diff --git a/PyTorch/built-in/others/OpenFold_for_PyTorch/README.md b/PyTorch/built-in/others/OpenFold_for_PyTorch/README.md index 8664ccd3dd91fecffe74cb17fb9ae68dc1025c7f..845521cae7e27af1216023c810783d4cf577b1f4 100644 --- a/PyTorch/built-in/others/OpenFold_for_PyTorch/README.md +++ b/PyTorch/built-in/others/OpenFold_for_PyTorch/README.md @@ -49,12 +49,6 @@ - 安装依赖。 - 创建python3.9的conda并激活 - ``` - conda create -n openfold_env python=3.9 - conda activate openfold_env - ``` - 在模型源码包根目录下执行命令,安装模型对应PyTorch版本需要的依赖。 ``` pip install -r 2.1_requirements.txt # PyTorch2.1版本 @@ -67,9 +61,15 @@ pip install git+https://github.com/NVIDIA/dllogger.git pip install torch==2.1.0 - conda install -c bioconda -c conda-forge hhsuite - conda install -c bioconda kalign2 - conda install -c bioconda -c conda-forge mmseqs2 + wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz + tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz + export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH" + + pip install git+https://github.com/TimoLassmann/kalign.git + + wget https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz + tar xvfz mmseqs-linux-avx2.tar.gz + export PATH=$(pwd)/mmseqs/bin/:$PATH ``` - 构建安装openfold。 diff --git a/PyTorch/built-in/others/OpenFold_for_PyTorch/scripts/install_third_party_dependencies.sh b/PyTorch/built-in/others/OpenFold_for_PyTorch/scripts/install_third_party_dependencies.sh index 4d142a8192a71c436f54647e055215821906c6e3..4d79849ad156639991ad724361280ed5c98c9eed 100644 --- a/PyTorch/built-in/others/OpenFold_for_PyTorch/scripts/install_third_party_dependencies.sh +++ b/PyTorch/built-in/others/OpenFold_for_PyTorch/scripts/install_third_party_dependencies.sh @@ -12,7 +12,4 @@ ln -rs openfold/resources/stereo_chemical_props.txt tests/test_data/alphafold/co gunzip -c tests/test_data/sample_feats.pickle.gz > tests/test_data/sample_feats.pickle # This setting is used to fix a worker assignment issue during data loading -conda env config vars set KMP_AFFINITY=none - -export LIBRARY_PATH=$CONDA_PREFIX/lib:$LIBRARY_PATH -export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH +export KMP_AFFINITY=none diff --git a/PyTorch/built-in/others/OpenFold_for_PyTorch/test/val_openfold_8p.sh b/PyTorch/built-in/others/OpenFold_for_PyTorch/test/val_openfold_8p.sh index 8f352d8b82b1c01a6dc4e45f6b454eb5381a6483..750c8598e21dde0db4034d6c6889b650ddff0f0c 100644 --- a/PyTorch/built-in/others/OpenFold_for_PyTorch/test/val_openfold_8p.sh +++ b/PyTorch/built-in/others/OpenFold_for_PyTorch/test/val_openfold_8p.sh @@ -45,7 +45,7 @@ python3 train_openfold.py $data_path/pdb_data/mmcif_files \ wait # 提取最后一行中的 val/loss 小数值并赋值给变量 -val_loss=$(tac openfold_val_8p.log | grep -m1 'val/loss' | sed -n 's/.*val\/loss[[:space:]]\+\([0-9.]\+\).*/\1/p') +val_loss=$(grep 'val/loss' openfold_val_8p.log | tail -n1 | awk '{print $(NF-1)}') # 输出结果 echo "val/loss: $val_loss" \ No newline at end of file