amber16在linux安装教程,在linux系统下怎么安装amber tools20呢？

Amber20和以前版本安装有很大差别，且自动生成安装目录amber20,安装文件采用cmake_run文件安装，每部安装要设置其中的参数，这两天刚装好，采用官方提供的benchmark验证成功：

tar xvf Amber20.tar.bz2

tar xvf AmberTools20.tar.bz2

export AMBERHOME=/home/user/amber2020/amber20_src

一、串行安装

cd amber20_src/build

# optional: edit the run_cmake script to make any needed changes;

# most users should not need to do this

./run_cmake

# Next, build and install the code:

make install

source /home/xzhfood/amber2020/amber20/amber.sh

cd $AMBERHOME

make test.serial

二、并行安装

#compile the parallel (MPI)

cd $AMBERHOME/AmberTools/src

./configure_mpich gnu

You must download MPICH and extract it here

(for example, type 'tar xvfz mpich-3.3.2.tar.gz')

tar xvf mpich-3.3.tar.gz

cd /home/user/amber2020/amber20_src/build

# edit the run_cmake script to set -DMPI=TRUE

./run_cmake

make install

source /home/user/amber2020/amber20/amber.sh

# To run tests: Note the value below may depend on your MPI implementation

export DO_PARALLEL="mpirun -np 28"

cd $AMBERHOME

source amber.sh

make test.parallel

# Note, some tests, like the replica exchange tests, require more

# than 2 threads, so we suggest that you test with either 4 or 8

# threads as well

export DO_PARALLEL="mpirun -np 4"

make test.parallel

三、单GPU安装

Building and Testing the GPU code

export CUDA_HOME=/usr/local/cuda-9.2

cd build

# edit the run_cmake script to set -DCUDA=TRUE (you should also be using the GNU compilers here)

./run_cmake

make install

cd $AMBERHOME

export CUDA_VISIBLE_DEVICES=0

make test.cuda.serial

(choose the GPU id you wish to test)

四、多GPU安装

Building pmemd.cuda.MPI

cd build

# edit the run_cmake script to have -DMPI=TRUE -DCUDA=TRUE

./run_cmake

make install

cd $AMBERHOME

export DO_PARALLEL="mpirun -np 28" # for bash/sh

make test.cuda.parallel