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MAGICS-LAB / DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
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"indexSelectLargeIndex: block: [313,0,0], thread: [32,0,0] Assertion `srcIndex < srcSelectDimSize` failed." after evaluation. #61

Open Time-Rune opened 9 months ago

Time-Rune commented 9 months ago

When I try "sh scripts/run_dnabert2.sh /home/DNABERT_2"

I get the following error message:

(base) root@f442fb5fbe89:/home/DNABERT_2/finetune# sh scripts/run_dnabert2.sh /home/DNABERT_2
The provided data_path is /home/DNABERT_2
Using the `WANDB_DISABLED` environment variable is deprecated and will be removed in v5. Use the --report_to flag to control the integrations used for logging result (for instance --report_to none).
WARNING:root:Perform single sequence classification...
WARNING:root:Perform single sequence classification...
WARNING:root:Perform single sequence classification...
/root/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/1d020b803b871a976f5f3d5565f0eac8f2c7bb81/bert_layers.py:125: UserWarning: Unable to import Triton; defaulting MosaicBERT attention implementation to pytorch (this will reduce throughput when using this model).
  warnings.warn(
Some weights of the model checkpoint at zhihan1996/DNABERT-2-117M were not used when initializing BertForSequenceClassification: ['cls.predictions.transform.dense.bias', 'cls.predictions.transform.dense.weight', 'cls.predictions.decoder.weight', 'cls.predictions.transform.LayerNorm.bias', 'cls.predictions.decoder.bias', 'cls.predictions.transform.LayerNorm.weight']
- This IS expected if you are initializing BertForSequenceClassification from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPreTraining model).
- This IS NOT expected if you are initializing BertForSequenceClassification from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).
Some weights of BertForSequenceClassification were not initialized from the model checkpoint at zhihan1996/DNABERT-2-117M and are newly initialized: ['classifier.bias', 'bert.pooler.dense.bias', 'classifier.weight', 'bert.pooler.dense.weight']
You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.
Using cuda_amp half precision backend
***** Running training *****
  Num examples = 11,971
  Num Epochs = 3
  Instantaneous batch size per device = 8
  Total train batch size (w. parallel, distributed & accumulation) = 32
  Gradient Accumulation steps = 1
  Total optimization steps = 1,125
  Number of trainable parameters = 117,070,082
  0%|                                                                                                                   | 0/1125 [00:00<?, ?it/s]/root/miniconda3/lib/python3.9/site-packages/torch/nn/parallel/_functions.py:68: UserWarning: Was asked to gather along dimension 0, but all input tensors were scalars; will instead unsqueeze and return a vector.
  warnings.warn('Was asked to gather along dimension 0, but all '
  3%|██▊                                                                                                       | 30/1125 [00:31<15:53,  1.15it/s]***** Running Evaluation *****
  Num examples = 1497
  Batch size = 64
{'eval_loss': 0.16505089402198792, 'eval_accuracy': 0.5584502338009352, 'eval_f1': 0.5569191296151599, 'eval_matthews_correlation': 0.12047851210237737, 'eval_precision': 0.5607909809982725, 'eval_recall': 0.5596925384326958, 'eval_runtime': 10.8475, 'eval_samples_per_second': 138.004, 'eval_steps_per_second': 2.212, 'epoch': 0.08}
  3%|██▊                                                                                                       | 30/1125 [00:42<15:53,  1.15it/sSaving model checkpoint to output/dnabert2/checkpoint-30                                                                                          
Configuration saved in output/dnabert2/checkpoint-30/config.json
Model weights saved in output/dnabert2/checkpoint-30/pytorch_model.bin
tokenizer config file saved in output/dnabert2/checkpoint-30/tokenizer_config.json
Special tokens file saved in output/dnabert2/checkpoint-30/special_tokens_map.json
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [32,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [33,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [34,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [35,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [36,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [37,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [38,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [39,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [40,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [41,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [42,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [43,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [44,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [45,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [46,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [47,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [48,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [49,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [50,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [51,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [52,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [53,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [54,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [55,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [56,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [57,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [58,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [59,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [60,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [61,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [62,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
../aten/src/ATen/native/cuda/Indexing.cu:1146: indexSelectLargeIndex: block: [313,0,0], thread: [63,0,0] Assertion `srcIndex < srcSelectDimSize` failed.
Traceback (most recent call last):
  File "/home/DNABERT_2/finetune/train.py", line 311, in <module>
    train()
  File "/home/DNABERT_2/finetune/train.py", line 291, in train
    trainer.train()
  File "/root/miniconda3/lib/python3.9/site-packages/transformers/trainer.py", line 1664, in train
    return inner_training_loop(
  File "/root/miniconda3/lib/python3.9/site-packages/transformers/trainer.py", line 1940, in _inner_training_loop
    tr_loss_step = self.training_step(model, inputs)
  File "/root/miniconda3/lib/python3.9/site-packages/transformers/trainer.py", line 2735, in training_step
    loss = self.compute_loss(model, inputs)
  File "/root/miniconda3/lib/python3.9/site-packages/transformers/trainer.py", line 2767, in compute_loss
    outputs = model(**inputs)
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/parallel/data_parallel.py", line 171, in forward
    outputs = self.parallel_apply(replicas, inputs, kwargs)
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/parallel/data_parallel.py", line 181, in parallel_apply
    return parallel_apply(replicas, inputs, kwargs, self.device_ids[:len(replicas)])
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/parallel/parallel_apply.py", line 89, in parallel_apply
    output.reraise()
  File "/root/miniconda3/lib/python3.9/site-packages/torch/_utils.py", line 644, in reraise
    raise exception
RuntimeError: Caught RuntimeError in replica 3 on device 3.
Original Traceback (most recent call last):
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/parallel/parallel_apply.py", line 64, in _worker
    output = module(*input, **kwargs)
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/root/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/1d020b803b871a976f5f3d5565f0eac8f2c7bb81/bert_layers.py", line 862, in forward
    outputs = self.bert(
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/root/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/1d020b803b871a976f5f3d5565f0eac8f2c7bb81/bert_layers.py", line 608, in forward
    encoder_outputs = self.encoder(
  File "/root/miniconda3/lib/python3.9/site-packages/torch/nn/modules/module.py", line 1501, in _call_impl
    return forward_call(*args, **kwargs)
  File "/root/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/1d020b803b871a976f5f3d5565f0eac8f2c7bb81/bert_layers.py", line 426, in forward
    hidden_states, indices, cu_seqlens, _ = unpad_input(
  File "/root/.cache/huggingface/modules/transformers_modules/zhihan1996/DNABERT-2-117M/1d020b803b871a976f5f3d5565f0eac8f2c7bb81/bert_padding.py", line 104, in unpad_input
    indices = torch.nonzero(attention_mask.flatten(), as_tuple=False).flatten()
RuntimeError: CUDA error: device-side assert triggered
CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.
Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.

The model trained correctly on both the training and test sets, but as it continued training, errors occurred