关于我：全国7*24高效代维服务

联系我：lianglab@126.com

淘宝店：全国7*24高效代维服务

CentOS 7.6 安装部署Gromacs 2023 布朗动力学模拟

安装步骤

tar xfz gromacs-2023.3.tar.gz
cd gromacs-2023.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

下载地址： https://ftp.gromacs.org/gromacs/gromacs-2023.3.tar.gz

CentOS 7.6 安装部署Gromacs 2023 布朗动力学模拟

目录

安装要求：

获取最新版本的C和C++编译器。
使用：gcc版本9.3，路径加入到bashrc

检查您是否拥有CMake 3.18.4或更高版本。
使用：cmake-3.23.5
获取并打开GROMACS tarball的最新版本。
制作一个单独的生成目录并对其进行更改。
以源路径为参数运行cmake
运行make、make check和make install
来源GMXRC以访问GROMACS

这里对gromcas的编译依赖于python3版本和gcc的高版本（最低要求是5.x版本）
但是在Centos里，默认的python是2.x版本，gcc默认是4.x版本。使用yum对gcc的升级最多到4.x版本。

软件下载地址：

gcc
http://mirror.centos.org/centos/7/extras/x86_64/Packages/centos-release-scl-2-3.el7.centos.noarch.rpm
cmake
https://cmake.org/files/v3.25/

主题简述

Gromacs是研究生物大分子体系的动力学模拟软件，在国内外有着广泛的应用。目前Gromacs只发布了基于Linux/Unix的安装程序包，本教程将介绍在VMware虚拟机上安装Gromacs正式版本2019.6。

工具/原料

VMware 虚拟机容器和Linux系统CentOS7对应镜像文件——官网下载

Cmake和Gromacs程序包——官网下载（Gromacs官网和cmake官网下载安装程序包(http://manual.gromacs.org/documentation/ 以及 https://cmake.org/download/）

Gromacs详细安装教程

1、检查和安装C/C++

检查命令

gcc -v

安装命令

sudo yum install gcc  (这里sudo是获取临时root权限，需要管理员密码；另外用"su"命令进行root操作也可以)

CentOS7.6 gcc9.3安装方法

更新gcc版本

sudo yum install -y http://mirror.centos.org/centos/7/extras/x86_64/Packages/centos-release-scl-2-3.el7.centos.noarch.rpm

[root@lianglab tmp]# yum -y install centos-release-scl-2-3.el7.centos.noarch.rpm
Loaded plugins: fastestmirror
Examining centos-release-scl-2-3.el7.centos.noarch.rpm: centos-release-scl-2-3.el7.centos.noarch
Marking centos-release-scl-2-3.el7.centos.noarch.rpm to be installed
Resolving Dependencies

2.安装devtoolset：
这里需要注意一下，如果想安装7.版本的，就改成devtoolset-7-gcc，以此类推.
sudo yum install devtoolset-9-gcc-c++
3. 激活对应的devtoolset:

scl enable devtoolset-9 bash
或者
source /opt/rh/devtoolset-9/enable

[root@lianglab tmp]# scl enable devtoolset-9 bash

[root@lianglab tmp]# source /opt/rh/devtoolset-9/enable
[root@lianglab tmp]# gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-9/root/usr --mandir=/opt/rh/devtoolset-9/root/usr/share/man --infodir=/opt/rh/devtoolset-9/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --with-default-libstdcxx-abi=gcc4-compatible --enable-plugin --enable-initfini-array --with-isl=/builddir/build/BUILD/gcc-9.3.1-20200408/obj-x86_64-redhat-linux/isl-install --disable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 9.3.1 20200408 (Red Hat 9.3.1-2) (GCC)
[root@lianglab tmp]#





若是重新安装gcc，从而提高gcc的版本，就很费时费磁盘空间，这里介绍一种普遍的方法来暂时的更新gcc：

yum安装相关依赖，将gcc提高到8.x版本：
 

yum install centos -release-scl -y
 
yum install devtoolset-8 -y
安装成功后，输入如下命令，打开一个新bash，在里面暂时更新gcc的版本：

scl enable devtoolset-8 bash
查看gcc的版本：

gcc --version
若是上面的方法不能更新gcc，可以使用如下方法使用devtoolset-8的内置脚本：

source /opt/rh/devtoolset-8/enable
这个就不会新开bahs，检查gcc版本：



gcc --version

image-20231201003811477

image-20231201003900643

image-20231201003919658

image-20231201004012273

查看gcc版本

image-20231201004106677

2、检查cmake

cmake -version

说明：

如果没有安装cmake或版本过低，需要到网上下载，yum资源库中的cmake版本一般较低:

下载安装包: https://cmake.org/files/v3.10/cmake-3.10.2-Linux-x86_64.tar.gz
wget https://github.com/Kitware/CMake/releases/download/v3.23.5/cmake-3.23.5-linux-x86_64.tar.gz
(用系统自带的下载工具下载)
3、cmake安装步骤
$ tar zxvf cmake-3.25.1-linux-x86_64.tar.gz  (解压安装包)

cd /opt && mkdir cmake
cd cmake

wget -c https://cmake.org/files/v3.25/cmake-3.25.1-linux-x86_64.tar.gz

tar -zxvf cmake-3.25.1-linux-x86_64.tar.gz

vi /etc/profile.d/cmakeenv.sh
export CMAKE_HOME=/opt/cmake/cmake-3.25.1-linux-x86_64/bin
export PATH=$CMAKE_HOME:$PATH


source /etc/profile


cmake --version

image-20231201005828774

4、Python3安装
解决依赖关系：
yum install zlib-devel bzip2-devel openssl-devel ncurses-devel sqlite-devel readline-devel tk-devel libffi-devel 



tar -zxf Python-3.7.12.tgz -C . 
 
cd Python-3.7.12 && ./configure prefix=/usr/local/python3
进行安装：

make && make -j 4 install

Generating grammar tables from /usr/local/python3/lib/python3.7/lib2to3/PatternGrammar.txt
Writing grammar tables to /usr/local/python3/lib/python3.7/lib2to3/PatternGrammar3.7.12.final.0.pickle
if test "xupgrade" != "xno"  ; then \
        case upgrade in \
                upgrade) ensurepip="--upgrade" ;; \
                install|*) ensurepip="" ;; \
        esac; \
         ./python -E -m ensurepip \
                $ensurepip --root=/ ; \
fi
Looking in links: /tmp/tmpudhcmddy
Processing /tmp/tmpudhcmddy/setuptools-47.1.0-py3-none-any.whl
Processing /tmp/tmpudhcmddy/pip-20.1.1-py2.py3-none-any.whl
Installing collected packages: setuptools, pip
  WARNING: The script easy_install-3.7 is installed in '/usr/local/python3/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts pip3 and pip3.7 are installed in '/usr/local/python3/bin' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed pip-20.1.1 setuptools-47.1.0
[root@lianglab Python-3.7.12]#



编译安装成功后，进入到/usr/local/python3文件夹里查看是否成功安装：

[root@lianglab Python-3.7.12]# cd /usr/local/python3/bin && ll
total 31600
lrwxrwxrwx. 1 root root        8 Dec  1 01:07 2to3 -> 2to3-3.7
-rwxr-xr-x. 1 root root      109 Dec  1 01:07 2to3-3.7
-rwxr-xr-x. 1 root root      246 Dec  1 01:08 easy_install-3.7
lrwxrwxrwx. 1 root root        7 Dec  1 01:07 idle3 -> idle3.7
-rwxr-xr-x. 1 root root      107 Dec  1 01:07 idle3.7
-rwxr-xr-x. 1 root root      237 Dec  1 01:08 pip3
-rwxr-xr-x. 1 root root      237 Dec  1 01:08 pip3.7
lrwxrwxrwx. 1 root root        8 Dec  1 01:07 pydoc3 -> pydoc3.7
-rwxr-xr-x. 1 root root       92 Dec  1 01:07 pydoc3.7
lrwxrwxrwx. 1 root root        9 Dec  1 01:07 python3 -> python3.7
-rwxr-xr-x. 2 root root 16161800 Dec  1 01:07 python3.7
lrwxrwxrwx. 1 root root       17 Dec  1 01:07 python3.7-config -> python3.7m-config
-rwxr-xr-x. 2 root root 16161800 Dec  1 01:07 python3.7m
-rwxr-xr-x. 1 root root     2910 Dec  1 01:07 python3.7m-config
lrwxrwxrwx. 1 root root       16 Dec  1 01:07 python3-config -> python3.7-config
lrwxrwxrwx. 1 root root       10 Dec  1 01:07 pyvenv -> pyvenv-3.7
-rwxr-xr-x. 1 root root      449 Dec  1 01:07 pyvenv-3.7
[root@lianglab bin]#

使用软连接将python3编译器和pip链接到/usr/bin里，方便在命令行里调用：
 

ln -s /usr/local/python3/bin/python3 /usr/bin/python3
ln -s /usr/local/python3/bin/pip3 /usr/bin/pip3

[root@lianglab bin]# ln -s /usr/local/python3/bin/python3 /usr/bin/python3
[root@lianglab bin]# ln -s /usr/local/python3/bin/pip3 /usr/bin/pip3
[root@lianglab bin]#



最后在命令行里输入python3查看能否打开python3编译器：

[root@lianglab bin]# python3
Python 3.7.12 (default, Dec  1 2023, 01:06:32)
[GCC 9.3.1 20200408 (Red Hat 9.3.1-2)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

————————————————

wget https://www.python.org/ftp/python/3.7.12/Python-3.7.12.tgz

image-20231201010132320

image-20231201010014264

image-20231201010320398

image-20231201010449438

image-20231201010907663

image-20231201011028364

image-20231201011314266

image-20231201011341530

5、安装Gromacs
官网下载

下载安称耍装包: https://ftp.gromacs.org/gromacs/gromacs-2023.3.tar.gz
(用辞泥系统自带的下载工具下载) (如下图)

$   tar xfz gromacs-2019.6.tar.gz  (解压安装包)
$   cd gromacs-2019.6   (进入目录)
$   mkdir build    (新建文件夹build)  (如下图)
$   cd build     (进入目录)
$   cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.6  (要求安装过程中自动下载FFTW库文件，指定程序安装到目录/usr/local/gromacs-2019.6)
$   make   (编译时间比较长)
$   make check 
$   sudo make install   (安装)

tar xfz gromacs-2023.3.tar.gz
cd gromacs-2023.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC


[root@lianglab tmp]# tar zxvf gromacs-2023.3.tar.gz

[root@lianglab tmp]# cd gromacs-2023.3
[root@lianglab gromacs-2023.3]# ls
admin  AUTHORS       cmake           COPYING          CPackInit.cmake    docs     python_packaging  scripts  src
api    CITATION.cff  CMakeLists.txt  COPYING.derived  CTestConfig.cmake  INSTALL  README            share    tests
[root@lianglab gromacs-2023.3]# mkdir build
[root@lianglab gromacs-2023.3]# cd build
[root@lianglab build]# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
------------------------------省略---------------------------
-- [download 99% complete]
-- [download 100% complete]
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "4.0.0")
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/gromacs-2023.3/build
[root@lianglab build]# make
------------------------------省略---------------------------
[ 98%] Linking CXX shared library ../../lib/libnblib_gmx.so
[ 98%] Built target nblib
[ 98%] Building CXX object api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o
[ 98%] Linking CXX executable ../../../bin/argon-forces-integration
[ 98%] Built target argon-forces-integration
[ 98%] Building CXX object api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o
[100%] Linking CXX executable ../../../bin/methane-water-integration
[100%] Built target methane-water-integration
[100%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
[100%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o
[100%] Built target mdrun_objlib
[100%] Building CXX object src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o
[100%] Building CXX object src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o
[100%] Built target gmx_objlib
[100%] Linking CXX executable ../../bin/gmx
[100%] Built target gmx
[root@lianglab build]# make check

      Start 84: regressiontests/complex
84/87 Test #84: regressiontests/complex ...................   Passed   77.63 sec
      Start 85: regressiontests/freeenergy
85/87 Test #85: regressiontests/freeenergy ................   Passed   41.03 sec
      Start 86: regressiontests/rotation
86/87 Test #86: regressiontests/rotation ..................   Passed    2.48 sec
      Start 87: regressiontests/essentialdynamics
87/87 Test #87: regressiontests/essentialdynamics .........   Passed    1.54 sec

100% tests passed, 0 tests failed out of 87

Label Time Summary:
GTest              = 245.07 sec*proc (81 tests)
IntegrationTest    = 199.80 sec*proc (25 tests)
MpiTest            = 217.99 sec*proc (19 tests)
QuickGpuTest       =  75.73 sec*proc (17 tests)
SlowGpuTest        = 279.87 sec*proc (18 tests)
SlowTest           =  43.14 sec*proc (13 tests)
UnitTest           =   2.13 sec*proc (43 tests)

Total Test time (real) = 367.83 sec
[100%] Built target run-ctest-nophys
[100%] Built target check
[root@lianglab build]#
[root@lianglab build]#
[root@lianglab build]# make install


[root@lianglab build]# source /usr/local/gromacs/bin/GMXRC

image-20231201011525593

image-20231201011623167

image-20231201011701919

image-20231201011904800

image-20231201020811492

image-20231201020923779

image-20231201024550009

image-20231201024616831

image-20231201024631695

6、备注说明：
首先申明不推荐老系统安装新的软件，太费事了

安装软件的话，首先要考虑环境

首要任务：升级gcc和g++，这块比较顺畅
posted @ 2023-12-01 14:50  亮亮实验室  阅读(627)  评论(0)    收藏  举报