Encountered several errors while testing SurfDock #42
Description
Hello, after completing the installation, I encountered several errors while testing SurfDock. Could you please provide some suggestions to help resolve them? Thank you in advance!
"bash eval_samples.sh
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EnvironmentNameNotFound: Could not find conda environment: SurfDock
You can list all discoverable environments with conda info --envs.
SurfDockdir : /data/mark/SurfDock
------------------------------------ Step1 : Setup Params --------------------------------------
Using GPU devices: 0
Target structure has been processed, skipping this step.
----------------------------- Step1 : Compute Target Surface -----------------------------------
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 64.86it/s]100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 4.02it/s]-------------------------------- Step2 : Get Input CSV File -----------------------------------
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 5622.39it/s]-------------------------------- Step3 : Get Pocket ESM Embedding ----------------------------
Traceback (most recent call last):
File "/data/mark/SurfDock/datasets/esm_embedding_preparation.py", line 51, in
df = pd.read_csv(args.protein_ligand_csv)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1448, in init
self._engine = self._make_engine(f, self.engine)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine
return mapping[engine](f, **self.options)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "parsers.pyx", line 586, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
Traceback (most recent call last):
File "/data/mark/SurfDock/esm/scripts/extract.py", line 140, in
main()
File "/data/mark/SurfDock/esm/scripts/extract.py", line 137, in main
run(args)
File "/data/mark/SurfDock/esm/scripts/extract.py", line 74, in run
dataset = FastaBatchedDataset.from_file(args.fasta_file)
File "/data/mark/SurfDock/esm/esm/data.py", line 39, in from_file
with open(fasta_file, "r") as infile:
FileNotFoundError: [Errno 2] No such file or directory: '/data/mark/Eval_result/processed_data/SurfDock_eval_samples_skip_target_processed/test_samples_esmbedding/test_samples.fasta'
Traceback (most recent call last):
File "/data/mark/SurfDock/datasets/get_pocket_embedding.py", line 22, in
df = pd.read_csv(args.protein_pocket_csv)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1448, in init
self._engine = self._make_engine(f, self.engine)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine
return mapping[engine](f, **self.options)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self.reader = parsers.TextReader(src, **kwds)
File "parsers.pyx", line 586, in pandas.libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
Traceback (most recent call last):
File "/data/mark/SurfDock/datasets/esm_pocket_embeddings_to_pt.py", line 15, in
for filename in tqdm(os.listdir(args.esm_embeddings_path)):
FileNotFoundError: [Errno 2] No such file or directory: '/data/mark/Eval_result/processed_data/SurfDock_eval_samples_skip_target_processed/test_samples_esmbedding/esm_embedding_pocket_output'
------------------------ Step3 : Start Sampling Ligand Confromers ----------------------------
/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/wandb/sdk/launch/builder/build.py:11: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
The following values were not passed to accelerate launch and had defaults used instead:
--num_machines was set to a value of 1
--mixed_precision was set to a value of 'no'
--dynamo_backend was set to a value of 'no'
To avoid this warning pass in values for each of the problematic parameters or run accelerate config.
/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/wandb/sdk/launch/builder/build.py:11: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/torch_geometric/typing.py:54: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version GLIBC_2.27' not found (required by /data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/libpyg.so) warnings.warn(f"An issue occurred while importing 'pyg-lib'. " /data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/torch_geometric/typing.py:110: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /lib64/libm.so.6: version GLIBC_2.27' not found (required by /data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/libpyg.so)
warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 201/201 [01:28<00:00, 2.27it/s]100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 201/201 [02:05<00:00, 1.60it/s]/data/mark/SurfDock/utils/torus.py:41: RuntimeWarning: invalid value encountered in divide
score = grad(x, sigma[:, None], N=100) / p
2025-07-27 20:28:14.138 | INFO | main::90 - Runing inference script in path: /data/mark/Eval_result/processed_data/SurfDock_eval_samples_skip_target_processed/test_samples_8A_surface
2025-07-27 20:28:14.138 | INFO | main::91 - Runing inference with args: Namespace(config=None, data_csv='/data/mark/Eval_result/processed_data/SurfDock_eval_samples_skip_target_processed/input_csv_files//test_samples.csv', model_dir='/data/mark/SurfDock/model_weights/docking', ckpt='best_ema_inference_epoch_model.pt', confidence_model_dir='/data/mark/SurfDock/model_weights/posepredict', confidence_ckpt='best_model.pt', save_docking_result=True, ligand_to_pocket_center=False, keep_input_pose=False, use_noise_to_rank=False, num_cpu=None, run_name='/data/mark/SurfDock/model_weights/posepredict_test_dist_3', project='SurfDock_eval_samples_skip_target_processed', surface_path='/PDBBind_processed_8A_surface/', esm_embeddings_path='/data/mark/Eval_result/processed_data/SurfDock_eval_samples_skip_target_processed/test_samples_esmbedding/esm_embedding_pocket_output_for_train/esm2_3billion_pdbbind_embeddings.pt', out_dir='/data/mark/Eval_result/docking_result/SurfDock_eval_samples_skip_target_processed', batch_size=40, batch_size_molecule=1, cache_path='/PDBBIND/cache_PDBBIND_pocket_8A', data_dir='/PDBBIND/PDBBind_pocket_8A/', split_path='/data/splits/timesplit_test', no_overlap_names_path='~/data/splits/timesplit_test_no_rec_overlap', no_model=False, no_random=False, no_final_step_noise=False, ode=False, wandb=False, wandb_dir='/data/mark/docking_result/test_workdir', inference_steps=20, limit_complexes=0, num_workers=1, num_process=20, tqdm=False, save_visualisation=False, samples_per_complex=40, save_docking_result_number=40, actual_steps=None, inference_mode='evaluate', head_index=0, tail_index=10000, ligandsMaxAtoms=80, random_seed=42, force_optimize=False, mdn_dist_threshold_test=3.0)
2025-07-27 20:28:24.351 | INFO | main:main_function:165 - loaded model weight for score model
2025-07-27 20:28:27.601 | INFO | main:main_function:188 - t schedule:[1. 0.95 0.9 0.85 0.8 0.75 0.7 0.65 0.6 0.55 0.5 0.45 0.4 0.35
0.3 0.25 0.2 0.15 0.1 0.05]
2025-07-27 20:28:27.601 | INFO | main:main_function:189 - Loading data ...........
Traceback (most recent call last):
File "/data/mark/SurfDock/inference_accelerate.py", line 470, in
main_function()
File "/data/mark/SurfDock/inference_accelerate.py", line 195, in main_function
df = pd.read_csv(args.data_csv)[args.head_index:args.tail_index]
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1448, in init
self._engine = self._make_engine(f, self.engine)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine
return mapping[engine](f, **self.options)
File "/data/mark/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "parsers.pyx", line 586, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
[2025-07-27 20:28:31,505] torch.distributed.elastic.multiprocessing.api: [ERROR] failed (exitcode: 1) local_rank: 0 (pid: 127967) of binary: /data/mark/mambaforge/envs/SurfDock/bin/python3.10
/ | _ _ _ __ / | _ \ ___ | | __ / | __ _ _ __ ___ _ __ | () __ __ _ | _ \ ___ _ __ | |
_ | | | | '| || | | |/ _ \ / | |/ / _ \ / | '_ _ | ' | | | ' \ / ` | | | | |/ _ | ' \ / _ \ |
) | || | | | | || | () | (| < ) | (| | | | | | | |) | | | | | | (| | | || | () | | | | __/|
|/ _,|| || |/ _/ _||_\ |/ _,|| || || .__/|||| ||_, | |/ ___/|| ||___()
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____ _ _ _ _ _ _ ____ _ _____ ____ _ _ ____ _ _ ____ _ ____ _ _"