e-5, rtol=1e-5)
 
 
+def test_load_from_converted_checkpoint(te_model_checkpoint):
+    from esm.modeling_esm_te import NVEsmForMaskedLM
+
+    NVEsmForMaskedLM.from_pretrained(te_model_checkpoint)
+
+
 def test_qkv_unpacking():
     """Test that QKV unpacking works correctly."""
     from esm.convert import convert_esm_hf_to_te, convert_esm_te_to_hf

bionemo-recipes/models/esm2/tests/test_distributed_fp8.py

@@ -38,10 +38,12 @@ def requires_fp8(func):
     "strategy", ["ddp", "fsdp2", pytest.param("mfsdp", marks=pytest.mark.xfail(reason="BIONEMO-2999"))]
 )
 @requires_fp8
-def test_single_process_attaches_correct_fp8_recipe(strategy):
+def test_single_process_attaches_correct_fp8_recipe(strategy, unused_tcp_port):
     cmd = [
         "torchrun",
         "--nproc_per_node=1",
+        "--rdzv-backend=c10d",
+        f"--rdzv-endpoint=localhost:{unused_tcp_port}",
         os.path.relpath(__file__),
         "--strategy",
         strategy,
@@ -66,10 +68,12 @@ def test_single_process_attaches_correct_fp8_recipe(strategy):
 )
 @requires_fp8
 @requires_multi_gpu
-def test_multi_process_fp8_recipes_are_synced(strategy):
+def test_multi_process_fp8_recipes_are_synced(strategy, unused_tcp_port):
     cmd = [
         "torchrun",
         "--nproc_per_node=2",
+        "--rdzv-backend=c10d",
+        f"--rdzv-endpoint=localhost:{unused_tcp_port}",
         os.path.relpath(__file__),
         "--strategy",
         strategy,
@@ -207,11 +211,14 @@ def is_main_process(self) -> bool:
 
         outputs.loss.backward()
 
-    fp8_extra_states = {key: val for key, val in model.state_dict().items() if key.endswith("_extra_state")}
-
-    # For some reason, this one doesn't get an fp8 recipe? It's the only te.LayerNorm.
-    key = filter(lambda x: x.endswith("encoder.emb_layer_norm_after._extra_state"), fp8_extra_states.keys())
-    fp8_extra_states.pop(next(key))
+    # Access FP8 extra states directly from modules instead of state_dict()
+    # since state_dict() now filters them out for HuggingFace compatibility
+    fp8_extra_states = {}
+    for name, module in model.named_modules():
+        if hasattr(module, "_extra_state") and callable(module._extra_state):
+            extra_state = module._extra_state()
+            if extra_state is not None and len(extra_state) > 0:
+                fp8_extra_states[f"{name}._extra_state"] = extra_state
 
     # lm_head.dense and lm_head.decoder are BF16, not FP8, so exclude them from FP8 checks
     fp8_extra_states = {key: val for key, val in fp8_extra_states.items() if "lm_head." not in key}

bionemo-recipes/models/esm2/tests/test_distributed_strategies.py

@@ -41,10 +41,12 @@
     ],
 )
 @pytest.mark.parametrize("backend", ["te", "eager"])
-def test_ddp_vs_fsdp_single_gpu(strategy, backend):
+def test_ddp_vs_fsdp_single_gpu(strategy, backend, unused_tcp_port):
     cmd = [
         "torchrun",
         "--nproc_per_node=1",
+        "--rdzv-backend=c10d",
+        f"--rdzv-endpoint=localhost:{unused_tcp_port}",
         os.path.relpath(__file__),
         "--strategy",
         strategy,
@@ -69,10 +71,12 @@ def test_ddp_vs_fsdp_single_gpu(strategy, backend):
 @requires_multi_gpu
 @pytest.mark.parametrize("strategy", ["fsdp2", pytest.param("mfsdp", marks=pytest.mark.xfail(reason="BIONEMO-2726"))])
 @pytest.mark.parametrize("backend", ["te", "eager"])
-def test_ddp_vs_fsdp_multi_gpu(strategy, backend):
+def test_ddp_vs_fsdp_multi_gpu(strategy, backend, unused_tcp_port):
     cmd = [
         "torchrun",
         "--nproc_per_node=2",
+        "--rdzv-backend=c10d",
+        f"--rdzv-endpoint=localhost:{unused_tcp_port}",
         os.path.relpath(__file__),
         "--strategy",
         strategy,
@@ -160,20 +164,28 @@ def is_main_process(self) -> bool:
             return self.rank == 0
 
     def run_forward_backward(use_te: bool, strategy: Strategy, input_data: dict, dist_config: DistributedConfig):
+        # Set seed for reproducible model initialization across strategies
+        torch.manual_seed(42)
+        torch.cuda.manual_seed_all(42)
+
         device_mesh = init_device_mesh(
             "cuda",
-            mesh_shape=(dist_config.world_size,),
-            mesh_dim_names=("dp",),
+            mesh_shape=(dist_config.world_size, 1),
+            mesh_dim_names=("dp", "tp"),  # mfsdp requires us to give a tp mesh dimension.
         )
 
         device = f"cuda:{dist_config.local_rank}"
 
         if use_te:
-            model = AutoModelForMaskedLM.from_pretrained(
-                "nvidia/esm2_t6_8M_UR50D",
+            # Import local model classes to avoid using outdated code from HF Hub
+            from esm.modeling_esm_te import NVEsmConfig, NVEsmForMaskedLM
+
+            config = NVEsmConfig.from_pretrained(
+                "facebook/esm2_t6_8M_UR50D",
                 dtype=torch.bfloat16,
-                trust_remote_code=True,
+                revision="c731040f",
             )
+            model = NVEsmForMaskedLM(config)
             transformer_layers = model.esm.encoder.layers
         else:
             model = AutoModelForMaskedLM.from_pretrained(

bionemo-recipes/models/esm2/tests/test_meta_device_init.py

@@ -44,10 +44,6 @@
 )
 
 
-def msg(x):
-    return f"Mismatch in module {name}: {x}"
-
-
 def verify_model_parameters_initialized_correctly(
     model: NVEsmForMaskedLM, atol=1e-3, rtol=1e-4, should_be_fp8: bool = False
 ):
@@ -57,6 +53,10 @@ def verify_model_parameters_initialized_correctly(
         assert str(parameter.device).startswith("cuda"), f"Parameter {name} is not on the cuda device"
 
     for name, module in model.named_modules():
+
+        def msg(x):
+            return f"Mismatch in module {name}: {x}"
+
         if isinstance(module, torch.nn.Embedding):
             torch.testing.assert_close(module.weight.mean().item(), 0.0, atol=atol, rtol=rtol, msg=msg)
             torch.testing.assert_close(
@@ -118,8 +118,12 @@ def verify_model_parameters_initialized_correctly(
             torch.testing.assert_close(module.inv_freq, expected_inv_freq, msg=msg)
 
 
-def verify_pretrained_model_sanity(model: NVEsmForTokenClassification, atol=1e-3, rtol=1e-4):
+def verify_pretrained_model_sanity(model: NVEsmForTokenClassification, atol=1e-2, rtol=1e-3):
     for name, p in model.named_parameters():
+
+        def msg(x):
+            return f"Mismatch in parameter {name}: {x}"
+
         assert p.numel() > 0, f"{name} is empty"
         assert torch.isfinite(p).all(), f"{name} has NaN/Inf"
 
@@ -187,14 +191,12 @@ def test_meta_fp8_init(fp8_recipe):
 
 
 def test_model_for_token_classification_init(te_model_checkpoint):
-    config = NVEsmConfig.from_pretrained(te_model_checkpoint, trust_remote_code=True)
-
     set_seed(42)
-    model = NVEsmForTokenClassification.from_pretrained(
-        te_model_checkpoint, config=config, dtype=torch.bfloat16, trust_remote_code=True
-    )
-    model.to("cuda")
 
+    config = NVEsmConfig.from_pretrained(te_model_checkpoint)
+    model = NVEsmForTokenClassification.from_pretrained(te_model_checkpoint, config=config, dtype=torch.bfloat16)
+    # model.classifier.reset_parameters()
+    model.to("cuda")
     verify_pretrained_model_sanity(model)