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typing_extensions issue

Open Khyati-Microcrispr opened this issue 1 year ago • 1 comments

Hi, I followed this set up conda create -n tf2.3 python=3.7 conda activate tf2.3 conda install -c conda-forge cudatoolkit=10.1 cudnn=7.6 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/ then installed the requirements sucessfully but while running AIONER, I am getting this error. Please help resolving this issue as soon as possible. Thank you for this advance tool

AIONER-main$ python src/AIONER_Run.py -i ../example/input/ -m ../pretrained_models/AIONER/Bioformer-softmax-AIONER.h5 -v ../vocab/AIO_label.vocab -e ALL -o ../example/output/ 2024-05-31 16:20:56.266464: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcudart.so.10.1 2024-05-31 16:20:58.052726: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcuda.so.1 2024-05-31 16:20:58.093898: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1716] Found device 0 with properties: pciBusID: 0000:31:00.0 name: NVIDIA GeForce RTX 4090 computeCapability: 8.9 coreClock: 2.52GHz coreCount: 128 deviceMemorySize: 23.64GiB deviceMemoryBandwidth: 938.86GiB/s 2024-05-31 16:20:58.093962: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcudart.so.10.1 2024-05-31 16:20:58.096369: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcublas.so.10 2024-05-31 16:20:58.098784: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcufft.so.10 2024-05-31 16:20:58.099218: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcurand.so.10 2024-05-31 16:20:58.101683: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcusolver.so.10 2024-05-31 16:20:58.102992: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcusparse.so.10 2024-05-31 16:20:58.108054: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcudnn.so.7 2024-05-31 16:20:58.108705: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1858] Adding visible gpu devices: 0 Num GPUs Available: 1 Traceback (most recent call last): File "src/AIONER_Run.py", line 27, in import stanza File "/home/khyati/anaconda3/envs/tf2.3/lib/python3.7/site-packages/stanza/init.py", line 1, in from stanza.pipeline.core import Pipeline File "/home/khyati/anaconda3/envs/tf2.3/lib/python3.7/site-packages/stanza/pipeline/core.py", line 20, in from stanza.pipeline.langid_processor import LangIDProcessor File "/home/khyati/anaconda3/envs/tf2.3/lib/python3.7/site-packages/stanza/pipeline/langid_processor.py", line 5, in import emoji File "/home/khyati/anaconda3/envs/tf2.3/lib/python3.7/site-packages/emoji/init.py", line 47, in from emoji.core import * File "/home/khyati/anaconda3/envs/tf2.3/lib/python3.7/site-packages/emoji/core.py", line 12, in from typing_extensions import Literal, Match, TypedDict ImportError: cannot import name 'Match' from 'typing_extensions' (/home/khyati/anaconda3/envs/tf2.3/lib/python3.7/site-packages/typing_extensions.py)

Khyati-Microcrispr avatar May 31 '24 10:05 Khyati-Microcrispr

Hi, this issue is likely due to an incompatibility between the versions of the emoji and typing_extensions libraries installed in your environment, but not AIONER. Could you list the versions of the libraries in your environment?

lingluodlut avatar Jun 12 '24 00:06 lingluodlut

python = 3.7 absl-py==2.1.0 AmberUtils==21.0 astunparse==1.6.3 attrs==24.2.0 backcall==0.2.0 bioc==2.0.post4 blis==0.7.11 cachetools==5.5.0 catalogue==2.0.10 certifi @ file:///croot/certifi_1671487769961/work/certifi charset-normalizer==3.4.0 click==8.0.4 cycler==0.11.0 cymem==2.0.8 debugpy==1.7.0 decorator==5.1.1 edgembar==3.0 emoji==2.12.0 entrypoints==0.4 filelock==3.12.2 flatbuffers==24.3.25 fonttools==4.38.0 fsspec==2023.1.0 gast==0.3.3 google-auth==2.36.0 google-auth-oauthlib==0.4.6 google-pasta==0.2.0 grpcio==1.62.3 h5py==2.10.0 huggingface-hub==0.16.4 idna==3.10 importlib-metadata==6.7.0 intervaltree==3.1.0 ipykernel==6.16.2 ipython==7.34.0 jedi==0.19.2 Jinja2==3.1.4 joblib==1.3.2 jsonlines==3.1.0 jupyter_client==7.4.9 jupyter_core==4.12.0 keras==2.11.0 Keras-Preprocessing==1.1.2 kiwisolver==1.4.5 langcodes==3.3.0 libclang==18.1.1 lxml==5.3.0 Markdown==3.4.4 MarkupSafe==2.1.5 matplotlib==3.5.3 matplotlib-inline==0.1.6 MMPBSA.py==16.0 murmurhash==1.0.10 ndfes==3.0 nest-asyncio==1.6.0 numpy==1.21.6 nvidia-cublas-cu11==11.10.3.66 nvidia-cuda-nvrtc-cu11==11.7.99 nvidia-cuda-runtime-cu11==11.7.99 nvidia-cudnn-cu11==8.5.0.96 oauthlib==3.2.2 opt-einsum==3.3.0 packaging==24.0 packmol_memgen==2024.3.27 pandas==1.3.5 ParmEd==0+unknown parso==0.8.4 pathy==0.10.3 pdb4amber==22.0 pexpect==4.9.0 pickleshare==0.7.5 Pillow==9.5.0 preshed==3.0.9 prompt_toolkit==3.0.48 protobuf==3.19.6 psutil==6.1.0 ptyprocess==0.7.0 pyasn1==0.5.1 pyasn1-modules==0.3.0 pydantic==1.8.2 Pygments==2.17.2 pyMSMT==22.0 pyparsing==3.1.4 python-dateutil==2.9.0.post0 pytraj==2.0.6 pytz==2024.2 PyYAML==6.0.1 pyzmq==26.2.0 regex==2024.4.16 requests==2.31.0 requests-oauthlib==2.0.0 rsa==4.9 sacremoses==0.0.53 sander==22.0 scipy==1.4.1 six==1.16.0 smart-open==6.4.0 sortedcontainers==2.4.0 spacy==3.2.4 spacy-legacy==3.0.12 spacy-loggers==1.0.5 srsly==2.4.8 stanza==1.4.0 tensorboard==2.11.2 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.1 tensorflow==2.11.0 tensorflow-addons==0.12.1 tensorflow-estimator==2.11.0 tensorflow-io-gcs-filesystem==0.34.0 termcolor==2.3.0 thinc==8.0.17 tokenizers==0.12.1 torch==1.13.1 tornado==6.2 tqdm==4.67.0 traitlets==5.9.0 transformers==4.18.0 typeguard==2.13.3 typer==0.4.2 typing-extensions==3.7.4.3 urllib3==2.0.7 wasabi==0.10.1 wcwidth==0.2.13 Werkzeug==2.2.3 wrapt==1.16.0 zipp==3.15.0

Khyati-Microcrispr avatar Nov 21 '24 12:11 Khyati-Microcrispr

please help, I have sent the library versions in my envionment, can you tell me cuda and cudnn versions?

Khyati-Microcrispr avatar Nov 21 '24 12:11 Khyati-Microcrispr

I was facing the same issue and solved it by running pip install --upgrade emoji. I was able to run AIONER with the following package versions:

  • emoji 2.14.1
  • stanza 1.4.0
  • typing_extensions 4.7.1

Hope this helps!

alejoaa avatar Jul 16 '25 07:07 alejoaa