microsoft / microsoft/Graphormer
Error with customized dataset
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Description
Hallo everone,
I wanted to train a customized dataset. Following the instructions in https://graphormer.readthedocs.io/en/latest/Datasets.html#id5
I added my code before the create_customized_dataset function to build a dgl dataset class. Then I wrote a shell file to run the training process. But I got ModuleNotFoundError error when I started the training.
Here was the error information
Traceback (most recent call last):
File "/root/anaconda3/envs/graphormer/bin/fairseq-train", line 8, in <module>
sys.exit(cli_main())
File "/root/anaconda3/envs/graphormer/lib/python3.9/site-packages/fairseq_cli/train.py", line 528, in cli_main
distributed_utils.call_main(cfg, main)
File "/root/anaconda3/envs/graphormer/lib/python3.9/site-packages/fairseq/distributed/utils.py", line 369, in call_main
main(cfg, **kwargs)
File "/root/anaconda3/envs/graphormer/lib/python3.9/site-packages/fairseq_cli/train.py", line 85, in main
task = tasks.setup_task(cfg.task)
File "/root/anaconda3/envs/graphormer/lib/python3.9/site-packages/fairseq/tasks/__init__.py", line 46, in setup_task
return task.setup_task(cfg, **kwargs)
File "/workspace/Graphormer/graphormer/tasks/graph_prediction.py", line 179, in setup_task
return cls(cfg)
File "/workspace/Graphormer/graphormer/tasks/graph_prediction.py", line 142, in __init__
self.__import_user_defined_datasets(cfg.user_data_dir)
File "/workspace/Graphormer/graphormer/tasks/graph_prediction.py", line 165, in __import_user_defined_datasets
importlib.import_module(module_name)
File "/root/anaconda3/envs/graphormer/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 984, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'customized_dataset'
Here was the shell file
#!/usr/bin/env bash
CUDA_VISIBLE_DEVICES=0 fairseq-train \
--user-dir ../../graphormer \
--user-data-dir /workspace/Graphormer/examples/customized_dataset \
--num-workers 16 \
--ddp-backend=legacy_ddp \
--dataset-name MonomerTg_dataset \
--task graph_prediction \
--criterion l1_loss \
--arch graphormer_slim \
--num-classes 1 \
--attention-dropout 0.1 --act-dropout 0.1 --dropout 0.0 \
--optimizer adam --adam-betas '(0.9, 0.999)' --adam-eps 1e-8 --clip-norm 5.0 --weight-decay 0.01 \
--lr-scheduler polynomial_decay --power 1 --warmup-updates 60000 --total-num-update 400000 \
--lr 2e-4 --end-learning-rate 1e-9 \
--batch-size 64 \
--fp16 \
--data-buffer-size 20 \
--encoder-layers 12 \
--encoder-embed-dim 80 \
--encoder-ffn-embed-dim 80 \
--encoder-attention-heads 8 \
--max-epoch 10000 \
--save-dir ./ckpts
Anyone knows why it happens and maybe a solution for it?
Thank you very much!
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in graphormer/tasks/graph_prediction.py, especially __import_user_defined_datasets, and compare it with the --user-data-dir value in the provided shell command. Check how the customized_dataset module is expected to be discovered, then rerun the command; done means training proceeds without the reported ModuleNotFoundError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100