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openvax / mhcflurry

Peptide-MHC I binding affinity prediction
http://openvax.github.io/mhcflurry/
Apache License 2.0
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excessive warnings generated from tensorflow due to deprecation of Model.state_updates #208

Open jgbaum opened 2 years ago

jgbaum commented 2 years ago

Running the example prediction, on both MacOS, Debian 11, and CentOS 8 Stream under Python 3.8 generates excessive warnings, seemingly due to imminent deprecation of Model.state_updates.

root@033e54d4560b:/# mhcflurry-predict \
>        --alleles HLA-A0201 HLA-A0301 \
>        --peptides SIINFEKL SIINFEKD SIINFEKQ \
>        --out /tmp/predictions.csv
Forcing tensorflow backend.
2022-10-13 20:12:41.110302: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-10-13 20:12:41.228251: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2022-10-13 20:12:41.228314: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2022-10-13 20:12:41.249984: E tensorflow/stream_executor/cuda/cuda_blas.cc:2981] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2022-10-13 20:12:41.915179: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory
2022-10-13 20:12:41.915392: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory
2022-10-13 20:12:41.915442: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
2022-10-13 20:12:42.431776: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-10-13 20:12:42.434182: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2022-10-13 20:12:42.434223: W tensorflow/stream_executor/cuda/cuda_driver.cc:263] failed call to cuInit: UNKNOWN ERROR (303)
2022-10-13 20:12:42.434304: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (033e54d4560b): /proc/driver/nvidia/version does not exist
2022-10-13 20:12:42.725107: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:354] MLIR V1 optimization pass is not enabled
WARNING:root:No flanking information provided. Specify --no-flanking to silence this warning
Predicting processing.
  0%|                                                                                                                                                                                         | 0/1 [00:00<?, ?it/s]/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
/usr/local/lib/python3.8/site-packages/mhcflurry/flanking_encoding.py:173: FutureWarning: The default dtype for empty Series will be 'object' instead of 'float64' in a future version. Specify a dtype explicitly to silence this warning.
  n_flanks = pandas.Series([""] * len(df))
/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:03<00:00,  3.19s/it]
Predicting affinities.
  0%|                                                                                                                                                                                         | 0/2 [00:00<?, ?it/s]/usr/local/lib/python3.8/site-packages/keras/engine/training_v1.py:2356: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2/2 [00:06<00:00,  3.40s/it]
Wrote: /tmp/predictions.csv
ZoeChao2001 commented 9 months ago

Hello, @jgbaum. May I ask if you have already resolved this issue? If so, how did you solve it? I‘ll appreciate it if you could provide a response.

jgbaum commented 9 months ago

@ZoeChao2001, unfortunately not.

timodonnell commented 9 months ago

Are you still seeing these in the latest mhcflurry version?

I haven't tried it but I am also wondering if running export PYTHONWARNINGS=ignore in your shell before you run the predict command helps?