fix bug

Dockerfile

 FROM image.sourcefind.cn:5000/dcu/admin/base/jax:0.4.23-ubuntu20.04-dtk24.04.1-py3.10
 
-# RUN apt update
+RUN apt update
 
-# WORKDIR /app
+RUN sudo apt install hmmer -y
 
-# WORKDIR /app/softwares
+RUN sudo apt install doxygen -y
 
-# RUN git clone https://github.com/soedinglab/hh-suite.git
+WORKDIR /app
 
-# RUN mkdir -p hh-suite/build && cd hh-suite/build && cmake -DCMAKE_INSTALL_PREFIX=. .. && make -j 4 && make install
+COPY . /app/alphafold2
+
+# hh-suite
+
+WORKDIR /app/softwares
+
+RUN git clone https://github.com/soedinglab/hh-suite.git
+
+# # for intel cpu
+# RUN mkdir -p hh-suite/build && cd hh-suite/build && lscpu | grep 'Model name' | grep -q 'Intel' && cmake -DCMAKE_INSTALL_PREFIX=. .. && make -j 4 && make install || echo "not for intel"
+
+# # RUN which hhsearch && echo "already build for intel" || echo ""
+
+# # for others
+# RUN lscpu | grep 'Model name' | grep -vq 'Intel' && cmake -DHAVE_AVX2=1 -DCMAKE_INSTALL_PREFIX=. .. && make -j 4 && make install && echo "already build for hygon or amd" || echo "not for others"
+
+# # RUN which hhsearch
 
 # ENV PATH=/app/softwares/hh-suite/build/bin:/app/softwares/hh-suite/build/scripts:$PATH
 
-# WORKDIR /app/softwares
+# RUN which hhsearch
+
+# kalign
+
+WORKDIR /app/softwares
+
+RUN wget https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.4.0.zip && unzip v3.4.0.zip && cd kalign-3.4.0 && mkdir build && cd build && cmake .. && make && sudo make install
+
+# openmm
+
+WORKDIR /app/softwares
 
-# RUN wget https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.4.0.zip && unzip v3.4.0.zip && cd kalign-3.4.0 && mkdir build && cd build && cmake .. && make && make install
+RUN wget https://github.com/openmm/openmm/archive/refs/tags/8.0.0.zip && unzip 8.0.0.zip
 
-# WORKDIR /app/softwares
+# RUN mkdir build build-hip install
 
-# RUN sudo apt install doxygen -y
+# RUN cd build && cmake ../openmm-8.0.0/ -D CMAKE_INSTALL_PREFIX=../install -D OPENMM_BUILD_COMMON=ON -D OPENMM_PYTHON_USER_INSTALL=ON && make && sudo make install && sudo make PythonInstall
 
-# RUN wget https://github.com/openmm/openmm/archive/refs/tags/8.0.0.zip && unzip 8.0.0.zip && cd openmm-8.0.0 && mkdir build && cd build && cmake .. && make && sudo make install && sudo make PythonInstall
+# hip
+WORKDIR /app/softwares
 
-# WORKDIR /app/softwares
+RUN git clone https://github.com/amd/openmm-hip.git
 
-# RUN wget https://github.com/openmm/pdbfixer/archive/refs/tags/1.9.zip && unzip 1.9.zip && cd pdbfixer-1.9 && python setup.py install 
+# RUN cd build-hip && cmake ../openmm-hip/ -D OPENMM_DIR=../install -D OPENMM_SOURCE_DIR=../openmm-8.0.0 -D CMAKE_INSTALL_PREFIX=../install && make && sudo make install
 
-# RUN sudo apt install hmmer -y
+# ENV LD_LIBRARY_PATH=/app/softwares/build-hip/:$LD_LIBRARY_PATH
 
-# WORKDIR /app
+# ENV OPENMM_PLUGIN_DIR=/app/softwares/install/lib/plugins
 
-# COPY . /app/alphafold2
+# ENV OPENMM_FFT_BACKEND=1
 
-# RUN ls
+# RUN python docker_test.py | grep -q 'HIP'
 
-# RUN pip install --no-cache-dir -r /app/alphafold2/requirements_dcu.txt -i https://mirrors.ustc.edu.cn/pypi/web/simple
+# pdbfixer
 
-# RUN pip install dm-haiku==0.0.11 flax==0.7.1 jmp==0.0.2 tabulate==0.8.9 --no-deps jax -i https://mirrors.ustc.edu.cn/pypi/web/simple
+WORKDIR /app/softwares
 
-# RUN pip install orbax==0.1.6 orbax-checkpoint==0.1.6 optax==0.2.2 -i https://mirrors.ustc.edu.cn/pypi/web/simple
+RUN wget https://github.com/openmm/pdbfixer/archive/refs/tags/1.9.zip && unzip 1.9.zip && cd pdbfixer-1.9 && python setup.py install 
 
-# WORKDIR /app/alphafold2
+# pip
+RUN ls
 
-# RUN python setup.py install
+RUN pip install --no-cache-dir -r /app/alphafold2/requirements_dcu.txt -i https://mirrors.ustc.edu.cn/pypi/web/simple
 
+RUN pip install dm-haiku==0.0.11 flax==0.7.1 jmp==0.0.2 tabulate==0.8.9 --no-deps jax -i https://mirrors.ustc.edu.cn/pypi/web/simple
 
+RUN pip install orbax==0.1.6 orbax-checkpoint==0.1.6 optax==0.2.2 -i https://mirrors.ustc.edu.cn/pypi/web/simple
 
+WORKDIR /app/alphafold2
 
+RUN python setup.py install

README.md

@@ -16,69 +16,35 @@ AlphaFold2通过从蛋白质序列和结构数据中提取信息，使用神经
 
 ## 环境配置
 
-### Docker（方法一）
+<!-- ### Docker
 
-    # 使用该方法不需要下载本仓库，镜像中已包含可运行代码，但需要挂载相应的数据文件
+    # 使用该方法不需要下载本仓库，镜像中已包含可运行代码，只需要挂载相应的数据文件
 
     docker pull image.sourcefind.cn:5000/dcu/admin/base/custom:alphafold2-dtk24.04.1-py310
 
     docker run --shm-size 100g --network=host --name=alphafold2 --privileged --device=/dev/kfd --device=/dev/dri --group-add video --cap-add=SYS_PTRACE --security-opt seccomp=unconfined -v 本地数据地址:镜像数据地址 -v /opt/hyhal:/opt/hyhal:ro -it <your IMAGE ID> bash
 
-    # 该镜像在intel-cpu上编译，若在其他cpu上使用，需要重新编译hh-suite
-    cd /app/softwares/hh-suite && rm -rf build
-    mkdir build && cd build 
-    cmake -DHAVE_AVX2=1 -DCMAKE_INSTALL_PREFIX=. ..
-    make -j 4 && sudo make install
-    export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"
+    cd /app/alphafold2/dcu_build
 
-### Docker（方法二）
+    # 此过程较为耗时
+    bash build.sh
 
-    docker pull image.sourcefind.cn:5000/dcu/admin/base/jax:0.4.23-ubuntu20.04-dtk24.04.1-py3.10
+    source env.sh -->
 
-    docker run --shm-size 50g --network=host --name=alphafold2 --privileged --device=/dev/kfd --device=/dev/dri --group-add video --cap-add=SYS_PTRACE --security-opt seccomp=unconfined -v 项目地址(绝对路径):/home/ -v /opt/hyhal:/opt/hyhal:ro -it <your IMAGE ID> bash
+### Dockerfile
 
-    # 1. 一般依赖项安装
-    pip install -r requirements_dcu.txt
+    # 下载本仓库
 
-    pip install dm-haiku==0.0.11 flax==0.7.1 jmp==0.0.2 tabulate==0.8.9 --no-deps jax
+    docker build -t alphafold2:v1 .
 
-    pip install orbax==0.1.6 orbax-checkpoint==0.1.6 optax==0.2.2
-
-    python setup.py install
-
-    sudo apt install hmmer -y
-
-    # 2、hh-suite 
-
-    git clone https://github.com/soedinglab/hh-suite.git
-    mkdir -p hh-suite/build && cd hh-suite/build
-    cmake -DCMAKE_INSTALL_PREFIX=. ..
-    make -j 4 && make install
-    export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"
-
-    wget https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.4.0.zip
-    unzip v3.4.0.zip && cd kalign-3.4.0
-    mkdir build 
-    cd build
-    cmake .. 
-    make 
-    make test 
-    make install
-
-    # 3. openmm + pdbfixer
-
-    sudo apt install doxygen
-
-    wget https://github.com/openmm/openmm/archive/refs/tags/8.0.0.zip
-
-    unzip 8.0.0.zip && cd openmm-8.0.0 && mkdir build && cd build
-
-    cmake .. && make && sudo make install && sudo make PythonInstall
+    docker run --shm-size 100g --network=host --name=alphafold2 --privileged --device=/dev/kfd --device=/dev/dri --group-add video --cap-add=SYS_PTRACE --security-opt seccomp=unconfined -v 本地数据地址:镜像数据地址 -v /opt/hyhal:/opt/hyhal:ro -it <your IMAGE ID> bash
 
-    wget https://github.com/openmm/pdbfixer/archive/refs/tags/1.9.zip
+    cd /app/alphafold2/dcu_build
 
-    unzip 1.9.zip && cd pdbfixer-1.9 && python setup.py install 
+    # 此过程较为耗时
+    bash build.sh
 
+    source env.sh
 
 ## 数据集
 推荐使用AlphaFold2中的开源数据集，包括BFD、MGnify、PDB70、Uniclust、Uniref90等,数据集大小约2.62TB。数据集格式如下：

alphafold/relax/amber_minimize.py

@@ -92,7 +92,7 @@ def _openmm_minimize(
     _add_restraints(system, pdb, stiffness, restraint_set, exclude_residues)
 
   integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
-  platform = openmm.Platform.getPlatformByName("CUDA" if use_gpu else "CPU")
+  platform = openmm.Platform.getPlatformByName("HIP" if use_gpu else "CPU")
   simulation = openmm_app.Simulation(
       pdb.topology, system, integrator, platform)
   simulation.context.setPositions(pdb.positions)

dcu_build/build.sh

+#!/bin/bash
+
+# /*即使下载了镜像依旧可能无法使用，因此在这里对一些容易出问题的库编译*/
+
+# hh-suite
+
+platform_is_intel=`lscpu | grep 'Model name' | grep -q "Intel" && echo "true" || echo "false"` 
+
+echo $platform_is_intel
+
+if [ "${platform_is_intel}" = "true" ]; then
+    echo "build for intel"
+    cd /app/softwares/hh-suite
+    rm -rf build
+    mkdir -p build && cd build && cmake -DCMAKE_INSTALL_PREFIX=. .. && make -j 8 && make install
+else
+    echo "build for others"
+    cd /app/softwares/hh-suite
+    rm -rf build
+    mkdir -p build && cd build && cmake -DHAVE_AVX2=1 -DCMAKE_INSTALL_PREFIX=. .. && make -j 8 && make install
+fi
+
+# openmm-8.0.0
+
+echo "build openmm-8.0.0"
+
+cd /app/softwares
+
+rm -rf build build-hip install
+
+mkdir build build-hip install
+
+cd build && cmake ../openmm-8.0.0/ -D CMAKE_INSTALL_PREFIX=../install -D OPENMM_BUILD_COMMON=ON -D OPENMM_PYTHON_USER_INSTALL=ON && make && sudo make install && sudo make PythonInstall
+
+# openmm-hip
+
+cd /app/softwares
+
+cd build-hip && cmake ../openmm-hip/ -D OPENMM_DIR=../install -D OPENMM_SOURCE_DIR=../openmm-8.0.0 -D CMAKE_INSTALL_PREFIX=../install && make && sudo make install
+

dcu_build/env.sh

+#!/bin/bash
+
+export LD_LIBRARY_PATH=/app/softwares/build-hip/:$LD_LIBRARY_PATH
+export OPENMM_PLUGIN_DIR=/app/softwares/install/lib/plugins
+export OPENMM_FFT_BACKEND=1
+
+export PATH=/app/softwares/hh-suite/build/bin:/app/softwares/hh-suite/build/scripts:$PATH

docker_test.py

+import openmm
+
+
+num_platform = openmm.Platform_getNumPlatforms()
+
+for i in range(num_platform):
+    gname = openmm.Platform_getPlatform(i).getName()
+    if gname == "HIP":
+        print(gname)
+        break

run_monomer.sh

  #!/bin/bash
  
- download_dir=/home/chuangkj/alphafold2_jax/downloads
+ download_dir=/path/to/data
  python3 run_alphafold.py \
  --fasta_paths=monomer.fasta \
  --output_dir=./ \

run_multimer.sh

  #!/bin/bash
  
- download_dir=/home/chuangkj/alphafold2_jax/downloads
+ download_dir=/path/to/data
  python3 run_alphafold.py \
  --fasta_paths=multimer.fasta \
  --output_dir=./ \