Comments (6)
I executed all the processes in the README and found no problems.
The possible reason is that you did not clone the repository correctly, causing some files to be damaged.
bash scripts/train.sh 1 12333 (CrossMatch)
[2024-05-16 17:19:25,385][ INFO] {'T': 1.0,
'batch_size': 12,
'conf_thresh': 0.95,
'config': 'configs/acdc.yaml',
'crop_size': 256,
'data_root': './dataset/datasets/ACDC',
'dataset': 'acdc',
'drop_rate': 0.5,
'epochs': 300,
'eta': 0.3,
'labeled_id_path': 'splits/acdc/3/labeled.txt',
'local_rank': 0,
'lr': 0.01,
'nclass': 4,
'ngpus': 1,
'port': 12333,
'save_path': 'exp/acdc/train_cross_match_cross_match/unet/3/eta_0.3',
'unlabeled_id_path': 'splits/acdc/3/unlabeled.txt',
'use_threshold_relax': False}
[2024-05-16 17:19:25,466][ INFO] Total params: 1.8M
[2024-05-16 17:19:26,427][ INFO] ===========> Epoch: 0, LR: 0.01000, Previous best: 0.00, TH: 0.9500
[2024-05-16 17:19:32,535][ INFO] Iters: 0, Total loss: 0.821, Loss x: 1.175, Loss s: 0.693, Loss KD: 0.595, Mask ratio: 0.000
[2024-05-16 17:19:36,077][ INFO] Iters: 12, Total loss: 0.834, Loss x: 1.011, Loss s: 0.752, Loss KD: 0.738, Mask ratio: 0.001
fish: Job 1, 'bash scripts/train.sh 1 12333' has stopped
from crossmatch.
I executed all the processes in the README and found no problems. The possible reason is that you did not clone the repository correctly, causing some files to be damaged.
bash scripts/train.sh 1 12333 (CrossMatch) [2024-05-16 17:19:25,385][ INFO] {'T': 1.0, 'batch_size': 12, 'conf_thresh': 0.95, 'config': 'configs/acdc.yaml', 'crop_size': 256, 'data_root': './dataset/datasets/ACDC', 'dataset': 'acdc', 'drop_rate': 0.5, 'epochs': 300, 'eta': 0.3, 'labeled_id_path': 'splits/acdc/3/labeled.txt', 'local_rank': 0, 'lr': 0.01, 'nclass': 4, 'ngpus': 1, 'port': 12333, 'save_path': 'exp/acdc/train_cross_match_cross_match/unet/3/eta_0.3', 'unlabeled_id_path': 'splits/acdc/3/unlabeled.txt', 'use_threshold_relax': False} [2024-05-16 17:19:25,466][ INFO] Total params: 1.8M [2024-05-16 17:19:26,427][ INFO] ===========> Epoch: 0, LR: 0.01000, Previous best: 0.00, TH: 0.9500 [2024-05-16 17:19:32,535][ INFO] Iters: 0, Total loss: 0.821, Loss x: 1.175, Loss s: 0.693, Loss KD: 0.595, Mask ratio: 0.000 [2024-05-16 17:19:36,077][ INFO] Iters: 12, Total loss: 0.834, Loss x: 1.011, Loss s: 0.752, Loss KD: 0.738, Mask ratio: 0.001 fish: Job 1, 'bash scripts/train.sh 1 12333' has stopped
[2024-05-16 16:12:13,033][ INFO] ===========> Epoch: 62, LR: 0.00812, Previous best: 81.34, TH: 0.9500
[2024-05-16 16:12:17,256][ INFO] Iters: 0, Total loss: 0.068, Loss x: 0.038, Loss s: 0.051, Loss KD: 0.115, Mask ratio: 0.977
[2024-05-16 16:12:18,553][ INFO] Iters: 3, Total loss: 0.048, Loss x: 0.040, Loss s: 0.031, Loss KD: 0.075, Mask ratio: 0.979
[2024-05-16 16:12:19,844][ INFO] Iters: 6, Total loss: 0.055, Loss x: 0.041, Loss s: 0.035, Loss KD: 0.089, Mask ratio: 0.978
Traceback (most recent call last):
File "/home/mnt/lee/Med/CrossMatch/ACDC/train_cross_match.py", line 420, in <module>
main()
File "/home/mnt/lee/Med/CrossMatch/ACDC/train_cross_match.py", line 183, in main
for i, (
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 630, in __next__
data = self._next_data()
^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 1325, in _next_data
return self._process_data(data)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/utils/data/dataloader.py", line 1371, in _process_data
data.reraise()
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/_utils.py", line 694, in reraise
raise exception
OSError: Caught OSError in DataLoader worker process 9.
Original Traceback (most recent call last):
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/utils/data/_utils/worker.py", line 308, in _worker_loop
data = fetcher.fetch(index)
^^^^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/utils/data/_utils/fetch.py", line 51, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/utils/data/_utils/fetch.py", line 51, in <listcomp>
data = [self.dataset[idx] for idx in possibly_batched_index]
~~~~~~~~~~~~^^^^^
File "/home/mnt/lee/Med/CrossMatch/ACDC/dataset/acdc.py", line 37, in __getitem__
sample = h5py.File(os.path.join(self.root, id), 'r')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/h5py/_hl/files.py", line 562, in __init__
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/h5py/_hl/files.py", line 235, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 102, in h5py.h5f.open
OSError: [Errno 9] Unable to synchronously open file (unable to lock file, errno = 9, error message = 'Bad file descriptor')
[2024-05-16 16:12:22,257] torch.distributed.elastic.multiprocessing.api: [WARNING] Sending process 30 closing signal SIGTERM
[2024-05-16 16:12:22,258] torch.distributed.elastic.multiprocessing.api: [WARNING] Sending process 32 closing signal SIGTERM
[2024-05-16 16:12:22,258] torch.distributed.elastic.multiprocessing.api: [WARNING] Sending process 33 closing signal SIGTERM
[2024-05-16 16:12:22,377] torch.distributed.elastic.multiprocessing.api: [ERROR] failed (exitcode: 1) local_rank: 1 (pid: 31) of binary: /home/mnt/lee/miniconda3/envs/CrossMatch/bin/python
Traceback (most recent call last):
File "/home/mnt/lee/miniconda3/envs/CrossMatch/bin/torchrun", line 8, in <module>
sys.exit(main())
^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/distributed/elastic/multiprocessing/errors/__init__.py", line 346, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/distributed/run.py", line 806, in main
run(args)
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/distributed/run.py", line 797, in run
elastic_launch(
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/distributed/launcher/api.py", line 134, in __call__
return launch_agent(self._config, self._entrypoint, list(args))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mnt/lee/miniconda3/envs/CrossMatch/lib/python3.11/site-packages/torch/distributed/launcher/api.py", line 264, in launch_agent
raise ChildFailedError(
torch.distributed.elastic.multiprocessing.errors.ChildFailedError:
============================================================
train_cross_match.py FAILED
------------------------------------------------------------
Failures:
<NO_OTHER_FAILURES>
------------------------------------------------------------
Root Cause (first observed failure):
[0]:
time : 2024-05-16_16:12:22
host : pt-r5qx9yk4-worker-0.pt-r5qx9yk4.ns-sensetime2023-cb5b8530.svc.cluster.local
rank : 1 (local_rank: 1)
exitcode : 1 (pid: 31)
error_file: <N/A>
traceback : To enable traceback see: https://pytorch.org/docs/stable/elastic/errors.html
============================================================
from crossmatch.
Please try running the code below:
import h5py
import glob
import tqdm
ACDC_DIR = '/home/mnt/lee/Med/CrossMatch/ACDC/dataset/datasets/ACDC'
print("Checking the dataset... type: Slices")
for file_name in tqdm.tqdm(glob.glob(f'{ACDC_DIR}/data/slices/*.h5')):
sample = h5py.File(file_name, 'r')
img = sample['image'][:]
mask = sample['label'][:]
print("Finished!")
print("Checking the dataset... type: 3D Images")
for file_name in tqdm.tqdm(glob.glob(f'{ACDC_DIR}/data/*.h5')):
sample = h5py.File(file_name, 'r')
img = sample['image'][:]
mask = sample['label'][:]
print("Finished!")
to check if your dataset can be read correctly.
from crossmatch.
Please try running the code below:
import h5py import glob import tqdm ACDC_DIR = '/home/mnt/lee/Med/CrossMatch/ACDC/dataset/datasets/ACDC' print("Checking the dataset... type: Slices") for file_name in tqdm.tqdm(glob.glob(f'{ACDC_DIR}/data/slices/*.h5')): sample = h5py.File(file_name, 'r') img = sample['image'][:] mask = sample['label'][:] print("Finished!") print("Checking the dataset... type: 3D Images") for file_name in tqdm.tqdm(glob.glob(f'{ACDC_DIR}/data/*.h5')): sample = h5py.File(file_name, 'r') img = sample['image'][:] mask = sample['label'][:] print("Finished!")
from crossmatch.
from crossmatch.
Thanks for you to provide the solution
from crossmatch.
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from crossmatch.