求amber24和ambertools25的安装方法 - 计算化学公社

#!/usr/bin/env bash
# MIT License
#
# Copyright (c) 2025 Bundit Boonyarit
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
set -euo pipefail
export C_INCLUDE_PATH=${HOME}/amber-installer/ambertools25_src/AmberTools/src/boost:$C_INCLUDE_PATH
export C_INCLUDE_PATH=/usr/local/cuda-12.2/include:$C_INCLUDE_PATH
#export CPLUS_INCLUDE_PATH=/usr/local/cuda-12.2/include:$CPLUS_INCLUDE_PATH
export LD_LIBRARY_PATH=${HOME}/amber-installer/ambertools25_src/AmberTools/src/stage/lib:$LD_LIBRARY_PATH
#export LD_LIBRARY_PATH=/usr/local/cuda-12.2/lib64:$LD_LIBRARY_PATH
export PATH=/usr/local/cuda/bin:$PATH
#export MKL_HOME=/opt/intel/mkl:$MKL_HOME
# export C_INCLUDE_PATH="${HOME}/amber-installer/ambertools25_src/AmberTools/src/boost"
export CPLUS_INCLUDE_PATH="/usr/local/cuda-12.2/include"
# export LD_LIBRARY_PATH="${HOME}/amber-installer/ambertools25_src/AmberTools/src/stage/lib"
# export LD_LIBRARY_PATH="/usr/local/cuda-12.2/lib64"
# export PATH="/usr/local/cuda/bin"
export MKL_HOME="/opt/intel/mkl"
#export MKLROOT="/opt/intel/mkl"
# ----------------------------------------------------------------------------
# Colour codes
# ----------------------------------------------------------------------------
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
BLUE='\033[1;34m'
NC='\033[0m' # No Colour
# ----------------------------------------------------------------------------
# Default installation prefixes (separated as requested)
# ----------------------------------------------------------------------------
INSTALL_PREFIX_AMBERTOOLS="${HOME}/ambertools25"
INSTALL_PREFIX_PMEMD="${HOME}/pmemd24"
# ----------------------------------------------------------------------------
# Default build flags
# ----------------------------------------------------------------------------
BUILD_MPI=false
BUILD_CUDA=false
BUILD_AMBERTOOLS=false
BUILD_PMEMD=false
NPROC=$(nproc)
# ----------------------------------------------------------------------------
# Helper: usage message
# ----------------------------------------------------------------------------
usage() {
echo -e "${YELLOW}Usage: $0 [OPTIONS]${NC}\n"
echo "Options:"
echo " -cpu Build serial CPU version"
echo " -gpu Build serial GPU version with CUDA"
echo " -mpi_cpu Build MPI‑parallel CPU version"
echo " -mpi_gpu Build MPI‑parallel GPU version (MPI + CUDA)"
echo " -ambertools Build AmberTools25"
echo " -pmemd Build PMEMD24"
echo " -path_ambertools <path> Override AmberTools25 installation prefix"
echo " -path_pmemd <path> Override PMEMD24 installation prefix"
echo " -nproc <n> Number of CPU cores for compilation (default: all)"
echo " -h | --help Show this help message and exit"
exit 1
}
# ----------------------------------------------------------------------------
# CLI argument parsing
# ----------------------------------------------------------------------------
CPU_FLAG_SET=0
GPU_FLAG_SET=0
MPI_CPU_FLAG_SET=0
MPI_GPU_FLAG_SET=0
while [[ $# -gt 0 ]]; do
case "$1" in
-cpu) CPU_FLAG_SET=1; shift;;
-gpu) GPU_FLAG_SET=1; shift;;
-mpi_cpu) MPI_CPU_FLAG_SET=1;shift;;
-mpi_gpu) MPI_GPU_FLAG_SET=1;shift;;
-ambertools) BUILD_AMBERTOOLS=true; shift;;
-pmemd) BUILD_PMEMD=true; shift;;
-path_ambertools)
[[ $# -lt 2 ]] && { echo -e "${RED}Error: -path_ambertools requires an argument.${NC}"; usage; }
INSTALL_PREFIX_AMBERTOOLS="$2"; shift 2;;
-path_pmemd)
[[ $# -lt 2 ]] && { echo -e "${RED}Error: -path_pmemd requires an argument.${NC}"; usage; }
INSTALL_PREFIX_PMEMD="$2"; shift 2;;
-nproc)
[[ $# -lt 2 ]] && { echo -e "${RED}Error: -nproc requires an argument.${NC}"; usage; }
NPROC="$2"; shift 2;;
-h|--help) usage;;
*) echo -e "${RED}Unknown argument: $1${NC}"; usage;;
esac
done
TOTAL_FLAGS=$((CPU_FLAG_SET + GPU_FLAG_SET + MPI_CPU_FLAG_SET + MPI_GPU_FLAG_SET))
if [[ $TOTAL_FLAGS -ne 1 ]]; then
echo -e "${RED}Error: choose exactly one build type (-cpu, -gpu, -mpi_cpu, -mpi_gpu).${NC}"
usage
fi
if [[ "${BUILD_AMBERTOOLS}" = false && "${BUILD_PMEMD}" = false ]]; then
echo -e "${RED}Error: specify at least one of -ambertools or -pmemd.${NC}"
usage
fi
# ----------------------------------------------------------------------------
# Configure build type
# ----------------------------------------------------------------------------
if [[ $CPU_FLAG_SET -eq 1 ]]; then BUILD_MPI=false; BUILD_CUDA=false;
elif [[ $GPU_FLAG_SET -eq 1 ]]; then BUILD_MPI=false; BUILD_CUDA=true;
elif [[ $MPI_CPU_FLAG_SET -eq 1 ]]; then BUILD_MPI=true; BUILD_CUDA=false;
elif [[ $MPI_GPU_FLAG_SET -eq 1 ]]; then BUILD_MPI=true; BUILD_CUDA=true;
fi
# ----------------------------------------------------------------------------
# Environment‑modules handling (optional)
# ----------------------------------------------------------------------------
if command -v module &>/dev/null && [[ -n "${LMOD_CMD:-}" ]]; then
echo -e "${BLUE}Detected Lmod environment — purging loaded modules...${NC}"
module purge
fi
# ----------------------------------------------------------------------------
# Conda bootstrap (local Miniforge3) — unchanged from original script
# ----------------------------------------------------------------------------
if [[ -d ./miniforge3 ]]; then
echo -e "${BLUE}Activating existing conda environment...${NC}"
set +eu
source ./miniforge3/bin/activate
#set +eu
#SOURCE CONDA
conda activate amber-installer
else
MINIFORGE_INSTALLER="Miniforge3-$(uname)-$(uname -m).sh"
[[ -f "$MINIFORGE_INSTALLER" ]] || curl -LO "https://github.com/conda-forge/miniforge/releases/latest/download/$MINIFORGE_INSTALLER"
bash "$MINIFORGE_INSTALLER" -b -p ./miniforge3
source ./miniforge3/bin/activate
echo -e "${BLUE}Creating conda environment 'amber-installer'...${NC}"
conda env create -f env.yml
#set +eu
#SOURCE CONDA
set +eu
conda activate amber-installer
fi
# ----------------------------------------------------------------------------
# AmberTools25 build
# ----------------------------------------------------------------------------
if [[ "${BUILD_AMBERTOOLS}" = true ]]; then
[[ -f ambertools25.tar.bz2 ]] || {
echo -e "${RED}Error: ambertools25.tar.bz2 not found.${NC}\n${YELLOW}Download it from https://ambermd.org/GetAmber.php${NC}";
exit 1;
}
echo -e "${BLUE}Extracting AmberTools25...${NC}"
[[ -d ambertools25_src ]] || tar xvjf ambertools25.tar.bz2
pushd ambertools25_src > /dev/null
./update_amber --update
set +eu
conda activate amber-installer
# QUICK fix for mpi.h CMake flags (see original notes)
sed -i '/set(CMAKE_C_FLAGS "")/s/^/# /' AmberTools/src/quick/CMakeLists.txt
sed -i '/set(CMAKE_CXX_FLAGS "")/s/^/# /' AmberTools/src/quick/CMakeLists.txt
sed -i '/set(CMAKE_Fortran_FLAGS "")/s/^/# /' AmberTools/src/quick/CMakeLists.txt
mkdir -p build && cd build
which gfortran
echo -e "${BLUE}Configuring AmberTools25 (MPI=${BUILD_MPI}, CUDA=${BUILD_CUDA}, PREFIX=${INSTALL_PREFIX_AMBERTOOLS})...${NC}"
#[[ -d CMakeFiles ]] && { echo "CMakeFiles detected — running make clean"; make clean; }
cmake .. \
-DCUDA_cublas_LIBRARY="/usr/local/cuda-12.2/lib64/libcublas.so.12.2.1.16" \
-DMKL_HOME="/opt/intel/mkl" \
-DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
-DCMAKE_INSTALL_PREFIX="${INSTALL_PREFIX_AMBERTOOLS}" \
-DCOMPILER=GNU \
-DMPI="${BUILD_MPI}" \
-DCUDA="${BUILD_CUDA}" \
-DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE
echo -e "${BLUE}Building AmberTools25 with ${NPROC} cores...${NC}"
make -j"${NPROC}" && make install
popd > /dev/null
echo -e "${GREEN}AmberTools25 installed to ${INSTALL_PREFIX_AMBERTOOLS}${NC}"
fi
# ----------------------------------------------------------------------------
# PMEMD24 build
# ----------------------------------------------------------------------------
if [[ "${BUILD_PMEMD}" = true ]]; then
[[ -f pmemd24.tar.bz2 ]] || {
echo -e "${RED}Error: pmemd24.tar.bz2 not found.${NC}\n${YELLOW}Download it from https://ambermd.org/GetAmber.php${NC}";
exit 1;
}
echo -e "${BLUE}Extracting PMEMD24...${NC}"
[[ -d pmemd24_src ]] || tar xvjf pmemd24.tar.bz2
pushd pmemd24_src > /dev/null
./update_pmemd --update
mkdir -p build && cd build
echo -e "${BLUE}Configuring PMEMD24 (MPI=${BUILD_MPI}, CUDA=${BUILD_CUDA}, PREFIX=${INSTALL_PREFIX_PMEMD})...${NC}"
[[ -d CMakeFiles ]] && { echo "CMakeFiles detected — running make clean"; make clean; }
cmake .. \
-DCUDA_cublas_LIBRARY="/usr/local/cuda-12.2/lib64/libcublas.so.12.2.1.16" \
-DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
-DCMAKE_INSTALL_PREFIX="${INSTALL_PREFIX_PMEMD}" \
-DCOMPILER=GNU \
-DMPI="${BUILD_MPI}" \
-DCUDA="${BUILD_CUDA}" \
-DDOWNLOAD_MINICONDA=FALSE \
-DINSTALL_TESTS=TRUE \
-DBUILD_PYTHON=FALSE \
-DBUILD_PERL=FALSE \
-DBUILD_GUI=FALSE \
-DPMEMD_ONLY=TRUE \
-DCHECK_UPDATES=FALSE
echo -e "${BLUE}Building PMEMD24 with ${NPROC} cores...${NC}"
make -j"${NPROC}" && make install
popd > /dev/null
echo -e "${GREEN}PMEMD24 installed to ${INSTALL_PREFIX_PMEMD}${NC}"
fi
# ----------------------------------------------------------------------------
# Completion message
# ----------------------------------------------------------------------------
if [[ "${BUILD_AMBERTOOLS}" = true && "${BUILD_PMEMD}" = true ]]; then
echo -e "${GREEN}Both AmberTools25 and PMEMD24 installations completed successfully.${NC}"
elif [[ "${BUILD_AMBERTOOLS}" = true ]]; then
echo -e "${GREEN}AmberTools25 installation completed successfully.${NC}"
else
echo -e "${GREEN}PMEMD24 installation completed successfully.${NC}"
fi

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