File size: 14,524 Bytes
72c6b08 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 |
[Errno 2] No such file or directory: '/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/release_data/ccd_cache/components.v20240608.cif':
Traceback (most recent call last):
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/infer_data_pipeline.py", line 211, in __getitem__
data, atom_array, _ = self.process_one(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/infer_data_pipeline.py", line 101, in process_one
sample2feat = SampleDictToFeatures(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_to_feature.py", line 34, in __init__
self.input_dict = add_entity_atom_array(single_sample_dict)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_parser.py", line 605, in add_entity_atom_array
atom_info = build_polymer(entity_info)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_parser.py", line 345, in build_polymer
chain_array = _build_polymer_atom_array(ccd_seqs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/json_parser.py", line 290, in _build_polymer_atom_array
residue = ccd.get_component_atom_array(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/ccd.py", line 88, in get_component_atom_array
ccd_cif = biotite_load_ccd_cif()
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/data/ccd.py", line 45, in biotite_load_ccd_cif
return pdbx.CIFFile.read(COMPONENTS_FILE)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/biotite/structure/io/pdbx/cif.py", line 844, in read
with open(file, "r") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/release_data/ccd_cache/components.v20240608.cif'
[Rank 0]7r6r Protenix.get_pairformer_output() missing 1 required positional argument: 'pairformer_stack':
Traceback (most recent call last):
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 260, in infer_predict
prediction, label_dict = runner.predict(data)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 156, in predict
prediction, label_dict, _ = self.model(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 865, in forward
pred_dict, label_dict, log_dict, time_tracker = self.main_inference_loop(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 339, in main_inference_loop
pred_dict, log_dict, time_tracker = self._main_inference_loop(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 401, in _main_inference_loop
s_inputs, s, z = self.get_pairformer_output(
TypeError: Protenix.get_pairformer_output() missing 1 required positional argument: 'pairformer_stack'
[Rank 0]7r6r [Errno 28] No space left on device: '/n/home09/zaixizhang/.cache/torch_extensions/py310_cu121/evoformer_attn/lock':
Traceback (most recent call last):
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 260, in infer_predict
prediction, label_dict = runner.predict(data)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 156, in predict
prediction, label_dict, _ = self.model(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 866, in forward
pred_dict, label_dict, log_dict, time_tracker = self.main_inference_loop(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 339, in main_inference_loop
pred_dict, log_dict, time_tracker = self._main_inference_loop(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 401, in _main_inference_loop
s_inputs, s, z = self.get_pairformer_output(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 202, in get_pairformer_output
z = self.msa_module(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/modules/pairformer.py", line 732, in forward
msa_sample, z = checkpoint_blocks(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/utils/checkpointing.py", line 85, in checkpoint_blocks
return exec(blocks, args)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/utils/checkpointing.py", line 72, in exec
a = wrap(block(*a))
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/modules/pairformer.py", line 517, in forward
_, z = self.pair_stack(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/modules/pairformer.py", line 132, in forward
z += self.tri_att_start(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/model/triangular_attention.py", line 129, in forward
x = self._chunk(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/model/triangular_attention.py", line 74, in _chunk
return chunk_layer(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/utils/chunk_utils.py", line 285, in chunk_layer
output_chunk = layer(**chunks)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/model/primitives.py", line 560, in forward
o = _deepspeed_evo_attn(q, k, v, biases)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/openfold_local/model/primitives.py", line 730, in _deepspeed_evo_attn
o = DS4Sci_EvoformerAttention(q, k, v, biases)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/deepspeed4science/evoformer_attn.py", line 106, in DS4Sci_EvoformerAttention
return EvoformerFusedAttention.apply(Q, K, V, biases[0], biases[1])
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/autograd/function.py", line 598, in apply
return super().apply(*args, **kwargs) # type: ignore[misc]
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/deepspeed4science/evoformer_attn.py", line 71, in forward
o, lse = _attention(q, k, v, bias1_, bias2_)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/deepspeed4science/evoformer_attn.py", line 24, in _attention
kernel_ = EvoformerAttnBuilder().load()
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/op_builder/builder.py", line 508, in load
return self.jit_load(verbose)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/deepspeed/ops/op_builder/builder.py", line 555, in jit_load
op_module = load(name=self.name,
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1309, in load
return _jit_compile(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1696, in _jit_compile
if baton.try_acquire():
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/file_baton.py", line 29, in try_acquire
self.fd = os.open(self.lock_file_path, os.O_CREAT | os.O_EXCL)
OSError: [Errno 28] No space left on device: '/n/home09/zaixizhang/.cache/torch_extensions/py310_cu121/evoformer_attn/lock'
[Rank 0]7r6r 'profile':
Traceback (most recent call last):
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 260, in infer_predict
prediction, label_dict = runner.predict(data)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 156, in predict
prediction, label_dict, _ = self.model(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 866, in forward
pred_dict, label_dict, log_dict, time_tracker = self.main_inference_loop(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 339, in main_inference_loop
pred_dict, log_dict, time_tracker = self._main_inference_loop(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 523, in _main_inference_loop
s_inputs_clean, s_clean, z_clean = self.get_pairformer_output(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 159, in get_pairformer_output
s_inputs = self.input_embedder(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/modules/embedders.py", line 81, in forward
+ [
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/modules/embedders.py", line 82, in <listcomp>
input_feature_dict[name].reshape(*batch_shape, d)
KeyError: 'profile'
[Rank 0]7r6r too many values to unpack (expected 3):
Traceback (most recent call last):
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 260, in infer_predict
prediction, label_dict = runner.predict(data)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/runner/inference.py", line 156, in predict
prediction, label_dict, _ = self.model(
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1532, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/n/home09/zaixizhang/miniconda3/envs/pro_new/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1541, in _call_impl
return forward_call(*args, **kwargs)
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 867, in forward
pred_dict, label_dict, log_dict, time_tracker = self.main_inference_loop(
File "/n/holylabs/LABS/mzitnik_lab/Users/zaixizhang/Protenix_new/protenix/model/protenix_edit.py", line 339, in main_inference_loop
pred_dict, log_dict, time_tracker = self._main_inference_loop(
ValueError: too many values to unpack (expected 3)
|