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jiaor17 / DiffCSP

[NeurIPS 2023] The implementation for the paper "Crystal Structure Prediction by Joint Equivariant Diffusion"
MIT License
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Environmental configuration issues #9

Open gaole1111 opened 7 months ago

gaole1111 commented 7 months ago

(gl) root@ubuntu:/data2/gl/DiffCSP-main# python diffcsp/run.py data=perov_5 expname=reproduction_diffcsp_perov diffcsp/run.py:172: 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") /data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'default': Defaults list is missing _self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information warnings.warn(msg, UserWarning) /data1/anaconda3/envs/gl/lib/python3.8/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/1.2/upgrades/1.1_to_1.2/changes_to_job_working_dir/ for more information. ret = run_job( Global seed set to 42 [2024-03-06 20:05:23,548][hydra.utils][INFO] - Instantiating Error executing job with overrides: ['data=perov_5', 'expname=reproduction_diffcsp_perov'] Traceback (most recent call last): File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 644, in _locate obj = getattr(obj, part) AttributeError: module 'diffcsp.pl_data' has no attribute 'datamodule'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 650, in _locate obj = import_module(mod) File "/data1/anaconda3/envs/gl/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1014, in _gcd_import File "", line 991, in _find_and_load File "", line 975, in _find_and_load_unlocked File "", line 671, in _load_unlocked File "", line 843, in exec_module File "", line 219, in _call_with_frames_removed File "/data2/gl/DiffCSP-main/./diffcsp/pl_data/datamodule.py", line 15, in from diffcsp.common.data_utils import get_scaler_from_data_list File "/data2/gl/DiffCSP-main/./diffcsp/common/data_utils.py", line 8, in from pymatgen.core.structure import Structure ModuleNotFoundError: No module named 'pymatgen.core'

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 134, in _resolve_target target = _locate(target) File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 653, in _locate raise ImportError( ImportError: Error loading 'diffcsp.pl_data.datamodule.CrystDataModule': ModuleNotFoundError("No module named 'pymatgen.core'") Are you sure that 'datamodule' is importable from module 'diffcsp.pl_data'?

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "diffcsp/run.py", line 178, in main() File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/main.py", line 94, in decorated_main _run_hydra( File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 394, in _run_hydra _run_app( File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 457, in _run_app run_and_report( File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 223, in run_and_report raise ex File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 220, in run_and_report return func() File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/utils.py", line 458, in lambda: hydra.run( File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/internal/hydra.py", line 132, in run = ret.return_value File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/core/utils.py", line 260, in return_value raise self._return_value File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/core/utils.py", line 186, in run_job ret.return_value = task_function(task_cfg) File "diffcsp/run.py", line 174, in main run(cfg) File "diffcsp/run.py", line 93, in run datamodule: pl.LightningDataModule = hydra.utils.instantiate( File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 226, in instantiate return instantiate_node( File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 333, in instantiate_node target = _resolve_target(node.get(_Keys.TARGET), full_key) File "/data1/anaconda3/envs/gl/lib/python3.8/site-packages/hydra/_internal/instantiate/_instantiate2.py", line 139, in _resolve_target raise InstantiationException(msg) from e hydra.errors.InstantiationException: Error locating target 'diffcsp.pl_data.datamodule.CrystDataModule', set env var HYDRA_FULL_ERROR=1 to see chained exception. full_key: data.datamodule

gaole1111 commented 7 months ago

Hello, how to solve this problem

jiaor17 commented 7 months ago

Hi, it seems like the pymatgen package is not installed in your current environment, according to the error:

ModuleNotFoundError: No module named 'pymatgen.core'

You could install it by 

pip install pymatgen==2022.9.21
jiaor17 commented 7 months ago

Hi, we find that downloading the 2022.9.21 version of pymatgen via pip would encounter an error now. An available and compatible version is 2023.8.10. You could try again with 

pip install pymatgen==2023.8.10

Thanks quite a lot for pointing out the problem!

gaole1111 commented 7 months ago

(gl) root@ubuntu:/data2/gl/DiffCSP-main# python diffcsp/run.py data=perov_5 expname=test1 Global seed set to 42 [2024-03-08 16:56:18,016][hydra.utils][INFO] - Instantiating Segmentation fault

jiaor17 commented 7 months ago

Hi, could you please provide more details about your environment? This will help us reproduce the error and offer a solution.

Could you export the minimal Conda environment leading to the segmentation fault and share it with us? You can do this by running the following command:

conda env export > env.yaml

Once you've done that, please paste the contents of env.yaml here. With this information, we'll be better equipped to diagnose and resolve the problem you're facing.

yuuhaixia commented 4 months ago

(gl) root@ubuntu:/data2/gl/DiffCSP-main# python diffcsp/run.py data=perov_5 expname=test1 Global seed set to 42 [2024-03-08 16:56:18,016][hydra.utils][INFO] - Instantiating Segmentation fault

I have the same problem as you, have you solved it and can you reply me, thanks a lot!