Comments (4)
sorry for my poor English, Do you need more info?
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Hi @Whale-fall,
Thanks for your interest in our study. This problem is related to the computing environment. The model should still run despite the warnings. If you would like to use cuDNN for acceleration, please refer to the following post. https://www.tensorflow.org/api_docs/python/tf/keras/layers/LSTM.
Thanks!
from pmtnet.
Hi!
I am sorry to reply so late. I understand if cuDNN is unavailable.However,I noticed that when I run pMTnet, GPU computing power is basically unused.When tested on a file containing 1000 rows, It spends about 3mins!
My code looks like this:
time python /home/yiliang/software/pMTnet/pMTnet.py \
-input test.input \
-library /home/yiliang/software/pMTnet/library \
-output ./ -output_log ./test_log &
However, from my perspective, It is conflicts with the performance claimed in this issue. It says pMTnet can finish prediction in 2mins on a file containing 2M rows. Can you help me fix this?
This is My env info:
keras 2.4.3 pyhd8ed1ab_0 conda-forge
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
numpy 1.19.5 py37h3e96413_3 conda-forge
pandas 1.3.5 py37he8f5f7f_0 conda-forge
python 3.7.12 hf930737_100_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-flatbuffers 2.0 pyhd8ed1ab_0 conda-forge
python_abi 3.7 2_cp37m conda-forge
scikit-learn 1.0.2 py37hf9e9bfc_0 conda-forge
scipy 1.7.3 py37h492baa0_0 defaults
tensorflow 2.4.1 gpu_py37ha2e99fa_0 defaults
tensorflow-base 2.4.1 gpu_py37h29c2da4_0 defaults
tensorflow-estimator 2.6.0 py37hcd2ae1e_0 conda-forge
tensorflow-gpu 2.4.1 h30adc30_0 defaults
from pmtnet.
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Related Issues (20)
- TCR_encoder_30.h5 and other trained models in the repo HOT 1
- tensorflow.python.framework.errors_impl.InvalidArgumentError: input and filter must have the same depth: 76 vs 30 HOT 4
- A bug may be in pMTnet HOT 2
- Labelled training data used in pMTnet HOT 5
- Strange characters in the testing_data.csv and training_data.csv HOT 1
- HLA Pseudosequence generation HOT 3
- Full TCR sequences of validation data HOT 2
- Prediction with unknown antigen HOT 1
- Prediction with unknown HLA HOT 2
- Retrain Model pMTnet HOT 3
- How to calculate the AUC?
- How to filter the result by Rank HOT 1
- What does the negative rank mean HOT 1
- about the testing data
- Request for the support of MHC II molecule like "DRA1*02:01" HOT 2
- Understanding the model predictions- not CDR3 rank not influenced by HLA or peptide HOT 1
- Build my own background TCR HOT 2
- About Training TCR_encoder
- Error Predict Score on Neg_10k Data
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