cdvae
cdvae copied to clipboard
Published
20 hours ago •
txie-93
txie-93
matminer>=0.7.3 instead of =0.7.3
(base) PS C:\Users\sterg\Documents\GitHub\sgbaird-5DOF\cdvae> mamba env create -f env.yml
conda-forge/win-64 Using cache
conda-forge/noarch Using cache
bioconda/win-64 Using cache
bioconda/noarch Using cache
pkgs/main/win-64 No change
pkgs/r/win-64 No change
pkgs/main/noarch No change
pytorch/win-64 No change
pkgs/r/noarch No change
pytorch/noarch No change
pyg/win-64 No change
sgbaird/noarch No change
plotly/win-64 No change
plotly/noarch No change
pkgs/msys2/win-64 No change
pyg/noarch No change
pkgs/msys2/noarch No change
numba/noarch 589.0 B @ 630.0 B/s 0.2s
sgbaird/win-64 No change
numba/win-64 148.9kB @ 107.1kB/s 1.1s
Looking for: ['ase=3.22', 'autopep8', 'cudatoolkit=10.2', 'jupyterlab', "matminer[version='>=0.7.3']", 'matplotl]
warning libmamba Extracted package cache 'C:\Users\sterg\miniconda3\pkgs\winpty-0.4.3-4' has invalid size
warning libmamba Extracted package cache 'C:\Users\sterg\miniconda3\pkgs\winpty-0.4.3-4' has invalid SHA-256 chm
Transaction
Prefix: C:\Users\sterg\miniconda3\envs\cdvae
Updating specs:
- ase=3.22
- autopep8
- cudatoolkit=10.2
- jupyterlab
- matminer[version='>=0.7.3']
- matplotlib
- nglview
- pip
- pyg=2.0.1
- ipywidgets
- pylint
- pymatgen=2020.12.31
- python=3.8
- pytorch-lightning=1.3.8
- pytorch=1.8.1
- seaborn
- tqdm
Package Version Build Channel Size
---------------------------------------------------------------------------------------------------------------
Install:
---------------------------------------------------------------------------------------------------------------
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Summary:
Install: 290 packages
Total download: 1GB
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ninja 307.7kB @ 318.3kB/s 1.0s
mkl-include 778.6kB @ 449.4kB/s 1.7s
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Preparing transaction: done
Verifying transaction: done
Executing transaction: - "By downloading and using the CUDA Toolkit conda packages, you accept the terms and con
- Enabling notebook extension jupyter-js-widgets/extension...
- Validating: ok
done
Installing pip dependencies: | Ran pip subprocess with arguments:
['C:\\Users\\sterg\\miniconda3\\envs\\cdvae\\python.exe', '-m', 'pip', 'install', '-U', '-r', 'C:\\Users\\sterg\]
Pip subprocess output:
Collecting hydra-core==1.1.0
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Collecting hydra-joblib-launcher==1.1.5
Downloading hydra_joblib_launcher-1.1.5-py3-none-any.whl (5.2 kB)
Collecting p-tqdm==1.3.3
Downloading p_tqdm-1.3.3.tar.gz (4.3 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting pytest
Using cached pytest-7.1.2-py3-none-any.whl (297 kB)
Collecting python-dotenv
Downloading python_dotenv-0.20.0-py3-none-any.whl (17 kB)
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Collecting streamlit==0.79.0
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Collecting wandb==0.10.33
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Collecting antlr4-python3-runtime==4.8
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Preparing metadata (setup.py): started
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Collecting omegaconf==2.1.*
Downloading omegaconf-2.1.2-py3-none-any.whl (74 kB)
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Collecting pathos
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Collecting pydeck>=0.1.dev5
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Collecting gitpython
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Downloading base58-2.1.1-py3-none-any.whl (5.6 kB)
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Collecting astor
Downloading astor-0.8.1-py2.py3-none-any.whl (27 kB)
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Collecting validators
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Preparing metadata (setup.py): started
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Collecting sentry-sdk>=0.4.0
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Collecting urllib3<=1.25.11
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Collecting subprocess32>=3.5.3
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Preparing metadata (setup.py): started
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Collecting promise<3,>=2.0
Downloading promise-2.3.tar.gz (19 kB)
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Collecting configparser>=3.8.1
Downloading configparser-5.2.0-py3-none-any.whl (19 kB)
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Collecting docker-pycreds>=0.4.0
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Collecting iniconfig
Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting atomicwrites>=1.0
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Collecting py>=1.8.2
Using cached py-1.11.0-py2.py3-none-any.whl (98 kB)
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Collecting toolz
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Building wheels for collected packages: p-tqdm, antlr4-python3-runtime, promise, subprocess32, validators
Building wheel for p-tqdm (setup.py): started
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Building wheel for promise (setup.py): started
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Successfully built p-tqdm antlr4-python3-runtime promise subprocess32 validators
Installing collected packages: pathtools, iniconfig, antlr4-python3-runtime, watchdog, validators, urllib3, toolt
Attempting uninstall: urllib3
Found existing installation: urllib3 1.26.9
Uninstalling urllib3-1.26.9:
Successfully uninstalled urllib3-1.26.9
Successfully installed altair-4.2.0 antlr4-python3-runtime-4.8 astor-0.8.1 atomicwrites-1.4.0 base58-2.1.1 confi9
done
#
# To activate this environment, use
#
# $ conda activate cdvae
#
# To deactivate an active environment, use
#
# $ conda deactivate
Hmm...
(cdvae) PS C:\Users\sterg\Documents\GitHub\sgbaird-5DOF\cdvae> python cdvae/run.py data=perov expname=perov Traceback (most recent call last): File "cdvae/run.py", line 8, in <module> import pytorch_lightning as pl
File "C:\Users\sterg\Miniconda3\envs\cdvae\lib\site-packages\pytorch_lightning\__init__.py", line 20, in <module>
from pytorch_lightning import metrics # noqa: E402
File "C:\Users\sterg\Miniconda3\envs\cdvae\lib\site-packages\pytorch_lightning\metrics\__init__.py", line 15, in <module>
from pytorch_lightning.metrics.classification import ( # noqa: F401
File "C:\Users\sterg\Miniconda3\envs\cdvae\lib\site-packages\pytorch_lightning\metrics\classification\__init__.py", line 14, in <module>
from pytorch_lightning.metrics.classification.accuracy import Accuracy # noqa: F401
File "C:\Users\sterg\Miniconda3\envs\cdvae\lib\site-packages\pytorch_lightning\metrics\classification\accuracy.py", line 18, in <module>
from pytorch_lightning.metrics.utils import deprecated_metrics
File "C:\Users\sterg\Miniconda3\envs\cdvae\lib\site-packages\pytorch_lightning\metrics\utils.py", line 22, in <module>
from torchmetrics.utilities.data import get_num_classes as _get_num_classes
ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' (C:\Users\sterg\Miniconda3\envs\cdvae\lib\site-packages\torchmetrics\utilities\data.py)
Thanks for your contribution. I think to solve this problem, you need to use an older version of torchmetrics. Try:
conda install torchmetrics=0.7.3
@txie-93 Did you see the post in https://github.com/txie-93/cdvae/issues/2#issuecomment-1153000418?
@txie-93 @kyonofx
This Colab notebook shows that:
The user requested pymatgen==2020.12.31
matminer 0.7.3 depends on pymatgen>=2022.0.8
...
ERROR: ResolutionImpossible
hence my suggestion about matminer>=0.7.3 (pymatgen>=2022.0.8 might be a suitable alternative).
After loosening to matminer>=0.7.3 (also demonstrated above), the following Colab notebooks reproduce the error with get_num_classes (without pinning torchmetrics==0.7.3).
After pinning torchmetrics==0.7.3 with matminer>=0.7.3, cdvae-debug-strictest-torchmetrics==0.7.3.ipynb shows a new error:
/usr/local/lib/python3.7/dist-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}")
Traceback (most recent call last):
File "cdvae/run.py", line 8, in <module>
import pytorch_lightning as pl
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/__init__.py", line 20, in <module>
from pytorch_lightning import metrics # noqa: E402
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/metrics/__init__.py", line 15, in <module>
from pytorch_lightning.metrics.classification import ( # noqa: F401
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/metrics/classification/__init__.py", line 14, in <module>
from pytorch_lightning.metrics.classification.accuracy import Accuracy # noqa: F401
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/metrics/classification/accuracy.py", line 18, in <module>
from pytorch_lightning.metrics.utils import deprecated_metrics
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/metrics/utils.py", line 29, in <module>
from pytorch_lightning.utilities import rank_zero_deprecation
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/__init__.py", line 18, in <module>
from pytorch_lightning.utilities.apply_func import move_data_to_device # noqa: F401
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/apply_func.py", line 29, in <module>
if _compare_version("torchtext", operator.ge, "0.9.0"):
File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/imports.py", line 53, in _compare_version
pkg = importlib.import_module(package)
File "/usr/lib/python3.7/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/usr/local/lib/python3.7/dist-packages/torchtext/__init__.py", line 7, in <module>
from . import datasets
File "/usr/local/lib/python3.7/dist-packages/torchtext/datasets/__init__.py", line 3, in <module>
from .ag_news import AG_NEWS
File "/usr/local/lib/python3.7/dist-packages/torchtext/datasets/ag_news.py", line 5, in <module>
from torchtext.data.datasets_utils import (
File "/usr/local/lib/python3.7/dist-packages/torchtext/data/datasets_utils.py", line 11, in <module>
from torch.utils.data import functional_datapipe, IterDataPipe
ImportError: cannot import name 'functional_datapipe' from 'torch.utils.data' (/usr/local/lib/python3.7/dist-packages/torch/utils/data/__init__.py)
Related: Cannot import name 'functional_datapipe' from 'torch.utils.data'
Maybe after trying this again locally but with torchmetrics==0.7.3 and python==3.8.*, I might have some better luck. However, I've been chasing down error-after-error over the course of hours and days (coming up on weeks). It would be great if you could verify from a fresh installation that you're able to run to completion the instructions in the README. Ideally, this would be using a separate user account on your machine (in my case I just appended -alt to my usual username) or someone else's "fresh" machine. That would definitely give me some light at the end of the tunnel ⛰️🚋⛰️🌞
@sgbaird Thanks for documenting your struggle! :D I've also been wrestling with setting this repo up and fixing error after error for a few days... It's a shame since this library seems promising. Did you eventually manage to get it up and running?
Unfortunately, no. The only thing I don't think I've tried yet is running it on a purely Linux system (i.e., not just WSL2).
Thanks! I've been trying to run it on a remote Linux machine through ssh and vscode; still no luck.
