nablaDFT
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Published
20 hours ago •
AIRI-Institute
AIRI-Institute
Error on import
The import of NablaDFT:
from nablaDFT.dataset import NablaDFT
raises an error:
/home/kostanew/anaconda3/lib/python3.9/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension: libtorch_cuda_cu.so: cannot open shared object file: No such file or directory warn(f"Failed to load image Python extension: {e}")
OSError Traceback (most recent call last)
Input In [4], in <cell line: 1>()
----> 1 from nablaDFT.dataset import NablaDFT
File ~/anaconda3/lib/python3.9/site-packages/nablaDFT/__init__.py:1, in <module>
----> 1 from . import dataset
2 from . import schnet
3 from . import painn
File ~/anaconda3/lib/python3.9/site-packages/nablaDFT/dataset/__init__.py:1, in <module>
----> 1 from .nablaDFT_dataset import *
2 from .hamiltonian_database import HamiltonianDatabase
File ~/anaconda3/lib/python3.9/site-packages/nablaDFT/dataset/nablaDFT_dataset.py:11, in <module>
9 from ase.db import connect
10 from torch.utils.data import Subset
---> 11 from torch_geometric.data.lightning import LightningDataset
12 from torch_geometric.data import InMemoryDataset, Data
13 from schnetpack.data import AtomsDataFormat, AtomsDataModule, load_dataset
File ~/anaconda3/lib/python3.9/site-packages/torch_geometric/data/lightning/__init__.py:1, in <module>
----> 1 from .datamodule import LightningDataset, LightningNodeData, LightningLinkData
3 __all__ = classes = [
4 'LightningDataset',
5 'LightningNodeData',
6 'LightningLinkData',
7 ]
File ~/anaconda3/lib/python3.9/site-packages/torch_geometric/data/lightning/datamodule.py:20, in <module>
17 from torch_geometric.typing import InputEdges, InputNodes, OptTensor
19 try:
---> 20 from pytorch_lightning import LightningDataModule as PLLightningDataModule
21 no_pytorch_lightning = False
22 except (ImportError, ModuleNotFoundError):
File ~/anaconda3/lib/python3.9/site-packages/pytorch_lightning/__init__.py:27, in <module>
25 from lightning_fabric.utilities.seed import seed_everything # noqa: E402
26 from lightning_fabric.utilities.warnings import disable_possible_user_warnings # noqa: E402
---> 27 from pytorch_lightning.callbacks import Callback # noqa: E402
28 from pytorch_lightning.core import LightningDataModule, LightningModule # noqa: E402
29 from pytorch_lightning.trainer import Trainer # noqa: E402
File ~/anaconda3/lib/python3.9/site-packages/pytorch_lightning/callbacks/__init__.py:14, in <module>
1 # Copyright The Lightning AI team.
2 #
3 # Licensed under the Apache License, Version 2.0 (the "License");
(...)
12 # See the License for the specific language governing permissions and
13 # limitations under the License.
---> 14 from pytorch_lightning.callbacks.batch_size_finder import BatchSizeFinder
15 from pytorch_lightning.callbacks.callback import Callback
16 from pytorch_lightning.callbacks.checkpoint import Checkpoint
File ~/anaconda3/lib/python3.9/site-packages/pytorch_lightning/callbacks/batch_size_finder.py:24, in <module>
21 from typing import Optional
23 import pytorch_lightning as pl
---> 24 from pytorch_lightning.callbacks.callback import Callback
25 from pytorch_lightning.tuner.batch_size_scaling import _scale_batch_size
26 from pytorch_lightning.utilities.exceptions import MisconfigurationException, _TunerExitException
File ~/anaconda3/lib/python3.9/site-packages/pytorch_lightning/callbacks/callback.py:22, in <module>
19 from torch.optim import Optimizer
21 import pytorch_lightning as pl
---> 22 from pytorch_lightning.utilities.types import STEP_OUTPUT
25 class Callback:
26 r"""Abstract base class used to build new callbacks.
27
28 Subclass this class and override any of the relevant hooks
29
30 """
File ~/anaconda3/lib/python3.9/site-packages/pytorch_lightning/utilities/types.py:40, in <module>
38 from torch import Tensor
39 from torch.optim import Optimizer
---> 40 from torchmetrics import Metric
41 from typing_extensions import NotRequired, Required
43 from lightning_fabric.utilities.types import _TORCH_LRSCHEDULER, LRScheduler, ProcessGroup, ReduceLROnPlateau
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/__init__.py:14, in <module>
11 _PACKAGE_ROOT = os.path.dirname(__file__)
12 _PROJECT_ROOT = os.path.dirname(_PACKAGE_ROOT)
---> 14 from torchmetrics import functional # noqa: E402
15 from torchmetrics.aggregation import ( # noqa: E402
16 CatMetric,
17 MaxMetric,
(...)
22 SumMetric,
23 )
24 from torchmetrics.audio._deprecated import _PermutationInvariantTraining as PermutationInvariantTraining # noqa: E402
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/functional/__init__.py:14, in <module>
1 # Copyright The Lightning team.
2 #
3 # Licensed under the Apache License, Version 2.0 (the "License");
(...)
12 # See the License for the specific language governing permissions and
13 # limitations under the License.
---> 14 from torchmetrics.functional.audio._deprecated import _permutation_invariant_training as permutation_invariant_training
15 from torchmetrics.functional.audio._deprecated import _pit_permutate as pit_permutate
16 from torchmetrics.functional.audio._deprecated import (
17 _scale_invariant_signal_distortion_ratio as scale_invariant_signal_distortion_ratio,
18 )
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/functional/audio/__init__.py:14, in <module>
1 # Copyright The Lightning team.
2 #
3 # Licensed under the Apache License, Version 2.0 (the "License");
(...)
12 # See the License for the specific language governing permissions and
13 # limitations under the License.
---> 14 from torchmetrics.functional.audio.pit import permutation_invariant_training, pit_permutate
15 from torchmetrics.functional.audio.sdr import scale_invariant_signal_distortion_ratio, signal_distortion_ratio
16 from torchmetrics.functional.audio.snr import (
17 complex_scale_invariant_signal_noise_ratio,
18 scale_invariant_signal_noise_ratio,
19 signal_noise_ratio,
20 )
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/functional/audio/pit.py:23, in <module>
20 from torch import Tensor
21 from typing_extensions import Literal
---> 23 from torchmetrics.utilities import rank_zero_warn
24 from torchmetrics.utilities.imports import _SCIPY_AVAILABLE
26 # _ps_dict: cache of permutations
27 # it's necessary to cache it, otherwise it will consume a large amount of time
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/utilities/__init__.py:14, in <module>
1 # Copyright The Lightning team.
2 #
3 # Licensed under the Apache License, Version 2.0 (the "License");
(...)
12 # See the License for the specific language governing permissions and
13 # limitations under the License.
---> 14 from torchmetrics.utilities.checks import check_forward_full_state_property
15 from torchmetrics.utilities.data import apply_to_collection
16 from torchmetrics.utilities.distributed import class_reduce, reduce
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/utilities/checks.py:25, in <module>
22 import torch
23 from torch import Tensor
---> 25 from torchmetrics.metric import Metric
26 from torchmetrics.utilities.data import select_topk, to_onehot
27 from torchmetrics.utilities.enums import DataType
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/metric.py:30, in <module>
27 from torch import Tensor
28 from torch.nn import Module
---> 30 from torchmetrics.utilities.data import (
31 _flatten,
32 _squeeze_if_scalar,
33 apply_to_collection,
34 dim_zero_cat,
35 dim_zero_max,
36 dim_zero_mean,
37 dim_zero_min,
38 dim_zero_sum,
39 )
40 from torchmetrics.utilities.distributed import gather_all_tensors
41 from torchmetrics.utilities.exceptions import TorchMetricsUserError
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/utilities/data.py:22, in <module>
19 from torch import Tensor
21 from torchmetrics.utilities.exceptions import TorchMetricsUserWarning
---> 22 from torchmetrics.utilities.imports import _TORCH_GREATER_EQUAL_1_12, _XLA_AVAILABLE
23 from torchmetrics.utilities.prints import rank_zero_warn
25 METRIC_EPS = 1e-6
File ~/anaconda3/lib/python3.9/site-packages/torchmetrics/utilities/imports.py:48, in <module>
46 _GAMMATONE_AVAILABEL: bool = package_available("gammatone")
47 _TORCHAUDIO_AVAILABEL: bool = package_available("torchaudio")
---> 48 _TORCHAUDIO_GREATER_EQUAL_0_10: Optional[bool] = compare_version("torchaudio", operator.ge, "0.10.0")
49 _SACREBLEU_AVAILABLE: bool = package_available("sacrebleu")
50 _REGEX_AVAILABLE: bool = package_available("regex")
File ~/anaconda3/lib/python3.9/site-packages/lightning_utilities/core/imports.py:77, in compare_version(package, op, version, use_base_version)
68 """Compare package version with some requirements.
69
70 >>> compare_version("torch", operator.ge, "0.1")
(...)
74
75 """
76 try:
---> 77 pkg = importlib.import_module(package)
78 except (ImportError, pkg_resources.DistributionNotFound):
79 return False
File ~/anaconda3/lib/python3.9/importlib/__init__.py:127, in import_module(name, package)
125 break
126 level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)
File ~/anaconda3/lib/python3.9/site-packages/torchaudio/__init__.py:1, in <module>
----> 1 from torchaudio import ( # noqa: F401
2 _extension,
3 compliance,
4 datasets,
5 functional,
6 io,
7 kaldi_io,
8 models,
9 pipelines,
10 sox_effects,
11 transforms,
12 utils,
13 )
14 from torchaudio.backend import get_audio_backend, list_audio_backends, set_audio_backend
16 try:
File ~/anaconda3/lib/python3.9/site-packages/torchaudio/_extension.py:135, in <module>
127 if ta_version != t_version:
128 raise RuntimeError(
129 "Detected that PyTorch and TorchAudio were compiled with different CUDA versions. "
130 f"PyTorch has CUDA version {t_version} whereas TorchAudio has CUDA version {ta_version}. "
131 "Please install the TorchAudio version that matches your PyTorch version."
132 )
--> 135 _init_extension()
136 _check_cuda_version()
File ~/anaconda3/lib/python3.9/site-packages/torchaudio/_extension.py:105, in _init_extension()
102 except Exception:
103 pass
--> 105 _load_lib("libtorchaudio")
106 # This import is for initializing the methods registered via PyBind11
107 # This has to happen after the base library is loaded
108 from torchaudio import _torchaudio # noqa
File ~/anaconda3/lib/python3.9/site-packages/torchaudio/_extension.py:52, in _load_lib(lib)
50 if not path.exists():
51 return False
---> 52 torch.ops.load_library(path)
53 torch.classes.load_library(path)
54 return True
File ~/anaconda3/lib/python3.9/site-packages/torch/_ops.py:643, in _Ops.load_library(self, path)
638 path = _utils_internal.resolve_library_path(path)
639 with dl_open_guard():
640 # Import the shared library into the process, thus running its
641 # static (global) initialization code in order to register custom
642 # operators with the JIT.
--> 643 ctypes.CDLL(path)
644 self.loaded_libraries.add(path)
File ~/anaconda3/lib/python3.9/ctypes/__init__.py:382, in CDLL.__init__(self, name, mode, handle, use_errno, use_last_error, winmode)
379 self._FuncPtr = _FuncPtr
381 if handle is None:
--> 382 self._handle = _dlopen(self._name, mode)
383 else:
384 self._handle = handle
OSError: libtorch_cuda_cpp.so: cannot open shared object file: No such file or directory
Solution of this issue requires downgrading of CUDA below 12 version:
sudo apt-get install libcudnn8=8.8.1.3-1+cuda11.8
sudo apt-get install libcudnn8-dev=8.8.1.3-1+cuda11.8
This is a cuda-installation specific error, we will provide an up to date config with a major update, but unfortunately PyTorch and PyTorch geometric codes are not guaranteed to work with all the versions of drivers.
Errors are fixed with the recent release, so now we have a complete setup.py