Example training set fails with CUDA out of memory on CUDA 12.1 and PyTorch 2.1

[RJ3]

Trying to run the example training from here: https://openfold.readthedocs.io/en/latest/Training_OpenFold.html

Command:

python3 train_openfold.py $DATA_DIR/pdb_data/mmcif_files \
$DATA_DIR/alignment_data/ $DATA_DIR/pdb_data/mmcif_files $OUTPUT_DIR 2021-10-10 \  
--template_release_dates_cache_path ../../pdb_data/data_caches/mmcif_cache.json \
--train_chain_data_cache_path ../../pdb_data/data_caches/chain_data_cache.json \
--seed 1 --num_nodes 1  --config_preset initial_training --gpus 4 --precision bf16-mixed 

Epoch 0:   0%|                                                                                                                                                        | 0/20 [00:00<?, ?it/s]Traceback (most recent call last):
  File "/data/AF_Training/Public_GitHub/openfold/train_openfold.py", line 703, in <module>
    main(args)
  File "/data/AF_Training/Public_GitHub/openfold/train_openfold.py", line 452, in main
    trainer.fit(
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 538, in fit
    call._call_and_handle_interrupt(
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 46, in _call_and_handle_interrupt
    return trainer.strategy.launcher.launch(trainer_fn, *args, trainer=trainer, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/strategies/launchers/subprocess_script.py", line 105, in launch
    return function(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 574, in _fit_impl
    self._run(model, ckpt_path=ckpt_path)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 981, in _run
    results = self._run_stage()
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/trainer/trainer.py", line 1025, in _run_stage
    self.fit_loop.run()
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/fit_loop.py", line 205, in run
    self.advance()
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/fit_loop.py", line 363, in advance
    self.epoch_loop.run(self._data_fetcher)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/training_epoch_loop.py", line 140, in run
    self.advance(data_fetcher)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/training_epoch_loop.py", line 250, in advance
    batch_output = self.automatic_optimization.run(trainer.optimizers[0], batch_idx, kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/automatic.py", line 190, in run
    self._optimizer_step(batch_idx, closure)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/automatic.py", line 268, in _optimizer_step
    call._call_lightning_module_hook(
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 167, in _call_lightning_module_hook
    output = fn(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/core/module.py", line 1306, in optimizer_step
    optimizer.step(closure=optimizer_closure)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/core/optimizer.py", line 153, in step
    step_output = self._strategy.optimizer_step(self._optimizer, closure, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/strategies/ddp.py", line 270, in optimizer_step
    optimizer_output = super().optimizer_step(optimizer, closure, model, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 238, in optimizer_step
    return self.precision_plugin.optimizer_step(optimizer, model=model, closure=closure, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/plugins/precision/amp.py", line 75, in optimizer_step
    return super().optimizer_step(optimizer, model=model, closure=closure, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/plugins/precision/precision.py", line 122, in optimizer_step
    return optimizer.step(closure=closure, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/optim/lr_scheduler.py", line 68, in wrapper
    return wrapped(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/optim/optimizer.py", line 373, in wrapper
    out = func(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/optim/optimizer.py", line 76, in _use_grad
    ret = func(self, *args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/optim/adam.py", line 143, in step
    loss = closure()
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/plugins/precision/precision.py", line 108, in _wrap_closure
    closure_result = closure()
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/automatic.py", line 144, in __call__
    self._result = self.closure(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
    return func(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/automatic.py", line 129, in closure
    step_output = self._step_fn()
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/loops/optimization/automatic.py", line 317, in _training_step
    training_step_output = call._call_strategy_hook(trainer, "training_step", *kwargs.values())
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/trainer/call.py", line 319, in _call_strategy_hook
    output = fn(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 389, in training_step
    return self._forward_redirection(self.model, self.lightning_module, "training_step", *args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 640, in __call__
    wrapper_output = wrapper_module(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/parallel/distributed.py", line 1519, in forward
    else self._run_ddp_forward(*inputs, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/parallel/distributed.py", line 1355, in _run_ddp_forward
    return self.module(*inputs, **kwargs)  # type: ignore[index]
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/pytorch_lightning/strategies/strategy.py", line 633, in wrapped_forward
    out = method(*_args, **_kwargs)
  File "/data/AF_Training/Public_GitHub/openfold/train_openfold.py", line 104, in training_step
    outputs = self(batch)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "/data/AF_Training/Public_GitHub/openfold/train_openfold.py", line 63, in forward
    return self.model(batch)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "/data/AF_Training/Public_GitHub/openfold/openfold/model/model.py", line 568, in forward
    outputs, m_1_prev, z_prev, x_prev, early_stop = self.iteration(
  File "/data/AF_Training/Public_GitHub/openfold/openfold/model/model.py", line 393, in iteration
    z = self.extra_msa_stack(
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "/data/AF_Training/Public_GitHub/openfold/openfold/model/evoformer.py", line 1217, in forward
    m, z = b(m, z)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "/data/AF_Training/Public_GitHub/openfold/openfold/model/evoformer.py", line 642, in forward
    self.msa_att_row(
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "/data/AF_Training/Public_GitHub/openfold/openfold/model/msa.py", line 281, in forward
    m = self.mha(
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
    return forward_call(*args, **kwargs)
  File "/data/AF_Training/Public_GitHub/openfold/openfold/model/primitives.py", line 523, in forward
    o = attention_core(q, k, v, *((biases + [None] * 2)[:2]))
  File "micromamba/envs/openfold-pl-2/lib/python3.10/site-packages/torch/autograd/function.py", line 539, in apply
    return super().apply(*args, **kwargs)  # type: ignore[misc]
  File "/data/AF_Training/Public_GitHub/openfold/openfold/utils/kernel/attention_core.py", line 38, in forward
    attention_logits = torch.matmul(
torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 128.00 GiB. GPU 3 has a total capacty of 79.22 GiB of which 24.22 GiB is free. Including non-PyTorch memory, this process has 54.99 GiB memory in use. Of the allocated memory 40.00 GiB is allocated by PyTorch, and 13.91 GiB is reserved by PyTorch but unallocated. If reserved but unallocated memory is large try setting max_split_size_mb to avoid fragmentation.  See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF
[rank: 3] Child process with PID 11479 terminated with code 1. Forcefully terminating all other processes to avoid zombies 🧟
Killed

Setup: 4x H100 Torch 2.1.2 CUDA Toolkit 12.1 CUDA user-mode driver 12.5 (version visible top-right of nvidia-smi)