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agemagician / ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
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Error downloading pre-trained model (prot_t5_xl_uniref50) #85

Closed zengzishuo closed 2 years ago

zengzishuo commented 2 years ago

Hi,

In ProtTrans/Embedding/TensorFlow/Advanced/ProtT5-XL-UniRef50.ipynb

The command

model = TFT5EncoderModel.from_pretrained("Rostlab/prot_t5_xl_uniref50", from_pt=True)

gives me the following error and I have no clue how to fix it, please help. Thanks in advance!

Traceback (most recent call last): File "", line 1, in File "/Users/zishuozeng/tf_env/lib/python3.8/site-packages/transformers/modeling_tf_utils.py", line 844, in from_pretrained return load_pytorch_checkpoint_in_tf2_model(model, resolved_archive_file, allow_missing_keys=True) File "/Users/zishuozeng/tf_env/lib/python3.8/site-packages/transformers/modeling_tf_pytorch_utils.py", line 93, in load_pytorch_checkpoint_in_tf2_model pt_state_dict = torch.load(pt_path, map_location="cpu") File "/Users/zishuozeng/tf_env/lib/python3.8/site-packages/torch/serialization.py", line 527, in load with _open_zipfile_reader(f) as opened_zipfile: File "/Users/zishuozeng/tf_env/lib/python3.8/site-packages/torch/serialization.py", line 224, in init super(_open_zipfile_reader, self).init(torch._C.PyTorchFileReader(name_or_buffer)) RuntimeError: [enforce fail at inline_container.cc:143] . PytorchStreamReader failed reading zip archive: failed finding central directory frame #0: c10::ThrowEnforceNotMet(char const, int, char const, std::1::basic_string<char, std::__1::char_traits, std::1::allocator > const&, void const) + 191 (0x11077c0ff in libc10.dylib) frame #1: caffe2::serialize::PyTorchStreamReader::valid(char const, char const) + 115 (0x17a0c0b83 in libtorch.dylib) frame #2: caffe2::serialize::PyTorchStreamReader::init() + 315 (0x17a0bf95b in libtorch.dylib) frame #3: caffe2::serialize::PyTorchStreamReader::PyTorchStreamReader(std::1::basic_string<char, std::__1::char_traits, std::1::allocator > const&) + 143 (0x17a0bf79f in libtorch.dylib) frame #4: void pybind11::cpp_function::initialize<void pybind11::detail::initimpl::constructor<std::1::basic_string<char, std::__1::char_traits, std::1::allocator > >::execute<pybind11::class, 0>(pybind11::class&)::'lambda'(pybind11::detail::value_and_holder&, std::1::basic_string<char, std::__1::char_traits, std::1::allocator >), void, pybind11::detail::value_and_holder&, std::1::basic_string<char, std::__1::char_traits, std::1::allocator >, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_styleconstructor>(pybind11::class&&, void ()(pybind11::detail::value_and_holder&, std::1::basic_string<char, std::__1::char_traits, std::1::allocator >), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::detail::is_new_style_constructor const&)::'lambda'(pybind11::detail::function_call&)::operator()(pybind11::detail::function_call&) const + 147 (0x169c307c3 in libtorch_python.dylib) frame #5: pybind11::cpp_function::dispatcher(_object, _object, _object*) + 3382 (0x169628e66 in libtorch_python.dylib) frame #6: cfunction_call_varargs + 122 (0x1043c201a in python3.8) frame #7: _PyObject_MakeTpCall + 374 (0x1043c1a56 in python3.8) frame #8: method_vectorcall + 490 (0x1043c50aa in python3.8) frame #9: PyVectorcall_Call + 108 (0x1043c1dac in python3.8) frame #10: slot_tp_init + 319 (0x10441d53f in python3.8) frame #11: type_call + 292 (0x104418674 in python3.8) frame #12: _PyObject_MakeTpCall + 374 (0x1043c1a56 in python3.8) frame #13: call_function + 652 (0x1044a7b2c in python3.8) frame #14: _PyEval_EvalFrameDefault + 30253 (0x1044a422d in python3.8) frame #15: _PyEval_EvalCodeWithName + 3459 (0x1044a8b93 in python3.8) frame #16: _PyFunction_Vectorcall + 254 (0x1043c259e in python3.8) frame #17: _PyObject_FastCallDict + 268 (0x1043c18ac in python3.8) frame #18: _PyObject_Call_Prepend + 131 (0x1043c2fc3 in python3.8) frame #19: slot_tp_init + 180 (0x10441d4b4 in python3.8) frame #20: type_call + 292 (0x104418674 in python3.8) frame #21: _PyObject_MakeTpCall + 374 (0x1043c1a56 in python3.8) frame #22: call_function + 652 (0x1044a7b2c in python3.8) frame #23: _PyEval_EvalFrameDefault + 30422 (0x1044a42d6 in python3.8) frame #24: _PyEval_EvalCodeWithName + 3459 (0x1044a8b93 in python3.8) frame #25: _PyFunction_Vectorcall + 254 (0x1043c259e in python3.8) frame #26: call_function + 354 (0x1044a7a02 in python3.8) frame #27: _PyEval_EvalFrameDefault + 30610 (0x1044a4392 in python3.8) frame #28: _PyEval_EvalCodeWithName + 3459 (0x1044a8b93 in python3.8) frame #29: _PyFunction_Vectorcall + 254 (0x1043c259e in python3.8) frame #30: call_function + 354 (0x1044a7a02 in python3.8) frame #31: _PyEval_EvalFrameDefault + 30610 (0x1044a4392 in python3.8) frame #32: _PyEval_EvalCodeWithName + 3459 (0x1044a8b93 in python3.8) frame #33: _PyFunction_Vectorcall + 254 (0x1043c259e in python3.8) frame #34: method_vectorcall + 171 (0x1043c4f6b in python3.8) frame #35: call_function + 354 (0x1044a7a02 in python3.8) frame #36: _PyEval_EvalFrameDefault + 30610 (0x1044a4392 in python3.8) frame #37: _PyEval_EvalCodeWithName + 3459 (0x1044a8b93 in python3.8) frame #38: PyEval_EvalCode + 48 (0x10449cb60 in python3.8) frame #39: PyRun_InteractiveOneObjectEx + 689 (0x1044ef281 in python3.8) frame #40: PyRun_InteractiveLoopFlags + 169 (0x1044ee949 in python3.8) frame #41: PyRun_AnyFileExFlags + 60 (0x1044ee86c in python3.8) frame #42: Py_RunMain + 2640 (0x10450e970 in python3.8) frame #43: pymain_main + 406 (0x10450ed56 in python3.8) frame #44: Py_BytesMain + 43 (0x10450edab in python3.8) frame #45: start + 462 (0x20498452e in dyld) frame #46: 0x0 + 3 (0x3 in ???)

mheinzinger commented 2 years ago

I can not reproduce your error on my end. I have transformers=4.17.0, torch=1.10, python=3.7.9, cuda=11.6