Environment issues and some name inconsistency #2
Comments
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Thanks for reaching out @YKQ98 For the first question, it seems the step 'solving environment' is taking a very long time. But I was able to successfully install the conda packages after waiting several hours. I don't know why it takes so long to solve the environment though.. For the crystvae, these are some leftovers from the refactoring and sorry about that. They should be resolved in #1. Let me know if you have more errors after pulling the latest commits. |
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Thank you for the feedback! Actually I manually installed all the packages needed and the code works fine. |
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Seems like a good use-case for |
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A more useful error message produced by (base) PS C:\Users\sterg\Documents\GitHub\sgbaird-5DOF\cdvae> conda install -c conda-forge mamba
(base) PS C:\Users\sterg\Documents\GitHub\sgbaird-5DOF\cdvae> mamba env create -f env.yml
pkgs/main/win-64 No change
pytorch/noarch 5.4kB @ 7.2kB/s 0.8s
numba/noarch 589.0 B @ 602.0 B/s 0.2s
pyg/win-64 19.0kB @ 14.2kB/s 0.7s
pkgs/main/noarch No change
pkgs/msys2/noarch No change
pytorch/win-64 89.7kB @ 31.2kB/s 2.9s
bioconda/noarch 3.5MB @ 1.2MB/s 2.3s
sgbaird/win-64 143.0 B @ 43.0 B/s 0.5s
plotly/win-64 1.2kB @ 332.0 B/s 1.9s
pkgs/r/noarch No change
pkgs/msys2/win-64 No change
pyg/noarch 130.0 B @ 34.0 B/s 0.2snumba/win-64 148.9kB @ 36.3kB/s 0.8sconda-forge/noarch 8.4MB @ 2.0MB/s 4.9splotly/noarch 5.5kB @ 1.1kB/s 1.2sbioconda/win-64 122.0 B @ 25.0 B/s 0.8s
sgbaird/noarch 4.1kB @ 837.0 B/s 0.8s
pkgs/r/win-64 No change
conda-forge/win-64 15.1MB @ 2.4MB/s 7.5s
Looking for: ['ase=3.22', 'autopep8', 'cudatoolkit=10.2', 'jupyterlab', 'matminer=0.7.3', 'matplotlib', 'nglview]
Encountered problems while solving:
- nothing provides dscribe >=0.2.9 needed by matminer-0.7.3-pyhd8ed1ab_0 |
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My attempt at a manual install: conda create -n cdvae python==3.9.*
conda activate cdvae
conda install -c pytorch -c conda-forge -c defaults -c pyg ase autopep8 cudatoolkit jupyterlab matminer matplotlib nglview pip pyg ipywidgets pylint pymatgen pytorch-lightning pytorch seaborn tqdm
pip install hydra-core hydra-joblib-launcher p-tqdm pytest python-dotenv smact streamlit wandb
pip install -e .
Also tried Lightning-AI/pytorch-lightning#7110 (comment): pip install hydra-core --upgrade
Same error. Tried installing with: mamba install -c conda-forge pytorch-lightning=1.5.10Failed via mamba, possibly due to issue with mamba and WSL (it wasn't working before with using `mamba` instead of `conda` above)
(cdvae) sgbaird@Dell-G7:~/GitHub/sparks-baird/cdvae$ mamba install -c conda-forge pytorch-lightning=1.5.10
Trying: conda install -c conda-forge pytorch-lightning=1.5.10and it took maybe a few minutes to solve. It seems to be loading the CIF files now. (~30 min to load ~30k CIF files from string representation, so saving the pymatgen |
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So, first making sure that I'm actually in the WSL storage, the following seems to work: git clone https://github.com/txie-93/cdvae.git
cd cdvae
conda create -n cdvae python==3.9.*
conda activate cdvae
conda install -c pytorch -c conda-forge -c defaults -c pyg ase autopep8 cudatoolkit jupyterlab matminer matplotlib nglview pip pyg ipywidgets pylint pymatgen pytorch-lightning=1.5.10 pytorch seaborn tqdm
pip install hydra-core hydra-joblib-launcher p-tqdm pytest python-dotenv smact streamlit wandb
pip install -e .
I'm running this in debugging mode with VS Code. My and just in case, also set it in a custom launch file: {
// Use IntelliSense to learn about possible attributes.
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [
{
"name": "CDVAE MP-20",
"type": "python",
"request": "launch",
"program": "${file}",
"console": "integratedTerminal",
"justMyCode": false,
"args": [
"data=mp_20",
"expname=mp_20"
],
"env": {
"PROJECT_ROOT": "/home/sgbaird/cdvae",
"HYDRA_JOBS": "/home/sgbaird/hydra",
"WABDB_DIR": "/home/sgbaird/wabdb"
}
}
]
} |
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Still ran into an error eventually: Exception has occurred: InstantiationException (note: full exception trace is shown but execution is paused at: _run_module_as_main)
Error in call to target 'cdvae.pl_modules.model.CDVAE':
InstantiationException("Error in call to target 'cdvae.pl_modules.gnn.DimeNetPlusPlusWrap':\nRuntimeError('a leaf Variable that requires grad is being used in an in-place operation.')\nfull_key: encoder")
full_key: model
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 92, in _call_target
return _target_(*args, **kwargs)
File "/home/sgbaird/cdvae/cdvae/pl_modules/gnn.py", line 327, in __init__
super(DimeNetPlusPlusWrap, self).__init__(
File "/home/sgbaird/cdvae/cdvae/pl_modules/gnn.py", line 223, in __init__
self.rbf = BesselBasisLayer(num_radial, cutoff, envelope_exponent)
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/torch_geometric/nn/models/dimenet.py", line 59, in __init__
self.reset_parameters()
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/torch_geometric/nn/models/dimenet.py", line 62, in reset_parameters
torch.arange(1, self.freq.numel() + 1, out=self.freq).mul_(PI)
The above exception was the direct cause of the following exception:
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 92, in _call_target
return _target_(*args, **kwargs)
File "/home/sgbaird/cdvae/cdvae/pl_modules/model.py", line 140, in __init__
self.encoder = hydra.utils.instantiate(
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 222, in instantiate
return instantiate_node(
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 339, in instantiate_node
return _call_target(_target_, partial, args, kwargs, full_key)
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 97, in _call_target
raise InstantiationException(msg) from e
The above exception was the direct cause of the following exception:
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 97, in _call_target
raise InstantiationException(msg) from e
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 339, in instantiate_node
return _call_target(_target_, partial, args, kwargs, full_key)
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 222, in instantiate
return instantiate_node(
File "/home/sgbaird/cdvae/cdvae/run.py", line 94, in run
model: pl.LightningModule = hydra.utils.instantiate(
File "/home/sgbaird/cdvae/cdvae/run.py", line 166, in main
run(cfg)
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/core/utils.py", line 186, in run_job
ret.return_value = task_function(task_cfg)
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/core/utils.py", line 260, in return_value
raise self._return_value
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/hydra.py", line 132, in run
_ = ret.return_value
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/utils.py", line 453, in <lambda>
lambda: hydra.run(
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/utils.py", line 216, in run_and_report
raise ex
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/utils.py", line 216, in run_and_report
raise ex
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/utils.py", line 452, in _run_app
run_and_report(
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/utils.py", line 389, in _run_hydra
_run_app(
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/main.py", line 90, in decorated_main
_run_hydra(
File "/home/sgbaird/cdvae/cdvae/run.py", line 170, in <module>
main()
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/runpy.py", line 268, in run_path
return _run_module_code(code, init_globals, run_name,
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/runpy.py", line 197, in _run_module_as_main (Current frame)
return _run_code(code, main_globals, None,Seems related: https://discuss.pytorch.org/t/leaf-variable-was-used-in-an-inplace-operation/308 Not sure if there are notifications on the closed issue: @YKQ98 @txie-93 |
Dear authors,
Hi, when I install the environment by running 'conda env create -f env.yml', I got stuck in the 'solving environment' step of conda.
Could you check this step? I think something might be wrong here ~.
Also, there are some errors when I run the training code. Some places you name it cdvae but you use crystalvae to refer it in the pipeline.
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