update

Dockerfile.gromacs_amber

@@ -1,4 +1,4 @@
-# syntax=docker/dockerfile:1
+# syntax=docker/dockerfile:1.3-labs
 # NOTE: Building this image require's docker version >= 23.0.
 #
 # For reference:
@@ -52,8 +52,29 @@ chmod 600 /root/.ssh/authorized_keys2
 mkdir /var/run/sshd
 echo "root:${ROOT_PASSWD}" | chpasswd
 mkdir -p ~/.pip
+# timezone
+apt-get install -y tzdata
+ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
+echo "Asia/Shanghai" > /etc/timezone
 # install pixi
-curl -fsSL https://pixi.sh/install.sh | bash
+# curl -fsSL https://pixi.sh/install.sh | bash
+EOT
+
+ENV PATH=/opt/modules/bin:$PATH
+ENV LIBRARY_PATH=/opt/modules/lib:$LIBRARY_PATH
+COPY ./file/modules-5.4.0.tar.gz /root
+## install modules to manage environment variables download from https://modules.sourceforge.net/
+# usage: https://nscc.mrzhenggang.com/user-manual/config-env-with-module
+RUN <<EOT
+#!/bin/bash
+# apt-get update && apt-get install -y tcl
+tar zxvf modules-5.4.0.tar.gz
+cd modules-5.4.0
+# ./configure --prefix=/opt/modules --bindir=/opt/modules/bin --libdir=/opt/modules/lib --with-tclsh=/usr/bin/tclsh
+./configure --prefix=/opt/modules --bindir=/opt/modules/bin --libdir=/opt/modules/lib --disable-libtclenvmodules
+make -j$(nproc)
+make install
+/opt/modules/bin/modulecmd --version
 EOT
 
 ARG FFTW_VERSION="3.3.10"
@@ -125,7 +146,7 @@ nvcc -o test_mpi_cuda test_mpi_cuda.cu -I${CUDA_HOME}/include -I${MPI_HOME}/incl
 EOT
 
 # 安装plumed
-ARG PLUMED_VERSION="2.9.1"
+ARG PLUMED_VERSION="2.9.2"
 ENV PLUMED_VERSION=${PLUMED_VERSION}
 ENV LD_LIBRARY_PATH=/usr/local/plumed/lib:$LD_LIBRARY_PATH
 ENV PATH=/usr/local/plumed:/usr/local/plumed/bin:$PATH
@@ -143,10 +164,12 @@ make install
 EOT
 
 # 安装gromacs
-ARG GROMACS_VERSION="2022.5"
+ARG GROMACS_VERSION="2021.7"
 ENV GROMACS_VERSION=${GROMACS_VERSION}
 ENV GROMACS_HOME=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}
 ENV PATH=PATH=$GROMACS_HOME/bin:$PATH
+ARG CUDA_ARCH="75;86;89"
+ENV CUDA_ARCH=${CUDA_ARCH}
 RUN <<EOT
 #!/bin/bash
 wget -c https://ftp.gromacs.org/gromacs/gromacs-${GROMACS_VERSION}.tar.gz
@@ -161,25 +184,56 @@ cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-${GROMACS_VERSION}-plumed-${P
          -DGMX_BUILD_OWN_FFTW=ON \
          -DREGRESSIONTEST_DOWNLOAD=ON \
          -DGMX_GPU=CUDA \
+         -DGMX_CUDA_TARGET_COMPUTE="75;86;89" \
+         -DGMX_CUDA_TARGET_SM="75;86;89" \
          -DGMX_MPI=ON
 make -j$(nproc)
 make install 
 echo "source /usr/local/gromacs-${GROMACS_VERSION}-plumed-${PLUMED_VERSION}/bin/GMXRC.bash" >> /root/.bashrc
 EOT
 
-COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
+# PyAutoFEP install support version: GROMACS 2021.7
+# GROMACS 2022.5 和 2023 中遇到的“排除原子距离超过截断距离”的问题，确保模拟的稳定性和自由能计算的收敛性。
+# https://github.com/luancarvalhomartins/PyAutoFEP/blob/master/docs/Manual.pdf
+# https://github.com/luancarvalhomartins/PyAutoFEP/tree/master/docs/tutorial01
+ENV CPLUS_INCLUDE_PATH=/usr/include/openbabel3
+ENV LIBRARY_PATH=/usr/lib:/usr/local/lib:${LIBRARY_PATH}
+RUN <<EOT
+#!/bin/bash
+sudo apt-get update
+sudo apt-get install openbabel libopenbabel-dev -y
+sudo apt-get install swig -y
+sudo ln -s /usr/include/openbabel3 /usr/local/include/openbabel3
+/usr/bin/python3 -m pip install ipython rdkit "networkx>2.0,<3.0" alchemlyb==0.6.0 pymbar==3.0.5 openbabel>3.0.0 matplotlib numpy biopython mdanalysis pytest packaging 
+# or openbabel use 2.4.1
+git clone https://github.com/luancarvalhomartins/PyAutoFEP.git 
+EOT
 
+COPY file/Amber24.tar.bz2 file/AmberTools24.tar.bz2 /root
+COPY file/l_HPCKit_p_2024.2.1.79_offline.sh file/l_onemkl_p_2024.2.2.17_offline.sh /root
+COPY boost_1_86_0.tar.gz /root
 ENV DOWNLOAD_MINICONDA="False"
 # install ambertools
 RUN <<EOT
 #!/bin/bash
 python3 -m pip install numpy scipy matplotlib
+chmod +x l_HPCKit_p_2024.2.1.79_offline.sh
+./l_HPCKit_p_2024.2.1.79_offline.sh -a --silent --eula accept --install-dir /opt/intel
+chmod +x l_onemkl_p_2024.2.2.17_offline.sh
+./l_onemkl_p_2024.2.2.17_offline.sh -a --silent --eula accept --install-dir /opt/intel/onemkl
+# install Boost from https://www.boost.org/users/download/
+tar zxvf boost_1_86_0.tar.gz
+cd boost_1_86_0
+./bootstrap.sh --prefix=/opt/boost --with-libraries=all --with-toolset=gcc
+echo "using mpi : /usr/local/openmpi/bin/mpicxx ;" >> project-config.jam
+# echo "using mpi : /opt/intel/mpi/2021.13/bin/mpicxx ;" >> project-config.jam
+./b2 -j$(nproc) --layout=tagged link=static,shared threading=multi install
 # 解压 Amber24
 tar -xjf Amber24.tar.bz2
 # 解压 AmberTools24
 tar -xjf AmberTools24.tar.bz2
 # 清理解压后的 .tar.bz2 文件（可选）
-rm Amber24.tar.bz2 AmberTools24.tar.bz2
+# rm Amber24.tar.bz2 AmberTools24.tar.bz2
 EOT
 
 RUN <<EOT