Environment issues and some name inconsistency

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.

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.

Thank you for the feedback!

Actually I manually installed all the packages needed and the code works fine.

Seems like a good use-case for mamba. @YKQ98 what did you run for installing the packages manually? Did you keep some of the requirements as concrete or convert them to abstract (unpinned) dependencies? I take it you probably used a two-step installation, one with conda and a second command with pip. Is that the case?

A more useful error message produced by mamba:

(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

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 .

Exception has occurred: ImportError       (note: full exception trace is shown but execution is paused at: _run_module_as_main)
cannot import name 'LearningRateMonitor' from 'pytorch_lightning.callbacks' (/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pytorch_lightning/callbacks/__init__.py)
  File "/home/sgbaird/GitHub/sparks-baird/cdvae/cdvae/run.py", line 12, in <module>
    from pytorch_lightning.callbacks import (
  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,

Also tried https://github.com/PyTorchLightning/pytorch-lightning/issues/7110#issuecomment-907967384:

pip install hydra-core --upgrade

Requirement already satisfied: hydra-core in /home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages (1.2.0)
Requirement already satisfied: antlr4-python3-runtime==4.9.* in /home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages (from hydra-core) (4.9.3)
Requirement already satisfied: omegaconf~=2.2 in /home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages (from hydra-core) (2.2.2)
Requirement already satisfied: packaging in /home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages (from hydra-core) (21.3)
Requirement already satisfied: PyYAML>=5.1.0 in /home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages (from omegaconf~=2.2->hydra-core) (6.0)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages (from packaging->hydra-core) (3.0.9)

Same error.

Tried installing with:

mamba install -c conda-forge pytorch-lightning=1.5.10

Failed 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

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.24.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['pytorch-lightning=1.5.10']

pkgs/r/linux-64                                               No change
pkgs/r/noarch                                                 No change
pkgs/main/noarch                                              No change
pkgs/main/linux-64                                            No change
conda-forge/noarch                                 @   1.5MB/s  5.8s
conda-forge/linux-64                               @   2.4MB/s 11.7s

Pinned packages:
  - python 3.9.*

Transaction

  Prefix: /home/sgbaird/miniconda3/envs/cdvae

  Updating specs:

   - pytorch-lightning=1.5.10
   - ca-certificates
   - certifi
   - openssl

  Package                  Version  Build           Channel                    Size
─────────────────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────────────────

  + fsspec                2022.5.0  pyhd8ed1ab_0    conda-forge/noarch         98kB
  + pydeprecate              0.3.2  pyhd8ed1ab_0    conda-forge/noarch         13kB
  + torchmetrics             0.9.1  pyhd8ed1ab_0    conda-forge/noarch        200kB

  Upgrade:
─────────────────────────────────────────────────────────────────────────────────────

  - ca-certificates      2022.4.26  h06a4308_0      pkgs/main                      
  + ca-certificates    2022.5.18.1  ha878542_0      conda-forge/linux-64     Cached
  - pytorch-lightning        0.8.5  py_0            conda-forge                    
  + pytorch-lightning       1.5.10  pyhd8ed1ab_0    conda-forge/noarch        308kB

  Downgrade:
─────────────────────────────────────────────────────────────────────────────────────

  - setuptools              61.2.0  py39h06a4308_0  pkgs/main                      
  + setuptools              59.5.0  py39hf3d152e_0  conda-forge/linux-64        1MB

  Summary:

  Install: 3 packages
  Upgrade: 2 packages
  Downgrade: 1 packages

  Total download: 2MB

─────────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] Y

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/home/sgbaird/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1114, in __call__
        return func(*args, **kwargs)
      File "/home/sgbaird/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 935, in exception_converter
        raise e
      File "/home/sgbaird/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 929, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/home/sgbaird/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 887, in _wrapped_main
        result = do_call(args, p)
      File "/home/sgbaird/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 750, in do_call
        exit_code = install(args, parser, "install")
      File "/home/sgbaird/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 586, in install
        transaction.fetch_extract_packages()
    RuntimeError: Download error (28) Timeout was reached [https://conda.anaconda.org/conda-forge/linux-64/setuptools-59.5.0-py39hf3d152e_0.tar.bz2]
    Connection timeout after 9064 ms

`$ /home/sgbaird/miniconda3/condabin/mamba install -c conda-forge pytorch-lightning=1.5.10`

  environment variables:
                 CIO_TEST=
        CONDA_DEFAULT_ENV=cdvae
                CONDA_EXE=/home/sgbaird/miniconda3/bin/conda
CONDA_MKL_INTERFACE_LAYER_BACKUP=
             CONDA_PREFIX=/home/sgbaird/miniconda3/envs/cdvae
           CONDA_PREFIX_1=/home/sgbaird/miniconda3
    CONDA_PROMPT_MODIFIER=(cdvae)
         CONDA_PYTHON_EXE=/home/sgbaird/miniconda3/bin/python
               CONDA_ROOT=/home/sgbaird/miniconda3
              CONDA_SHLVL=2
           CURL_CA_BUNDLE=
                     PATH=/home/sgbaird/.vscode-
                          server/bin/4af164ea3a06f701fe3e89a2bcbb421d2026b68f/bin/remote-cli:/ho
                          me/sgbaird/.local/bin:/home/sgbaird/miniconda3/envs/cdvae/bin:/home/sg
                          baird/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/us
                          r/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/P
                          ython310/Scripts:/mnt/c/Python310:/mnt/c/Program Files/NVIDIA GPU
                          Computing Toolkit/CUDA/v11.2/bin:/mnt/c/Program Files/NVIDIA GPU
                          Computing Toolkit/CUDA/v11.2/libnvvp:/mnt/c/Windows/system32:/mnt/c/Wi
                          ndows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowe
                          rShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program
                          Files/MATLAB/R2021a/runtime/win64:/mnt/c/Program
                          Files/MATLAB/R2021a/bin:/mnt/c/Program
                          Files/Git/cmd:/mnt/c/ProgramData/chocolatey/bin:/mnt/c/Program
                          Files/PuTTY:/mnt/c/Program Files (x86)/NVIDIA
                          Corporation/PhysX/Common:/mnt/c/Program Files/NVIDIA
                          Corporation/NVIDIA NvDLISR:/mnt/c/Program Files/NVIDIA
                          Corporation/Nsight Compute 2020.3.1:/mnt/c/WINDOWS/system32:/mnt/c/WIN
                          DOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPower
                          Shell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program
                          Files/P403n1x87/Austin:/mnt/c/Program Files/dotnet:/mnt/c/Program
                          Files/Wolfram Research/WolframScript:/mnt/c/Program Files/nodejs:/mnt/
                          c/Ruby31-x64/bin:/mnt/c/Users/sterg/AppData/Local/Programs/Python/Pyth
                          on38/Scripts:/mnt/c/Users/sterg/AppData/Local/Programs/Python/Python38
                          :/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/
                          mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/
                          OpenSSH:/mnt/c/Program Files/Wolfram
                          Research/WolframScript:/mnt/c/Program
                          Files/MATLAB/R2021a/runtime/win64:/mnt/c/Program
                          Files/MATLAB/R2021a/bin:/mnt/c/Program Files/Git/cmd:/mnt/c/Users/ster
                          g/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/sterg/AppData/Local
                          /atom/bin:/mnt/c/Users/sterg/AppData/Local/GitHubDesktop/bin:/mnt/c/Fu
                          llProf_Suite:/mnt/c/texlive/2021/bin/win32:/mnt/c/Users/sterg/AppData/
                          Local/Pandoc:/mnt/c/Users/sterg/AppData/Local/Programs/Microsoft VS
                          Code/bin:/mnt/c/Program Files/Graphviz/bin:/mnt/c/Users/sterg/AppData/
                          Local/Microsoft/WindowsApps:/mnt/c/Users/sterg/AppData/Local/Packages/
                          PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0/LocalCache/local-pac
                          kages/Python39/Scripts:/mnt/c/Users/sterg/AppData/Roaming/Python/Scrip
                          ts:/mnt/c/Users/sterg/Miniconda3:/mnt/c/Users/sterg/Miniconda3/scripts
                          :/mnt/c/Users/sterg/Miniconda3/Library/bin:/mnt/c/Users/sterg/AppData/
                          Roaming/npm:/snap/bin
       REQUESTS_CA_BUNDLE=
            SSL_CERT_FILE=

     active environment : cdvae
    active env location : /home/sgbaird/miniconda3/envs/cdvae
            shell level : 2
       user config file : /home/sgbaird/.condarc
 populated config files : 
          conda version : 4.13.0
    conda-build version : not installed
         python version : 3.9.5.final.0
       virtual packages : __linux=5.10.16.3=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/sgbaird/miniconda3  (writable)
      conda av data dir : /home/sgbaird/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/sgbaird/miniconda3/pkgs
                          /home/sgbaird/.conda/pkgs
       envs directories : /home/sgbaird/miniconda3/envs
                          /home/sgbaird/.conda/envs
               platform : linux-64
             user-agent : conda/4.13.0 requests/2.27.1 CPython/3.9.5 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.2 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

Trying:

conda install -c conda-forge pytorch-lightning=1.5.10

and 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 Structure objects directly would probably save some time, maybe not much compared to the time it takes to train though).

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 .

(cdvae) sgbaird@Dell-G7:~/cdvae$  /usr/bin/env /home/sgbaird/miniconda3/envs/cdvae/bin/python /home/sgbaird/.vscode-server/extensions/ms-python.python-2022.8.0/pythonFiles/lib/python/debugpy/launcher 38901 -- /home/sgbaird/cdvae/cdvae/run.py data=mp_20 expname=mp_20 
/home/sgbaird/cdvae/cdvae/run.py:164: UserWarning: 
The version_base parameter is not specified.
Please specify a compatability version level, or None.
Will assume defaults for version 1.1
  @hydra.main(config_path=str(PROJECT_ROOT / "conf"), config_name="default")
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'default': Defaults list is missing `_self_`. See https://hydra.cc/docs/upgrades/1.0_to_1.1/default_composition_order for more information
  warnings.warn(msg, UserWarning)
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/hydra/_internal/hydra.py:119: UserWarning: Future Hydra versions will no longer change working directory at job runtime by default.
See https://hydra.cc/docs/next/upgrades/1.1_to_1.2/changes_to_job_working_dir/ for more information.
  ret = run_job(
[2022-06-11 20:18:18,133][hydra.utils][INFO] - Instantiating <cdvae.pl_data.datamodule.CrystDataModule>
/home/sgbaird/cdvae/cdvae/pl_data/datamodule.py:142: UserWarning: 
The version_base parameter is not specified.
Please specify a compatability version level, or None.
Will assume defaults for version 1.1
  @hydra.main(config_path=str(PROJECT_ROOT / "conf"), config_name="default")
/home/sgbaird/cdvae/cdvae/pl_data/dataset.py:126: UserWarning: 
The version_base parameter is not specified.
Please specify a compatability version level, or None.
Will assume defaults for version 1.1
  @hydra.main(config_path=str(PROJECT_ROOT / "conf"), config_name="default")
  0%|                               | 0/27136 [00:00<?, ?it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                     | 3/27136 [00:01<2:54:47,  2.59it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                     | 4/27136 [00:02<5:21:44,  1.41it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                    | 12/27136 [00:03<1:03:16,  7.14it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                      | 34/27136 [00:04<27:10, 16.62it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                      | 36/27136 [00:04<34:19, 13.16it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                      | 46/27136 [00:05<28:25, 15.89it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                      | 81/27136 [00:08<32:59, 13.66it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  0%|                      | 87/27136 [00:08<30:14, 14.90it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  1%|                     | 159/27136 [00:13<21:29, 20.92it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  1%|▏                    | 162/27136 [00:13<28:57, 15.52it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
  2%|▍                    | 486/27136 [00:36<36:04, 12.31it/s]/home/sgbaird/miniconda3/envs/cdvae/lib/python3.9/site-packages/pymatgen/io/cif.py:1155: UserWarning: Issues encountered while parsing CIF: Some fractional coordinates rounded to ideal values to avoid issues with finite precision.
  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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  warnings.warn("Issues encountered while parsing CIF: " + "\n".join(self.warnings))
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I'm running this in debugging mode with VS Code.

My .env file:

export PROJECT_ROOT="/home/sgbaird/cdvae"
export HYDRA_JOBS="/home/sgbaird/hydra"
export WABDB_DIR="/home/sgbaird/wabdb"

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"
            }
        }
    ]
}

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,

Not sure if there are notifications on the closed issue: @YKQ98 @txie-93 @YKQ98 might be worth opening back up, otherwise I can open a fresh issue, too.

txie-93 / cdvae

Environment issues and some name inconsistency #2