Issues with running eval_samples.sh

[Yang-Wang-2020]

I got the following error when I was running the eval_samples.sh.

~/SurfDock/bash_scripts/test_scripts$ bash eval_samples.sh

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eval_samples.sh: line 15: /home/ywang/miniforge3/bin/activate: No such file or directory
SurfDockdir : /home/ywang/SurfDock
------------------------------------ Step1 : Setup Params --------------------------------------
Using GPU devices: 0
----------------------------- Step1 : Compute Target Surface -----------------------------------
Traceback (most recent call last):
File "/home/ywang/SurfDock/comp_surface/prepare_target/computeTargetMesh_test_samples.py", line 6, in
import pymesh
File "/home/ywang/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pymesh/init.py", line 25, in
from .Mesh import Mesh
File "/home/ywang/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pymesh/Mesh.py", line 5, in
import PyMesh
ImportError: /lib/x86_64-linux-gnu/libc.so.6: version GLIBC_2.34' not found (required by /home/ywang/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pymesh/lib/PyMesh.cpython-310-x86_64-linux-gnu.so) -------------------------------- Step2 : Get Input CSV File ----------------------------------- /home/ywang/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/core/computation/expressions.py:21: UserWarning: Pandas requires version '2.8.0' or newer of 'numexpr' (version '2.7.3' currently installed). from pandas.core.computation.check import NUMEXPR_INSTALLED 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 15827.56it/s] -------------------------------- Step3 : Get Pocket ESM Embedding ---------------------------- /home/ywang/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/core/computation/expressions.py:21: UserWarning: Pandas requires version '2.8.0' or newer of 'numexpr' (version '2.7.3' currently installed). from pandas.core.computation.check import NUMEXPR_INSTALLED 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 15.85it/s] python: can't open file '/home/ywang/SurfDock/esm/scripts/extract.py': [Errno 2] No such file or directory 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 9.81it/s] 0it [00:00, ?it/s] ------------------------ Step3 : Start Sampling Ligand Confromers ---------------------------- The following values were not passed to accelerate launchand had defaults used instead:--num_machineswas set to a value of1 --mixed_precisionwas set to a value of'no' --dynamo_backendwas set to a value of'no'To avoid this warning pass in values for each of the problematic parameters or runaccelerate config`.
/home/ywang/mambaforge/envs/SurfDock/lib/python3.10/site-packages/pandas/core/computation/expressions.py:21: UserWarning: Pandas requires version '2.8.0' or newer of 'numexpr' (version '2.7.3' currently installed).
from pandas.core.computation.check import NUMEXPR_INSTALLED

100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 201/201 [01:18<00:00, 2.56it/s]
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 201/201 [01:28<00:00, 2.26it/s]
/home/ywang/SurfDock/utils/torus.py:41: RuntimeWarning: invalid value encountered in divide
score_ = grad(x, sigma[:, None], N=100) / p_
2025-02-19 21:20:25.452 | INFO | main::90 - Runing inference script in path: /home/ywang/SurfDock/data/eval_sample_dirs/SurfDock_eval_samples/repeat_250102/test_samples_8A_surface
2025-02-19 21:20:25.453 | INFO | main::91 - Runing inference with args: Namespace(config=None, data_csv='/home/ywang/SurfDock/data/eval_sample_dirs/SurfDock_eval_samples/repeat_250102/input_csv_files/test_samples.csv', model_dir='/home/ywang/SurfDock/model_weights/docking', ckpt='best_ema_inference_epoch_model.pt', confidence_model_dir='/home/ywang/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='/home/ywang/SurfDock/model_weights/posepredict_test_dist_3', project='SurfDock_eval_samples/repeat_250102', surface_path='/PDBBind_processed_8A_surface/', esm_embeddings_path='/home/ywang/SurfDock/data/eval_sample_dirs/SurfDock_eval_samples/repeat_250102/test_samples_esmbedding/esm_embedding_pocket_output_for_train/esm2_3billion_pdbbind_embeddings.pt', out_dir='/home/ywang/docking_result/SurfDock_eval_samples/repeat_250102', 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='/home/ywang/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)
2025-02-19 21:20:28.841 | INFO | main:main_function:165 - loaded model weight for score model
2025-02-19 21:20:31.920 | 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]
2025-02-19 21:20:31.921 | INFO | main:main_function:189 - Loading data ...........
0%| | 0/1 [00:00<?, ?it/s]2025-02-19 21:20:31.923 | ERROR | main:main_function:433 - Some error failed for graph data. ligand_path: /home/ywang/SurfDock/data/eval_sample_dirs/test_samples/1a0q/1a0q_ligand.sdf,error of :'1a0q_protein_processed_8A'
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 5.02it/s]
Traceback (most recent call last):
File "/home/ywang/SurfDock/inference_accelerate.py", line 470, in
main_function()
File "/home/ywang/SurfDock/inference_accelerate.py", line 445, in main_function
logger.info('Docking time used for one moleculer: {}',docking_time/ all_molecules)
ZeroDivisionError: float division by zero
[2025-02-19 21:20:35,346] torch.distributed.elastic.multiprocessing.api: [ERROR] failed (exitcode: 1) local_rank: 0 (pid: 8333) of binary: /home/ywang/mambaforge/envs/SurfDock/bin/python3.10

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/ | _ _ _ __ / | _ \ ___ | | __ / | __ _ _ __ ___ _ __ | () __ __ _ | _ \ ___ _ __ | |
_ | | | | '| || | | |/ _ \ / | |/ / _ \ / | '_ _ | ' | | | ' \ / ` | | | | |/ _ | ' \ / _ \ |
) | || | | | | || | () | (| < ) | (| | | | | | | |) | | | | | | (| | | || | () | | | | __/|
|/ _,|| || |/ _/ _||_\ |/ _,|| || || .__/|||| ||_, | |/ ___/|| ||___()
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The whole process did not use any GPU.
It seems like there are more than one issues.
Could you help?

Thanks,
Yang

[CLG68]

Have a look at the closed issues such as: #16

There is an had coded PATH that you need to modify in the script