Schreenshot of the error message
I'm trying to run Alphafold on Google runtime, and I'm getting this error:
UnfilteredStackTrace Traceback (most recent call last)
<ipython-input-5-ca4ee2dc266d> in <module>
44 processed_feature_dict = model_runner.process_features(np_example, random_seed=0)
---> 45 prediction = model_runner.predict(processed_feature_dict, random_seed=random.randrange(sys.maxsize))
46
UnfilteredStackTrace: AttributeError: 'Config' object has no attribute 'jax_experimental_name_stack'
The stack trace below excludes JAX-internal frames.
The preceding is the original exception that occurred, unmodified.
--------------------
The above exception was the direct cause of the following exception:
AttributeError Traceback (most recent call last)
/opt/conda/lib/python3.7/site-packages/haiku/_src/module.py in wrapped(self, *args, **kwargs)
406 f = functools.partial(unbound_method, self)
407 f = functools.partial(run_interceptors, f, method_name, self)
--> 408 if jax.config.jax_experimental_name_stack and module_name:
409 local_module_name = module_name.split("/")[-1]
410 f = jax.named_call(f, name=local_module_name)
AttributeError: 'Config' object has no attribute 'jax_experimental_name_stack'
How do I resolve this error? The link for Alphafold is below.
https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb
Related
This error is shown when I run
config = config_util.get_configs_from_pipeline_file(CONFIG_PATH):
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-41-efc7822bb0d7> in <module>
----> 1 config = config_util.get_configs_from_pipeline_file(CONFIG_PATH)
~\anaconda3\lib\site-packages\object_detection\utils\config_util.py in get_configs_from_pipeline_file(pipeline_config_path, config_override)
92 """
93 pipeline_config = pipeline_pb2.TrainEvalPipelineConfig()
---> 94 with tf.io.gfile.GFile(pipeline_config_path, "r") as f:
95 proto_str = f.read()
96 text_format.Merge(proto_str, pipeline_config)
AttributeError: module 'tensorflow' has no attribute 'gfile'
I have a dataset (Kvasir data set) with several files that contains the features extraction in the format:
JCD:3.0,3.5,6.0...
Tamura:3.608455882352941,6.681779104634786,632.0,130.0...
ColorLayout:11.0,25.0,9.0,4.0,16.0...
EdgeHistogram:0.0,0.0,4.0,0.0,1.0,1.0,4.0...
AutoColorCorrelogram:13.0,13.0,12.0,12.0,13.0,13.0,12.0...
I'm trying to load all the features files with this code:
dat=sklearn.datasets.load_files("/MTU/Q3/kvasir-dataset-v2-features")
df=pd.DataFrame(data=dat.data,columns=dat.feature_names)
but I get this error:
KeyError Traceback (most recent call last)
C:\Python310\lib\site-packages\sklearn\utils\__init__.py in __getattr__(self, key)
116 try:
--> 117 return self[key]
118 except KeyError:
KeyError: 'feature_names'
During handling of the above exception, another exception occurred:
AttributeError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_22320/2380416560.py in <module>
----> 1 df=pd.DataFrame(data=dat.data,columns=dat.feature_names)
C:\Python310\lib\site-packages\sklearn\utils\__init__.py in __getattr__(self, key)
117 return self[key]
118 except KeyError:
--> 119 raise AttributeError(key)
120
121 def __setstate__(self, state):
AttributeError: feature_names
AttributeError Traceback (most recent call last)
C:\Users\BAMIGB~1\AppData\Local\Temp/ipykernel_15512/4291769960.py in <module>
----> 1 data = pd.read_xlsx ('HRDataset_v14 ().xlsx')
2 data
~\Anaconda3\lib\site-packages\pandas\__init__.py in __getattr__(name)
242 return _SparseArray
243
--> 244 raise AttributeError(f"module 'pandas' has no attribute '{name}'")
245
246
AttributeError: module 'pandas' has no attribute 'read_xlsx'
Instead of this [ data = pd.read_xlsx ('HRDataset_v14 ().xlsx') ] use
data = pd.read_excel ('filename.xlsx')
I'm using spaCy 2.0.18. I have trained a model using GPU but now I want to load this model for the predictions and run on CPU only.
I am able to load the model into memory but once I try to use it I get the following error:
import spacy
nlp = spacy.load("path_to_my_model")
# works fine up to this moment
result = nlp("Test") # throws the exception below:
Exception ignored in: <bound method Stream.__del__ of <cupy.cuda.stream.Stream object at 0x7fd288621be0>>
Traceback (most recent call last):
File "cupy/cuda/stream.pyx", line 161, in cupy.cuda.stream.Stream.__del__
AttributeError: 'Stream' object has no attribute 'ptr'
---------------------------------------------------------------------------
CUDARuntimeError Traceback (most recent call last)
<ipython-input-4-306c96b208c5> in <module>
----> 1 nlp("Yolo")
/opt/anaconda3/lib/python3.7/site-packages/spacy/language.py in __call__(self, text, disable)
344 if not hasattr(proc, '__call__'):
345 raise ValueError(Errors.E003.format(component=type(proc), name=name))
--> 346 doc = proc(doc)
347 if doc is None:
348 raise ValueError(Errors.E005.format(name=name))
nn_parser.pyx in spacy.syntax.nn_parser.Parser.__call__()
nn_parser.pyx in spacy.syntax.nn_parser.Parser.parse_batch()
/opt/anaconda3/lib/python3.7/site-packages/spacy/util.py in get_cuda_stream(require)
236
237 def get_cuda_stream(require=False):
--> 238 return CudaStream() if CudaStream is not None else None
239
240
cupy/cuda/stream.pyx in cupy.cuda.stream.Stream.__init__()
cupy/cuda/runtime.pyx in cupy.cuda.runtime.streamCreate()
cupy/cuda/runtime.pyx in cupy.cuda.runtime.streamCreate()
cupy/cuda/runtime.pyx in cupy.cuda.runtime.check_status()
CUDARuntimeError: cudaErrorNoDevice: no CUDA-capable device is detected
How to force spaCy to use CPU instead of GPU?
I'm a little confused. I'm working on a Python project where I load a resource file, read it as tsv and transform it into a dictionary with pattern objects as key for later usage. To load the file, so far I've used the pkg_resources package from setuptools. It basically looks like this:
from csv import DictReader
from pkg_resources import resource_string
def make_dict():
"""Make global dictionary."""
global event_dict
dictlines = [l.decode('utf8') for l in resource_string(
'pkgname.resources.tsv', 'event_dict.tsv').splitlines()]
reader = DictReader(dictlines, dialect='excel-tab')
for row in reader:
event = re.compile(r'\b{}\b'.format(re.escape(row['word'])))
classes = string_to_list(row['id'])
event_dict[event] = classes
So far, it worked well. However, once I started calling the module from another module, following error appeared:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
C:\Python\Python36\lib\site-packages\pkg_resources\__init__.py in get_provider(moduleOrReq)
430 try:
--> 431 module = sys.modules[moduleOrReq]
432 except KeyError:
KeyError: 'pkgname.resources.tsv'
During handling of the above exception, another exception occurred:
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-22-efa35954c76f> in <module>()
----> 1 make_event_dict()
<ipython-input-21-b318bc78e8fd> in make_event_dict()
4 global event_dict
5 dictlines = [l.decode('utf8') for l in resource_string(
----> 6 'pkgname.resources.tsv', 'event_classes_dict.tsv').splitlines()]
7 reader = DictReader(dictlines, dialect='excel-tab')
8 for row in reader:
C:\Python\Python36\lib\site-packages\pkg_resources\__init__.py in resource_string(self, package_or_requirement, resource_name)
1215 def resource_string(self, package_or_requirement, resource_name):
1216 """Return specified resource as a string"""
-> 1217 return get_provider(package_or_requirement).get_resource_string(
1218 self, resource_name
1219 )
C:\Python\Python36\lib\site-packages\pkg_resources\__init__.py in get_provider(moduleOrReq)
431 module = sys.modules[moduleOrReq]
432 except KeyError:
--> 433 __import__(moduleOrReq)
434 module = sys.modules[moduleOrReq]
435 loader = getattr(module, '__loader__', None)
ModuleNotFoundError: No module named 'pkgname'
Now I'm guessing something's wrong with my project setup, so this is what it's structured like:
|Pkg\
|----setup.py
|----pkg\
|--------__init__.py
|--------events.py
|--------resources\
|------------__init__.py
|------------tsv\
|----------------__init__.py
|----------------event_dict.tsv
What could be wrong? Not exactly sure if the __init__.py in the subfolders are needed, btw.