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google-deepmind / alphafold

Open source code for AlphaFold.
Apache License 2.0
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ValueError: Minimization failed after 100 attempts. #955

Open zcswnm opened 1 week ago

zcswnm commented 1 week ago

I0630 12:32:08.821609 140165856380736 run_docker.py:258] I0630 04:32:08.821140 133109636522624 run_alphafold.py:288] Total JAX model model_4_pred_0 on my_antibody predict time (includes compilation time, see --benchmark): 48.1s I0630 12:32:09.112607 140165856380736 run_docker.py:258] I0630 04:32:09.112085 133109636522624 run_alphafold.py:276] Running model model_5_pred_0 on my_antibody I0630 12:32:10.133877 140165856380736 run_docker.py:258] I0630 04:32:10.133128 133109636522624 model.py:165] Running predict with shape(feat) = {'aatype': (4, 122), 'residue_index': (4, 122), 'seq_length': (4,), 'is_distillation': (4,), 'seq_mask': (4, 122), 'msa_mask': (4, 512, 122), 'msa_row_mask': (4, 512), 'random_crop_to_size_seed': (4, 2), 'atom14_atom_exists': (4, 122, 14), 'residx_atom14_to_atom37': (4, 122, 14), 'residx_atom37_to_atom14': (4, 122, 37), 'atom37_atom_exists': (4, 122, 37), 'extra_msa': (4, 1024, 122), 'extra_msa_mask': (4, 1024, 122), 'extra_msa_row_mask': (4, 1024), 'bert_mask': (4, 512, 122), 'true_msa': (4, 512, 122), 'extra_has_deletion': (4, 1024, 122), 'extra_deletion_value': (4, 1024, 122), 'msa_feat': (4, 512, 122, 49), 'target_feat': (4, 122, 22)} I0630 12:32:57.888043 140165856380736 run_docker.py:258] I0630 04:32:57.887455 133109636522624 model.py:175] Output shape was {'distogram': {'bin_edges': (63,), 'logits': (122, 122, 64)}, 'experimentally_resolved': {'logits': (122, 37)}, 'masked_msa': {'logits': (512, 122, 23)}, 'predicted_lddt': {'logits': (122, 50)}, 'structure_module': {'final_atom_mask': (122, 37), 'final_atom_positions': (122, 37, 3)}, 'plddt': (122,), 'ranking_confidence': ()} I0630 12:32:57.888131 140165856380736 run_docker.py:258] I0630 04:32:57.887570 133109636522624 run_alphafold.py:288] Total JAX model model_5_pred_0 on my_antibody predict time (includes compilation time, see --benchmark): 47.8s I0630 12:32:59.009247 140165856380736 run_docker.py:258] I0630 04:32:59.008977 133109636522624 amber_minimize.py:178] alterations info: {'nonstandard_residues': [], 'removed_heterogens': set(), 'missing_residues': {}, 'missing_heavy_atoms': {}, 'missing_terminals': {<Residue 121 (SER) of chain 0>: ['OXT']}, 'Se_in_MET': [], 'removed_chains': {0: []}} I0630 12:32:59.061411 140165856380736 run_docker.py:258] I0630 04:32:59.060884 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 1 of 100. I0630 12:32:59.152712 140165856380736 run_docker.py:258] I0630 04:32:59.152203 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:32:59.306290 140165856380736 run_docker.py:258] I0630 04:32:59.305938 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:32:59.307225 140165856380736 run_docker.py:258] I0630 04:32:59.306909 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 2 of 100. I0630 12:32:59.398853 140165856380736 run_docker.py:258] I0630 04:32:59.398281 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:32:59.553482 140165856380736 run_docker.py:258] I0630 04:32:59.552931 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:32:59.554854 140165856380736 run_docker.py:258] I0630 04:32:59.554430 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 3 of 100. I0630 12:32:59.647076 140165856380736 run_docker.py:258] I0630 04:32:59.646550 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:32:59.801911 140165856380736 run_docker.py:258] I0630 04:32:59.801356 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:32:59.803255 140165856380736 run_docker.py:258] I0630 04:32:59.802931 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 4 of 100. I0630 12:33:00.626900 140165856380736 run_docker.py:258] I0630 04:33:00.626338 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:00.783391 140165856380736 run_docker.py:258] I0630 04:33:00.782771 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:00.784864 140165856380736 run_docker.py:258] I0630 04:33:00.784483 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 5 of 100. I0630 12:33:00.878914 140165856380736 run_docker.py:258] I0630 04:33:00.878278 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:01.034142 140165856380736 run_docker.py:258] I0630 04:33:01.033510 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:01.035675 140165856380736 run_docker.py:258] I0630 04:33:01.035180 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 6 of 100. I0630 12:33:01.127528 140165856380736 run_docker.py:258] I0630 04:33:01.126949 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:01.284192 140165856380736 run_docker.py:258] I0630 04:33:01.283556 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:01.285357 140165856380736 run_docker.py:258] I0630 04:33:01.285058 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 7 of 100. I0630 12:33:01.377079 140165856380736 run_docker.py:258] I0630 04:33:01.376507 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:01.532669 140165856380736 run_docker.py:258] I0630 04:33:01.532121 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:01.533706 140165856380736 run_docker.py:258] I0630 04:33:01.533267 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 8 of 100. I0630 12:33:01.625478 140165856380736 run_docker.py:258] I0630 04:33:01.624895 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:01.781855 140165856380736 run_docker.py:258] I0630 04:33:01.781188 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:01.783256 140165856380736 run_docker.py:258] I0630 04:33:01.782602 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 9 of 100. I0630 12:33:01.876392 140165856380736 run_docker.py:258] I0630 04:33:01.875791 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:02.031495 140165856380736 run_docker.py:258] I0630 04:33:02.030891 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:02.032497 140165856380736 run_docker.py:258] I0630 04:33:02.032057 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 10 of 100. I0630 12:33:02.124000 140165856380736 run_docker.py:258] I0630 04:33:02.123421 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:02.280451 140165856380736 run_docker.py:258] I0630 04:33:02.279947 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:02.281279 140165856380736 run_docker.py:258] I0630 04:33:02.280932 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 11 of 100. I0630 12:33:02.372062 140165856380736 run_docker.py:258] I0630 04:33:02.371413 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:02.527497 140165856380736 run_docker.py:258] I0630 04:33:02.526856 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:02.528245 140165856380736 run_docker.py:258] I0630 04:33:02.527851 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 12 of 100. I0630 12:33:02.618776 140165856380736 run_docker.py:258] I0630 04:33:02.618151 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:02.773318 140165856380736 run_docker.py:258] I0630 04:33:02.772627 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:02.773875 140165856380736 run_docker.py:258] I0630 04:33:02.773437 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 13 of 100. I0630 12:33:02.863324 140165856380736 run_docker.py:258] I0630 04:33:02.862694 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:04.403079 140165856380736 run_docker.py:258] I0630 04:33:04.401817 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:04.404426 140165856380736 run_docker.py:258] I0630 04:33:04.403784 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 14 of 100. I0630 12:33:04.496526 140165856380736 run_docker.py:258] I0630 04:33:04.495868 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:04.648131 140165856380736 run_docker.py:258] I0630 04:33:04.647549 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:04.648512 140165856380736 run_docker.py:258] I0630 04:33:04.648259 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 15 of 100. I0630 12:33:04.737198 140165856380736 run_docker.py:258] I0630 04:33:04.736543 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:04.888443 140165856380736 run_docker.py:258] I0630 04:33:04.887692 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:04.888692 140165856380736 run_docker.py:258] I0630 04:33:04.888430 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 16 of 100. I0630 12:33:04.977293 140165856380736 run_docker.py:258] I0630 04:33:04.976697 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:05.133301 140165856380736 run_docker.py:258] I0630 04:33:05.132572 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:05.133794 140165856380736 run_docker.py:258] I0630 04:33:05.133417 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 17 of 100. I0630 12:33:05.223014 140165856380736 run_docker.py:258] I0630 04:33:05.222356 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:05.377067 140165856380736 run_docker.py:258] I0630 04:33:05.376565 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:05.377328 140165856380736 run_docker.py:258] I0630 04:33:05.377096 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 18 of 100. I0630 12:33:05.465735 140165856380736 run_docker.py:258] I0630 04:33:05.465162 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:05.619338 140165856380736 run_docker.py:258] I0630 04:33:05.618874 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:05.620059 140165856380736 run_docker.py:258] I0630 04:33:05.619789 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 19 of 100. I0630 12:33:05.708222 140165856380736 run_docker.py:258] I0630 04:33:05.707706 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:05.863344 140165856380736 run_docker.py:258] I0630 04:33:05.862727 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:05.864081 140165856380736 run_docker.py:258] I0630 04:33:05.863630 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 20 of 100. I0630 12:33:06.742609 140165856380736 run_docker.py:258] I0630 04:33:06.742092 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:06.896276 140165856380736 run_docker.py:258] I0630 04:33:06.895841 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:06.896701 140165856380736 run_docker.py:258] I0630 04:33:06.896488 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 21 of 100. I0630 12:33:06.987391 140165856380736 run_docker.py:258] I0630 04:33:06.986734 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:07.143651 140165856380736 run_docker.py:258] I0630 04:33:07.143073 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:07.144317 140165856380736 run_docker.py:258] I0630 04:33:07.144083 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 22 of 100. I0630 12:33:07.233405 140165856380736 run_docker.py:258] I0630 04:33:07.232877 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:07.388918 140165856380736 run_docker.py:258] I0630 04:33:07.388276 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:07.389374 140165856380736 run_docker.py:258] I0630 04:33:07.389020 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 23 of 100. I0630 12:33:07.477793 140165856380736 run_docker.py:258] I0630 04:33:07.477229 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:07.634958 140165856380736 run_docker.py:258] I0630 04:33:07.634272 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:07.635119 140165856380736 run_docker.py:258] I0630 04:33:07.634882 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 24 of 100. I0630 12:33:07.722703 140165856380736 run_docker.py:258] I0630 04:33:07.721917 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:07.877725 140165856380736 run_docker.py:258] I0630 04:33:07.877122 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:07.878275 140165856380736 run_docker.py:258] I0630 04:33:07.877899 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 25 of 100. I0630 12:33:07.965848 140165856380736 run_docker.py:258] I0630 04:33:07.965224 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:09.501865 140165856380736 run_docker.py:258] I0630 04:33:09.500586 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:09.503146 140165856380736 run_docker.py:258] I0630 04:33:09.502184 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 26 of 100. I0630 12:33:09.593094 140165856380736 run_docker.py:258] I0630 04:33:09.592452 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:09.749852 140165856380736 run_docker.py:258] I0630 04:33:09.749172 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:09.750274 140165856380736 run_docker.py:258] I0630 04:33:09.749869 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 27 of 100. I0630 12:33:09.837826 140165856380736 run_docker.py:258] I0630 04:33:09.837146 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:09.993509 140165856380736 run_docker.py:258] I0630 04:33:09.993147 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:09.994118 140165856380736 run_docker.py:258] I0630 04:33:09.993818 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 28 of 100. I0630 12:33:10.081269 140165856380736 run_docker.py:258] I0630 04:33:10.080692 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:10.237029 140165856380736 run_docker.py:258] I0630 04:33:10.236296 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:10.237178 140165856380736 run_docker.py:258] I0630 04:33:10.236927 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 29 of 100. I0630 12:33:10.324691 140165856380736 run_docker.py:258] I0630 04:33:10.324046 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:10.515269 140165856380736 run_docker.py:258] I0630 04:33:10.514692 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:10.515648 140165856380736 run_docker.py:258] I0630 04:33:10.515222 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 30 of 100. I0630 12:33:10.602689 140165856380736 run_docker.py:258] I0630 04:33:10.602033 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:10.761917 140165856380736 run_docker.py:258] I0630 04:33:10.761231 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:10.762842 140165856380736 run_docker.py:258] I0630 04:33:10.762274 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 31 of 100. I0630 12:33:10.852550 140165856380736 run_docker.py:258] I0630 04:33:10.852025 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:11.011585 140165856380736 run_docker.py:258] I0630 04:33:11.011016 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:11.011858 140165856380736 run_docker.py:258] I0630 04:33:11.011663 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 32 of 100. I0630 12:33:11.099923 140165856380736 run_docker.py:258] I0630 04:33:11.099307 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:11.259402 140165856380736 run_docker.py:258] I0630 04:33:11.258646 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:11.259658 140165856380736 run_docker.py:258] I0630 04:33:11.259330 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 33 of 100. I0630 12:33:11.349226 140165856380736 run_docker.py:258] I0630 04:33:11.348594 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:11.507418 140165856380736 run_docker.py:258] I0630 04:33:11.506944 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:11.507793 140165856380736 run_docker.py:258] I0630 04:33:11.507447 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 34 of 100. I0630 12:33:11.595523 140165856380736 run_docker.py:258] I0630 04:33:11.594794 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:11.755104 140165856380736 run_docker.py:258] I0630 04:33:11.754662 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:11.755617 140165856380736 run_docker.py:258] I0630 04:33:11.755355 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 35 of 100. I0630 12:33:11.844382 140165856380736 run_docker.py:258] I0630 04:33:11.843786 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:12.003288 140165856380736 run_docker.py:258] I0630 04:33:12.002863 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:12.003747 140165856380736 run_docker.py:258] I0630 04:33:12.003443 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 36 of 100. I0630 12:33:12.882605 140165856380736 run_docker.py:258] I0630 04:33:12.881947 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:13.041629 140165856380736 run_docker.py:258] I0630 04:33:13.041068 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:13.042462 140165856380736 run_docker.py:258] I0630 04:33:13.042010 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 37 of 100. I0630 12:33:13.130999 140165856380736 run_docker.py:258] I0630 04:33:13.130336 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:13.290310 140165856380736 run_docker.py:258] I0630 04:33:13.289800 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:13.290976 140165856380736 run_docker.py:258] I0630 04:33:13.290539 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 38 of 100. I0630 12:33:13.378651 140165856380736 run_docker.py:258] I0630 04:33:13.378093 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:13.539329 140165856380736 run_docker.py:258] I0630 04:33:13.538890 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:13.540220 140165856380736 run_docker.py:258] I0630 04:33:13.539562 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 39 of 100. I0630 12:33:13.627413 140165856380736 run_docker.py:258] I0630 04:33:13.626787 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:13.788333 140165856380736 run_docker.py:258] I0630 04:33:13.787948 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:13.788710 140165856380736 run_docker.py:258] I0630 04:33:13.788518 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 40 of 100. I0630 12:33:13.875749 140165856380736 run_docker.py:258] I0630 04:33:13.875290 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:14.037026 140165856380736 run_docker.py:258] I0630 04:33:14.036414 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:14.037406 140165856380736 run_docker.py:258] I0630 04:33:14.037076 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 41 of 100. I0630 12:33:14.124110 140165856380736 run_docker.py:258] I0630 04:33:14.123733 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:14.287545 140165856380736 run_docker.py:258] I0630 04:33:14.287166 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:14.288222 140165856380736 run_docker.py:258] I0630 04:33:14.287776 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 42 of 100. I0630 12:33:14.374461 140165856380736 run_docker.py:258] I0630 04:33:14.373919 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:14.538391 140165856380736 run_docker.py:258] I0630 04:33:14.537592 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:14.538732 140165856380736 run_docker.py:258] I0630 04:33:14.538254 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 43 of 100. I0630 12:33:14.625112 140165856380736 run_docker.py:258] I0630 04:33:14.624545 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:14.789495 140165856380736 run_docker.py:258] I0630 04:33:14.789053 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:14.789852 140165856380736 run_docker.py:258] I0630 04:33:14.789657 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 44 of 100. I0630 12:33:14.876608 140165856380736 run_docker.py:258] I0630 04:33:14.876067 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:16.340482 140165856380736 run_docker.py:258] I0630 04:33:15.036931 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:16.340620 140165856380736 run_docker.py:258] I0630 04:33:15.037551 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 45 of 100. I0630 12:33:16.340689 140165856380736 run_docker.py:258] I0630 04:33:15.123393 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:16.340752 140165856380736 run_docker.py:258] I0630 04:33:15.285819 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:16.340811 140165856380736 run_docker.py:258] I0630 04:33:15.286358 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 46 of 100. I0630 12:33:16.340869 140165856380736 run_docker.py:258] I0630 04:33:15.372119 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:16.340943 140165856380736 run_docker.py:258] I0630 04:33:15.534050 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:16.341017 140165856380736 run_docker.py:258] I0630 04:33:15.534672 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 47 of 100. I0630 12:33:16.341075 140165856380736 run_docker.py:258] I0630 04:33:15.622317 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:16.341132 140165856380736 run_docker.py:258] I0630 04:33:15.786929 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:16.341190 140165856380736 run_docker.py:258] I0630 04:33:15.787549 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 48 of 100. I0630 12:33:16.341247 140165856380736 run_docker.py:258] I0630 04:33:15.874139 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:16.341303 140165856380736 run_docker.py:258] I0630 04:33:16.038882 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:16.341361 140165856380736 run_docker.py:258] I0630 04:33:16.039502 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 49 of 100. I0630 12:33:16.341418 140165856380736 run_docker.py:258] I0630 04:33:16.126385 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:16.341475 140165856380736 run_docker.py:258] I0630 04:33:16.292575 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:16.341531 140165856380736 run_docker.py:258] I0630 04:33:16.293267 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 50 of 100. I0630 12:33:16.380627 140165856380736 run_docker.py:258] I0630 04:33:16.379971 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:16.563517 140165856380736 run_docker.py:258] I0630 04:33:16.563010 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:16.563852 140165856380736 run_docker.py:258] I0630 04:33:16.563554 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 51 of 100. I0630 12:33:17.404958 140165856380736 run_docker.py:258] I0630 04:33:17.404355 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:17.602005 140165856380736 run_docker.py:258] I0630 04:33:17.601462 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:17.602769 140165856380736 run_docker.py:258] I0630 04:33:17.602343 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 52 of 100. I0630 12:33:17.693159 140165856380736 run_docker.py:258] I0630 04:33:17.692603 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:17.943877 140165856380736 run_docker.py:258] I0630 04:33:17.943305 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:17.944391 140165856380736 run_docker.py:258] I0630 04:33:17.944084 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 53 of 100. I0630 12:33:18.035385 140165856380736 run_docker.py:258] I0630 04:33:18.034827 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:18.428151 140165856380736 run_docker.py:258] I0630 04:33:18.427122 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:18.429005 140165856380736 run_docker.py:258] I0630 04:33:18.428560 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 54 of 100. I0630 12:33:18.527001 140165856380736 run_docker.py:258] I0630 04:33:18.526366 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:18.772514 140165856380736 run_docker.py:258] I0630 04:33:18.771854 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:18.772774 140165856380736 run_docker.py:258] I0630 04:33:18.772447 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 55 of 100. I0630 12:33:18.860598 140165856380736 run_docker.py:258] I0630 04:33:18.860091 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:19.107903 140165856380736 run_docker.py:258] I0630 04:33:19.107378 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:19.108310 140165856380736 run_docker.py:258] I0630 04:33:19.107994 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 56 of 100. I0630 12:33:19.195773 140165856380736 run_docker.py:258] I0630 04:33:19.195193 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:19.395219 140165856380736 run_docker.py:258] I0630 04:33:19.394835 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:19.395541 140165856380736 run_docker.py:258] I0630 04:33:19.395300 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 57 of 100. I0630 12:33:19.483867 140165856380736 run_docker.py:258] I0630 04:33:19.483344 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:19.688328 140165856380736 run_docker.py:258] I0630 04:33:19.687628 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:19.688477 140165856380736 run_docker.py:258] I0630 04:33:19.688208 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 58 of 100. I0630 12:33:19.775359 140165856380736 run_docker.py:258] I0630 04:33:19.774799 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:19.981620 140165856380736 run_docker.py:258] I0630 04:33:19.981119 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:19.981911 140165856380736 run_docker.py:258] I0630 04:33:19.981733 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 59 of 100. I0630 12:33:20.068671 140165856380736 run_docker.py:258] I0630 04:33:20.068003 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:20.272300 140165856380736 run_docker.py:258] I0630 04:33:20.271828 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:20.272835 140165856380736 run_docker.py:258] I0630 04:33:20.272380 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 60 of 100. I0630 12:33:20.358663 140165856380736 run_docker.py:258] I0630 04:33:20.358119 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:20.574970 140165856380736 run_docker.py:258] I0630 04:33:20.574437 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:20.575258 140165856380736 run_docker.py:258] I0630 04:33:20.574914 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 61 of 100. I0630 12:33:20.661504 140165856380736 run_docker.py:258] I0630 04:33:20.660958 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:20.915315 140165856380736 run_docker.py:258] I0630 04:33:20.914574 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:20.915434 140165856380736 run_docker.py:258] I0630 04:33:20.915021 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 62 of 100. I0630 12:33:21.001267 140165856380736 run_docker.py:258] I0630 04:33:21.000741 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:21.236230 140165856380736 run_docker.py:258] I0630 04:33:21.235770 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:21.236506 140165856380736 run_docker.py:258] I0630 04:33:21.236230 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 63 of 100. I0630 12:33:21.322676 140165856380736 run_docker.py:258] I0630 04:33:21.322155 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:21.558003 140165856380736 run_docker.py:258] I0630 04:33:21.557455 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:21.558273 140165856380736 run_docker.py:258] I0630 04:33:21.557971 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 64 of 100. I0630 12:33:21.645992 140165856380736 run_docker.py:258] I0630 04:33:21.645453 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:21.864514 140165856380736 run_docker.py:258] I0630 04:33:21.864014 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:21.864740 140165856380736 run_docker.py:258] I0630 04:33:21.864498 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 65 of 100. I0630 12:33:21.951145 140165856380736 run_docker.py:258] I0630 04:33:21.950547 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:22.156967 140165856380736 run_docker.py:258] I0630 04:33:22.156433 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:22.157410 140165856380736 run_docker.py:258] I0630 04:33:22.157149 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 66 of 100. I0630 12:33:22.246091 140165856380736 run_docker.py:258] I0630 04:33:22.245471 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:22.453392 140165856380736 run_docker.py:258] I0630 04:33:22.452897 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:22.453684 140165856380736 run_docker.py:258] I0630 04:33:22.453441 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 67 of 100. I0630 12:33:23.540164 140165856380736 run_docker.py:258] I0630 04:33:23.539562 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:23.742459 140165856380736 run_docker.py:258] I0630 04:33:23.742080 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:23.743283 140165856380736 run_docker.py:258] I0630 04:33:23.742780 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 68 of 100. I0630 12:33:23.831450 140165856380736 run_docker.py:258] I0630 04:33:23.830911 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:24.033556 140165856380736 run_docker.py:258] I0630 04:33:24.033079 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:24.033882 140165856380736 run_docker.py:258] I0630 04:33:24.033611 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 69 of 100. I0630 12:33:24.123494 140165856380736 run_docker.py:258] I0630 04:33:24.122812 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:24.329952 140165856380736 run_docker.py:258] I0630 04:33:24.329361 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:24.330283 140165856380736 run_docker.py:258] I0630 04:33:24.330014 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 70 of 100. I0630 12:33:24.419495 140165856380736 run_docker.py:258] I0630 04:33:24.418884 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:24.623225 140165856380736 run_docker.py:258] I0630 04:33:24.622747 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:24.623542 140165856380736 run_docker.py:258] I0630 04:33:24.623354 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 71 of 100. I0630 12:33:24.711223 140165856380736 run_docker.py:258] I0630 04:33:24.710671 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:24.922855 140165856380736 run_docker.py:258] I0630 04:33:24.922289 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:24.923271 140165856380736 run_docker.py:258] I0630 04:33:24.922855 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 72 of 100. I0630 12:33:25.010597 140165856380736 run_docker.py:258] I0630 04:33:25.010063 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:25.214588 140165856380736 run_docker.py:258] I0630 04:33:25.214152 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:25.214897 140165856380736 run_docker.py:258] I0630 04:33:25.214725 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 73 of 100. I0630 12:33:25.302039 140165856380736 run_docker.py:258] I0630 04:33:25.301470 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:25.508266 140165856380736 run_docker.py:258] I0630 04:33:25.507651 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:25.508747 140165856380736 run_docker.py:258] I0630 04:33:25.508301 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 74 of 100. I0630 12:33:25.595489 140165856380736 run_docker.py:258] I0630 04:33:25.594795 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:25.800973 140165856380736 run_docker.py:258] I0630 04:33:25.800356 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:25.801096 140165856380736 run_docker.py:258] I0630 04:33:25.800813 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 75 of 100. I0630 12:33:25.933776 140165856380736 run_docker.py:258] I0630 04:33:25.933199 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:26.178470 140165856380736 run_docker.py:258] I0630 04:33:26.177976 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:26.178870 140165856380736 run_docker.py:258] I0630 04:33:26.178549 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 76 of 100. I0630 12:33:26.271264 140165856380736 run_docker.py:258] I0630 04:33:26.270624 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:26.493915 140165856380736 run_docker.py:258] I0630 04:33:26.493336 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:26.494331 140165856380736 run_docker.py:258] I0630 04:33:26.493954 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 77 of 100. I0630 12:33:26.580338 140165856380736 run_docker.py:258] I0630 04:33:26.579793 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:26.788237 140165856380736 run_docker.py:258] I0630 04:33:26.787625 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:26.788497 140165856380736 run_docker.py:258] I0630 04:33:26.788245 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 78 of 100. I0630 12:33:26.874225 140165856380736 run_docker.py:258] I0630 04:33:26.873585 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:27.082340 140165856380736 run_docker.py:258] I0630 04:33:27.081812 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:27.082561 140165856380736 run_docker.py:258] I0630 04:33:27.082271 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 79 of 100. I0630 12:33:27.168160 140165856380736 run_docker.py:258] I0630 04:33:27.167581 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:27.376721 140165856380736 run_docker.py:258] I0630 04:33:27.376213 133109636522624 amber_minimize.py:418] Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) I0630 12:33:27.376967 140165856380736 run_docker.py:258] I0630 04:33:27.376734 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 80 of 100. I0630 12:33:27.462772 140165856380736 run_docker.py:258] I0630 04:33:27.462107 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:27.531257 140165856380736 run_docker.py:258] I0630 04:33:27.530839 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:27.531699 140165856380736 run_docker.py:258] I0630 04:33:27.531400 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 81 of 100. I0630 12:33:27.616890 140165856380736 run_docker.py:258] I0630 04:33:27.616321 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:27.671317 140165856380736 run_docker.py:258] I0630 04:33:27.670797 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:27.671777 140165856380736 run_docker.py:258] I0630 04:33:27.671558 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 82 of 100. I0630 12:33:27.758620 140165856380736 run_docker.py:258] I0630 04:33:27.758213 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:27.814028 140165856380736 run_docker.py:258] I0630 04:33:27.813527 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:27.814634 140165856380736 run_docker.py:258] I0630 04:33:27.814345 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 83 of 100. I0630 12:33:28.683356 140165856380736 run_docker.py:258] I0630 04:33:28.682796 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.131273 140165856380736 run_docker.py:258] I0630 04:33:28.736963 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.131398 140165856380736 run_docker.py:258] I0630 04:33:28.737648 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 84 of 100. I0630 12:33:30.131457 140165856380736 run_docker.py:258] I0630 04:33:28.824766 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.131729 140165856380736 run_docker.py:258] I0630 04:33:28.880052 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.131806 140165856380736 run_docker.py:258] I0630 04:33:28.880649 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 85 of 100. I0630 12:33:30.131864 140165856380736 run_docker.py:258] I0630 04:33:28.970029 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.131916 140165856380736 run_docker.py:258] I0630 04:33:29.024402 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.131967 140165856380736 run_docker.py:258] I0630 04:33:29.024868 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 86 of 100. I0630 12:33:30.132031 140165856380736 run_docker.py:258] I0630 04:33:29.113197 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.132083 140165856380736 run_docker.py:258] I0630 04:33:29.167054 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.132133 140165856380736 run_docker.py:258] I0630 04:33:29.167627 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 87 of 100. I0630 12:33:30.132183 140165856380736 run_docker.py:258] I0630 04:33:29.255089 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.132232 140165856380736 run_docker.py:258] I0630 04:33:29.309079 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.132282 140165856380736 run_docker.py:258] I0630 04:33:29.309674 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 88 of 100. I0630 12:33:30.132332 140165856380736 run_docker.py:258] I0630 04:33:29.396072 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.132381 140165856380736 run_docker.py:258] I0630 04:33:29.448614 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.132430 140165856380736 run_docker.py:258] I0630 04:33:29.449223 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 89 of 100. I0630 12:33:30.132478 140165856380736 run_docker.py:258] I0630 04:33:29.535326 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.132528 140165856380736 run_docker.py:258] I0630 04:33:29.588721 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.132577 140165856380736 run_docker.py:258] I0630 04:33:29.589329 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 90 of 100. I0630 12:33:30.132625 140165856380736 run_docker.py:258] I0630 04:33:29.675157 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.132674 140165856380736 run_docker.py:258] I0630 04:33:29.728785 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.132725 140165856380736 run_docker.py:258] I0630 04:33:29.729245 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 91 of 100. I0630 12:33:30.132774 140165856380736 run_docker.py:258] I0630 04:33:29.815330 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.132824 140165856380736 run_docker.py:258] I0630 04:33:29.868527 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.132874 140165856380736 run_docker.py:258] I0630 04:33:29.868963 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 92 of 100. I0630 12:33:30.132924 140165856380736 run_docker.py:258] I0630 04:33:29.954258 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.132973 140165856380736 run_docker.py:258] I0630 04:33:30.011013 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.133032 140165856380736 run_docker.py:258] I0630 04:33:30.011528 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 93 of 100. I0630 12:33:30.133082 140165856380736 run_docker.py:258] I0630 04:33:30.096674 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.149953 140165856380736 run_docker.py:258] I0630 04:33:30.149527 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.150328 140165856380736 run_docker.py:258] I0630 04:33:30.150091 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 94 of 100. I0630 12:33:30.235997 140165856380736 run_docker.py:258] I0630 04:33:30.235446 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.289496 140165856380736 run_docker.py:258] I0630 04:33:30.289113 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.289698 140165856380736 run_docker.py:258] I0630 04:33:30.289543 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 95 of 100. I0630 12:33:30.376277 140165856380736 run_docker.py:258] I0630 04:33:30.375646 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.430535 140165856380736 run_docker.py:258] I0630 04:33:30.429925 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.430897 140165856380736 run_docker.py:258] I0630 04:33:30.430696 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 96 of 100. I0630 12:33:30.518128 140165856380736 run_docker.py:258] I0630 04:33:30.517550 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.572203 140165856380736 run_docker.py:258] I0630 04:33:30.571747 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.572522 140165856380736 run_docker.py:258] I0630 04:33:30.572304 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 97 of 100. I0630 12:33:30.658429 140165856380736 run_docker.py:258] I0630 04:33:30.657889 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.711863 140165856380736 run_docker.py:258] I0630 04:33:30.711441 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.712269 140165856380736 run_docker.py:258] I0630 04:33:30.711985 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 98 of 100. I0630 12:33:30.799564 140165856380736 run_docker.py:258] I0630 04:33:30.799000 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:30.853374 140165856380736 run_docker.py:258] I0630 04:33:30.852829 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:30.853630 140165856380736 run_docker.py:258] I0630 04:33:30.853340 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 99 of 100. I0630 12:33:31.719885 140165856380736 run_docker.py:258] I0630 04:33:31.719331 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:31.774508 140165856380736 run_docker.py:258] I0630 04:33:31.774141 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:31.774895 140165856380736 run_docker.py:258] I0630 04:33:31.774754 133109636522624 amber_minimize.py:408] Minimizing protein, attempt 100 of 100. I0630 12:33:31.863306 140165856380736 run_docker.py:258] I0630 04:33:31.862664 133109636522624 amber_minimize.py:69] Restraining 941 / 1852 particles. I0630 12:33:31.919448 140165856380736 run_docker.py:258] I0630 04:33:31.918951 133109636522624 amber_minimize.py:418] No compatible CUDA device is available I0630 12:33:31.919794 140165856380736 run_docker.py:258] Traceback (most recent call last): I0630 12:33:31.919901 140165856380736 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 570, in I0630 12:33:31.960604 140165856380736 run_docker.py:258] app.run(main) I0630 12:33:31.961039 140165856380736 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/absl/app.py", line 312, in run I0630 12:33:31.963929 140165856380736 run_docker.py:258] _run_main(main, args) I0630 12:33:31.964291 140165856380736 run_docker.py:258] File "/opt/conda/lib/python3.11/site-packages/absl/app.py", line 258, in _run_main I0630 12:33:31.964454 140165856380736 run_docker.py:258] sys.exit(main(argv)) I0630 12:33:31.964594 140165856380736 run_docker.py:258] ^^^^^^^^^^ I0630 12:33:31.964766 140165856380736 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 543, in main I0630 12:33:31.964901 140165856380736 run_docker.py:258] predict_structure( I0630 12:33:31.965281 140165856380736 run_docker.py:258] File "/app/alphafold/run_alphafold.py", line 361, in predict_structure I0630 12:33:31.965631 140165856380736 run_docker.py:258] relaxed_pdbstr, , violations = amber_relaxer.process( I0630 12:33:31.965737 140165856380736 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^ I0630 12:33:31.965818 140165856380736 run_docker.py:258] File "/app/alphafold/alphafold/relax/relax.py", line 62, in process I0630 12:33:31.966922 140165856380736 run_docker.py:258] out = amber_minimize.run_pipeline( I0630 12:33:31.967203 140165856380736 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ I0630 12:33:31.967347 140165856380736 run_docker.py:258] File "/app/alphafold/alphafold/relax/amber_minimize.py", line 476, in run_pipeline I0630 12:33:31.967509 140165856380736 run_docker.py:258] ret = _run_one_iteration( I0630 12:33:31.967633 140165856380736 run_docker.py:258] ^^^^^^^^^^^^^^^^^^^ I0630 12:33:31.967745 140165856380736 run_docker.py:258] File "/app/alphafold/alphafold/relax/amber_minimize.py", line 420, in _run_one_iteration I0630 12:33:31.967856 140165856380736 run_docker.py:258] raise ValueError(f"Minimization failed after {max_attempts} attempts.") I0630 12:33:31.967965 140165856380736 run_docker.py:258] ValueError: Minimization failed after 100 attempts.

zcswnm commented 1 week ago

ubuntu 24.04

python3 /home/zcs/alphafold-main/docker/run_docker.py --fasta_paths=my_antibody.fasta --max_template_date=2024-01-01 --model_preset=monomer --db_preset=reduced_dbs --data_dir=/home/zcs/database --output_dir=/home/zcs/pymol/alphafoldjob

zcswnm commented 4 days ago

--enable_gpu_relax=false Adding this flag will prevent errors during execution, it might be an issue with Amber calling the GPU.