diff --git a/README.md b/README.md index 78e0bb1..6f82c99 100644 --- a/README.md +++ b/README.md @@ -13,8 +13,28 @@ LocalColabFold is an installer script designed to make ColabFold functionality a - **No GPU limitations** - **NOT necessary to prepare the large database required for native AlphaFold2**. +## Note (Jun 18, 2022) + +ColabFold now depends on [JAX](https://github.com/google/jax) == 0.3.13 and jaxlib > 0.3.7, so you may encounter this error message after updating your localcolabfold using `./update_linux.sh`: + +``` + File "/path/to/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/jax/_src/lib/__init__.py", line 91, in check_jaxlib_version + raise RuntimeError(msg) +RuntimeError: jaxlib is version 0.1.72, but this version of jax requires version >= 0.3.7. +``` + +To fix this issue, please upgrade your jax and jaxlib: + +```bash +# '/path/to/your/colabfold_batch' should be substituted to your path, e.g. '/home/moriwaki/Desktop/colabfold_batch' +# install GPU-supported jaxlib +/path/to/your/colabfold_batch/colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.10+cuda11.cudnn82-cp37-none-manylinux2014_x86_64.whl +/path/to/your/colabfold_batch/colabfold-conda/bin/python3.7 -m pip install jax==0.3.13 +``` + ## New Updates +- 16Jun2022, version 1.4.0 released. See [Release v1.4.0](https://github.com/YoshitakaMo/localcolabfold/releases/tag/v1.4.0) - 07May2022, **Updated `update_linux.sh`.** See also [How to update](#how-to-update). Please use a new option `--use-gpu-relax` if GPU relaxation is required (recommended). - 12Apr2022, version 1.3.0 released. See [Release v1.3.0](https://github.com/YoshitakaMo/localcolabfold/releases/tag/v1.3.0) - 09Dec2021, version 1.2.0-beta released. easy-to-use updater scripts added. See [How to update](#how-to-update). diff --git a/README_ja.md b/README_ja.md index 7b4a6f2..43e06b8 100644 --- a/README_ja.md +++ b/README_ja.md @@ -4,6 +4,7 @@ ## アップデート情報 +- 2022年6月18日, version 1.4.0 リリース。[Release v1.4.0](https://github.com/YoshitakaMo/localcolabfold/releases/tag/v1.4.0) - 2021年12月9日, β版。簡単に使えるアップデートスクリプトを追加。[アップデートのやり方](#アップデートのやり方)を参照。 - 2021年12月4日, LocalColabFoldは最新版の[pipでインストール可能なColabFold](https://github.com/sokrypton/ColabFold#running-locally)に対応しました。このリポジトリではrelax(構造最適化)処理を行うために必要な他のパラメータファイルとともにColabFoldをインストールするためのスクリプトを提供しています。AlphaFoldとAlphaFold-Multimerの重みパラメータは初回の実行時に自動的にダウンロードされます。 diff --git a/install_colabbatch_M1mac.sh b/install_colabbatch_M1mac.sh index 1b8f07d..6bde81d 100755 --- a/install_colabbatch_M1mac.sh +++ b/install_colabbatch_M1mac.sh @@ -48,17 +48,14 @@ rm openmm.patch wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_M1mac.sh --no-check-certificate chmod +x update_M1mac.sh # install ColabFold and Jaxlib -colabfold-conda/bin/python3.8 -m pip install tensorflow-macos +colabfold-conda/bin/python3.8 -m pip install https://files.pythonhosted.org/packages/bd/57/88cea9e14dacaea82ca86fac2bf6ecb8b7fd99622d776e4131786ce5b65e/tensorflow_macos-2.7.0-cp38-cp38-macosx_11_0_arm64.whl colabfold-conda/bin/python3.8 -m pip install git+https://github.com/deepmind/tree.git colabfold-conda/bin/python3.8 -m pip install git+https://github.com/google/ml_collections.git -colabfold-conda/bin/python3.8 -m pip install dm-haiku==0.0.4 appdirs pandas absl-py==0.13.0 docker +colabfold-conda/bin/python3.8 -m pip install dm-haiku appdirs pandas absl-py docker colabfold-conda/bin/python3.8 -m pip install alphafold-colabfold --no-deps --no-color colabfold-conda/bin/python3.8 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" --no-deps --no-color -colabfold-conda/bin/python3.8 -m pip install jax==0.2.25 --no-deps --no-color -colabfold-conda/bin/python3.8 -m pip install jaxlib==0.1.74 -f "https://dfm.io/custom-wheels/jaxlib/index.html" --no-deps --no-color -colabfold-conda/bin/python3.8 -m pip install numpy==1.21.1 --no-deps --no-color -colabfold-conda/bin/python3.8 -m pip install chex --no-deps --no-color -colabfold-conda/bin/python3.8 -m pip install scipy --no-deps --no-color +colabfold-conda/bin/python3.8 -m pip install jaxlib==0.3.10 --no-deps --no-color +colabfold-conda/bin/python3.8 -m pip install jax==0.3.13 chex scipy toolz --no-deps --no-color # bin directory to run mkdir -p $COLABFOLDDIR/bin diff --git a/install_colabbatch_intelmac.sh b/install_colabbatch_intelmac.sh index 72c1e4d..70c09d9 100755 --- a/install_colabbatch_intelmac.sh +++ b/install_colabbatch_intelmac.sh @@ -48,8 +48,8 @@ wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/upda chmod +x update_intelmac.sh # install ColabFold and Jaxlib colabfold-conda/bin/python3.7 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" -colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/mac/jaxlib-0.1.74-cp37-none-macosx_10_9_x86_64.whl -colabfold-conda/bin/python3.7 -m pip install jax==0.2.25 +colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/mac/jaxlib-0.3.10-cp37-none-macosx_10_9_x86_64.whl +colabfold-conda/bin/python3.7 -m pip install jax==0.3.13 # bin directory to run mkdir -p $COLABFOLDDIR/bin diff --git a/install_colabbatch_linux.sh b/install_colabbatch_linux.sh index 95c1648..205d0ab 100755 --- a/install_colabbatch_linux.sh +++ b/install_colabbatch_linux.sh @@ -29,9 +29,8 @@ chmod +x update_linux.sh conda install -c conda-forge -c bioconda kalign3=3.2.2 hhsuite=3.3.0 -y # install ColabFold and Jaxlib colabfold-conda/bin/python3.7 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" -colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/cuda111/jaxlib-0.1.72+cuda111-cp37-none-manylinux2010_x86_64.whl -colabfold-conda/bin/python3.7 -m pip install jax==0.2.25 - +colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.10+cuda11.cudnn82-cp37-none-manylinux2014_x86_64.whl +colabfold-conda/bin/python3.7 -m pip install jax==0.3.13 # bin directory to run mkdir -p $COLABFOLDDIR/bin cd $COLABFOLDDIR/bin @@ -49,9 +48,6 @@ chmod +x colabfold_batch # hack to share the parameter files in a workstation. cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold sed -i -e "s#props_path = \"stereo_chemical_props.txt\"#props_path = \"${COLABFOLDDIR}/stereo_chemical_props.txt\"#" batch.py -# Use gpu-accelerated relaxation. -cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/alphafold/relax -sed -i -e 's/CPU/CUDA/g' amber_minimize.py # Use 'Agg' for non-GUI backend cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold sed -i -e "s#from matplotlib import pyplot as plt#import matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt#g" plot.py