Lightning-AI / Lightning-AI/pytorch-lightning
Epoch Skipping During Training After Multiple Jobs Submitted On Same Slurm Node
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Description
### Bug description
This has me stumped, can't finish an epoch without skipping. Submitting multiple jobs on a slurm cluster using one V100 GPU. The GPU nodes have 4 V100s each. Jobs can run on the same node, wondering if that could be the reason for the skipping? Can anyone suggest a way to debug this?
### What version are you seeing the problem on?
v2.0
### How to reproduce the bug
```python
# this is the setup in my trainer.py
checkpoint_callback = ModelCheckpoint( monitor="val_loss",
filename=str(args.model + '-epoch{epoch:02d}-val_loss{val/loss:.2f}'),
auto_insert_metric_name=False,
mode="min",
save_last=True,
save_top_k=3,)
accumulator = GradientAccumulationScheduler(scheduling={1000: 2, 2000:4})
trainer = pl.Trainer(
accelerator="gpu",
devices=[0], # set to -1 to use all avaliable gpus...
# strategy='ddp', # should be same as args.backend..., # stochastic_weight_avg=True, # pass to callbacks if required...
reload_dataloaders_every_n_epochs=1,
# limit_train_batches=0.2,
# limit_train_batches=0.7,
# limit_val_batches=0.5,
default_root_dir=model.hparams.root,
max_epochs=model.hparams.n_epochs*2,
check_val_every_n_epoch=1,
# log_gpu_memory='min_max',
sync_batchnorm=True,
log_every_n_steps=10,
precision="16",
callbacks=[checkpoint_callback, accumulator],
deterministic=True)
# log_every_n_steps=30)
trainer.fit(model)
```
### Error messages and logs
```
# This is what it prints, doesn't go through validation
Epoch 0: 8%|▊ | 41/522 [11:12<2:11:35, 16.41s/it, v_num=4, train_loss_step=8.190]tensor(25, device='cuda:0')
Epoch 1: 0%| | 0/522 [00:00
* CUDA:
- GPU: 1
- available: True
- version: 11.7
* Lightning:
- lightning: 2.0.6
- lightning-cloud: 0.5.37
- lightning-utilities: 0.9.0
- pytorch-lightning: 2.0.5
- torch: 2.0.1
- torchmetrics: 1.0.0
* Packages:
- acvl-utils: 0.2
- aiohttp: 3.8.4
- aiosignal: 1.3.1
- anyio: 3.7.1
- argparse: 1.4.0
- arrow: 1.2.3
- async-timeout: 4.0.2
- attrs: 23.1.0
- backoff: 2.2.1
- batchgenerators: 0.25
- beautifulsoup4: 4.12.2
- blessed: 1.20.0
- certifi: 2023.5.7
- charset-normalizer: 3.1.0
- click: 8.1.4
- cmake: 3.26.3
- connected-components-3d: 3.10.5
- contourpy: 1.0.7
- croniter: 1.4.1
- cycler: 0.11.0
- dateutils: 0.6.12
- deepdiff: 6.3.1
- dicom2nifti: 2.4.8
- dynamic-network-architectures: 0.2
- elasticdeform: 0.5.0
- fastapi: 0.100.0
- filelock: 3.12.0
- fonttools: 4.39.4
- frozenlist: 1.3.3
- fsspec: 2023.6.0
- future: 0.18.3
- graphviz: 0.20.1
- h11: 0.14.0
- h5py: 3.9.0
- hiddenlayer: 0.2
- idna: 3.4
- imagecodecs: 2023.3.16
- imageio: 2.29.0
- inquirer: 3.1.3
- itsdangerous: 2.1.2
- jinja2: 3.1.2
- joblib: 1.2.0
- kiwisolver: 1.4.4
- lazy-loader: 0.2
- lightning: 2.0.6
- lightning-cloud: 0.5.37
- lightning-utilities: 0.9.0
- linecache2: 1.0.0
- lit: 16.0.5
- markdown-it-py: 3.0.0
- markupsafe: 2.1.2
- matplotlib: 3.7.1
- mdurl: 0.1.2
- medpy: 0.4.0
- monai: 1.2.0
- mpmath: 1.3.0
- multidict: 6.0.4
- networkx: 3.1
- nibabel: 5.1.0
- nnunetv2: 2.1
- nptyping: 2.5.0
- numpy: 1.24.3
- nvidia-cublas-cu11: 11.10.3.66
- nvidia-cuda-cupti-cu11: 11.7.101
- nvidia-cuda-nvrtc-cu11: 11.7.99
- nvidia-cuda-runtime-cu11: 11.7.99
- nvidia-cudnn-cu11: 8.5.0.96
- nvidia-cufft-cu11: 10.9.0.58
- nvidia-curand-cu11: 10.2.10.91
- nvidia-cusolver-cu11: 11.4.0.1
- nvidia-cusparse-cu11: 11.7.4.91
- nvidia-nccl-cu11: 2.14.3
- nvidia-nvtx-cu11: 11.7.91
- opencv-python: 4.8.0.74
- ordered-set: 4.1.0
- packaging: 23.1
- pandas: 2.0.1
- pillow: 9.5.0
- pip: 23.1.2
- psutil: 5.9.5
- pydantic: 1.10.11
- pydicom: 2.3.1
- pygments: 2.15.1
- pyjwt: 2.7.0
- pynrrd: 1.0.0
- pyparsing: 3.0.9
- python-dateutil: 2.8.2
- python-editor: 1.0.4
- python-gdcm: 3.0.22
- python-multipart: 0.0.6
- pytorch-lightning: 2.0.5
- pytz: 2023.3
- pywavelets: 1.4.1
- pyyaml: 6.0
- readchar: 4.0.5
- requests: 2.31.0
- rich: 13.4.2
- scikit-image: 0.20.0
- scikit-learn: 1.2.2
- scipy: 1.10.1
- seaborn: 0.12.2
- setuptools: 67.7.2
- simpleitk: 2.2.1
- six: 1.16.0
- sniffio: 1.3.0
- soupsieve: 2.4.1
- starlette: 0.27.0
- starsessions: 1.3.0
- sympy: 1.12
- threadpoolctl: 3.1.0
- tifffile: 2023.4.12
- torch: 2.0.1
- torchmetrics: 1.0.0
- tqdm: 4.65.0
- traceback2: 1.4.0
- traitlets: 5.9.0
- triton: 2.0.0
- typing-extensions: 4.6.0
- tzdata: 2023.3
- unittest2: 1.1.0
- urllib3: 2.0.2
- uvicorn: 0.22.0
- wcwidth: 0.2.6
- websocket-client: 1.6.1
- websockets: 11.0.3
- wheel: 0.40.0
- yacs: 0.1.8
- yarl: 1.9.2
* System:
- OS: Linux
- architecture:
- 64bit
- ELF
- processor: x86_64
- python: 3.11.3
- release: 3.10.0-1160.36.2.el7.x86_64
- version: #1 SMP Wed Jul 21 11:57:15 UTC 2021
```
### More info
_No response_
cc @justusschock @awaelchli
Contributor guide
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
The reproduction is in trainer.py and uses ModelCheckpoint, GradientAccumulationScheduler, and a single GPU under Slurm. Start by reproducing the epoch transition with one job and with multiple jobs on the same node, then inspect the printed batch and epoch values. Done means identifying whether the skipped batches come from the training setup or the framework and documenting or fixing the confirmed cause.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, pytorch
- Domain
- distributed-systems, machine-learning
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100