linux怎么自学（linux怎么学知乎）

大家好，我是讯享网，很高兴认识大家。

gpaw 是一款效率比较高的第一性原理计算软件，在接近vasp的计算精度情况下，只消耗20%的时间。官网为：

安装介绍：Installation - GPAW

这个可以安装在自己的电脑，用来作为测试使用。

yum&nbsp;install&nbsp;epel-release&nbsp;#有些程序包在这里面&nbsp;yum&nbsp;install&nbsp;libxc-devel&nbsp;openblas-devel&nbsp;openmpi-devel&nbsp;fftw-devel&nbsp;yum&nbsp;install&nbsp;blacs-openmpi-devel&nbsp;scalapack-openmpi-devel

讯享网

.bashrc 加入：

OPENMPI=/usr/lib64/openmpi
export PATH= $OPENMPI/bin/:$PATH
export LD_LIBRARY_PATH= $OPENMPI/lib:$LD_LIBRARY_PATH
export GPAW_SETUP PATH=/home/yourusername/gpaw_setups/gpaw-setups-0.9.20000.tar.gz

其中setups文件从官网下载：https://setups/setups.html#installation-of-paw-datasets。

2. 安装gpaw:

讯享网pip&nbsp;install&nbsp;gpaw

讯享网

结果如上图所示，这种安装方式功能有限，并且因为为了方便，配置内容都放在了.bashrc，比较混乱。

yum&nbsp;install&nbsp;epel-release&nbsp;#有些程序包在这里面&nbsp;yum&nbsp;install&nbsp;libxc-devel&nbsp;openblas-devel&nbsp;openmpi-devel&nbsp;fftw-devel&nbsp;yum&nbsp;install&nbsp;blacs-openmpi-devel&nbsp;scalapack-openmpi-devel

从gitlab下载gpaw.tar.gz,，解压并修改配置文件siteconfig.py。（若没有可创建，或者更改已存在的siteconfig_exapmle.py 为siteconfig.py）：

讯享网tar&nbsp;-xf&nbsp;gpaw.tar.gz&nbsp; cd&nbsp;pgaw vim&nbsp;siteconfig.py

写入：

# FFTW3:
fftw = True
if fftw:
libraries = [‘fftw3’]

# openblas
openblas = True
if openblas :
libraries +=[‘openblas’]

# mpiblacs

mpiblacs = True
if mpiblacs :
libraries +=[‘mpiblacs’]

# ScaLAPACK (version 2.0.1+ required):
scalapack = True
if scalapack:
libraries += [‘scalapack’]

# xc:
xc = True
if xc:
libraries += [‘xc’]

# openmp
openmp = False
if openmp:
extra_compile_args += [‘-fopenmp’]
extra_link_args += [‘-fopenmp’]

保存文件，其中 openmp 在并行安装时使用。

2. 安装gpaw:

python&nbsp;setup.py&nbsp;install

结果如下图所示，推荐，其他辅助功能可按照类似方式配置。

ubuntu

注：ubuntu同centos，第一步依赖程序换成：

讯享网sudo&nbsp;apt&nbsp;install&nbsp;libopenblas-dev&nbsp;libxc-dev&nbsp;libscalapack-mpi-dev&nbsp;libfftw3-dev

对于能够联网intel服务器来说这里，可以参考第二种方式。关闭其中的openmp，同时需要在.bashrc文件中加入：

export PATH=/opt/intel2020/compilers_and_libraries_2020.0.166/linux/mpi/:$PATH export PATH=/opt/intel2020/compilers_and_libraries_2020.0.166/linux/mpi/intel64/bin/:$PATH
export PATH=/opt/intel2020/compilers_and_libraries_2020.0.166/linux/:\(PATH</blockquote><p class="ztext-empty-paragraph" style="margin-top: -0.8em; margin-bottom: -0.8em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);"> <p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">intel mpi下载请自行百度，一般使用过一段时间的服务器都已经安装好了，对应位置请自行设置。<p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">对于不能联网服务器，比如某些使用intel cpu的超算，安装最为麻烦，其他种类的cpu请参考他们的文档。<p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">Inter MPI:（不使用openmp）<p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">intel mpi下载请自行百度，一般使用过一段时间的服务器都已经安装好了，对应位置请自行设置。在.bashrc文件中加入：<blockquote style="margin: 1.4em 0px; padding-left: 1em; color: rgb(100, 100, 100); border-left: 3px solid rgb(211, 211, 211); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">export PATH=/opt/intel2020/compilers_and_libraries_2020.0.166/linux/mpi/:\)PATH
export PATH=/opt/intel2020/compilers_and_libraries_2020.0.166/linux/mpi/intel64/bin/:$PATH export PATH=/opt/intel2020/compilers_and_libraries_2020.0.166/linux/:$PATH

libxc:

wget http://www.pus/down.php?file=libxc/4.2.3/libxc-4.2.3.tar.gz -O libxc-4.2.3.tar.gz
tar -xf libxc-4.2.3.tar.gz
cd libxc-4.2.3
https://blog.sciencenet.cn/configure –enable-shared –disable-fortran –prefix=$HOME/libxc-4.2.3 make -j 10 make install</blockquote><p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">添加文件.bashrc:<blockquote style="margin: 1.4em 0px; padding-left: 1em; color: rgb(100, 100, 100); border-left: 3px solid rgb(211, 211, 211); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">XC=~/libxc-4.2.3 export C_INCLUDE_PATH=$XC/include
export LIBRARY_PATH=$XC/lib export LD_LIBRARY_PATH=$XC/lib

(这个过程中，可能会需要设置添加-std=c99, 或者直接更改xc-theshold.c文件第800+行，把i定义放在for循环外。不知道是不是bug? )

openblas （非必须）:

tar -xf openblas.tar.gz
cd openblas
https://blog.sciencenet.cn/configure –prefix=$HOME/openblas make -j 10 make install libraries = ['openblas'] library_dirs = ['path_to_myblas']</blockquote><p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">添加文件.bashrc:<blockquote style="margin: 1.4em 0px; padding-left: 1em; color: rgb(100, 100, 100); border-left: 3px solid rgb(211, 211, 211); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">export C_INCLUDE_PATH=$HOME/openblas/include/:$C_INCLUDE_PATH export LD_LIBRARY_PATH=$HOME/openblas/lib/:$LD_LIBRARY_PATH export LIBRARY_PATH=/$HOME/openblas/lib/:$LIBRARY_PATH export PATH=$HOME/openblas/bin/:\(PATH</blockquote><p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">fftw：<p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">没啥说的，和上面一样，编译安装，其中配置参数注意：<p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">(并行版本)<blockquote style="margin: 1.4em 0px; padding-left: 1em; color: rgb(100, 100, 100); border-left: 3px solid rgb(211, 211, 211); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">https://blog.sciencenet.cn/configure MPICC=mpicc --prefix=\)HOME/fftw –disable-fortran –enable-mpi –enable-shared

(非并行版本)

https://blog.sciencenet.cn/configure –prefix=$HOME/fftw --disable-fortran</blockquote><p style="margin-top: 1.4em; margin-bottom: 1.4em; color: rgb(18, 18, 18); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">添加文件.bashrc:<blockquote style="margin: 1.4em 0px; padding-left: 1em; color: rgb(100, 100, 100); border-left: 3px solid rgb(211, 211, 211); font-family: -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Microsoft YaHei", "Source Han Sans SC", "Noto Sans CJK SC", "WenQuanYi Micro Hei", sans-serif; font-size: medium; white-space: normal; background-color: rgb(255, 255, 255);">export LD_LIBRARY_PATH=/$HOME/fftw/lib/:$LD_LIBRARY_PATH export C_INCLUDE_PATH=$HOME/fftw/include/:$C_INCLUDE_PATH export LIBRARY_PATH=$HOME/fftw/lib/:$LIBRARY_PATH

其他的库请按照该方式自行安装。

2. gpaw：

tar&nbsp;-xf&nbsp;gpaw.tar.gz&nbsp; cd&nbsp;gpaw vim&nbsp;siteconfig.py

siteconfig.py 写入：

libraries += [‘openblas’]
library_dirs += [‘/data/home/wa/openblas/lib/’]

include_dirs +=["/data/home/wa/anaconda3/include/python3.8"]
include_dirs +=["/data/home/wa/anaconda3/lib/python3.8/site-packages/numpy/core/include"]

# FFTW3:
fftw=True

libraries += [‘fftw3’]
ff = ‘/data/home/wa/gpaw/fftw/’
include_dirs += [ff + ‘include’]
library_dirs += [ff + ‘lib’]
extra_link_args += [‘-Wl,-rpath={ff}lib’.format(ff=ff)]

# LibXC:

xc = ‘/data/home/wa/gpaw/libxc/’
include_dirs += [xc + ‘include’]
library_dirs += [xc + ‘lib’]
# You can use rpath to avoid changing LD_LIBRARY_PATH:
extra_link_args += [‘-Wl,-rpath={xc}lib’.format(xc=xc)]
if ‘xc’ not in libraries:
libraries.append(‘xc’)

setup.py 文件写入:

extra_compile_args = [‘-Wall’, ‘-Wno-unknown-pragmas’, ‘-std=c99’,"-Xlinker",]

运行：

讯享网python&nbsp;setup.py&nbsp;build_ext&nbsp;install

这样装完，基本都是动态链接。所以谨慎删除文件。

编辑于 2021-09-18 18:02

                                    <label style="font-size:13px; color:#850f0f">转载本文请联系原作者获取授权，同时请注明本文来自吕铁羽科学网博客。<br />链接地址：</label>https://blog.sciencenet.cn/blog-3471958-1328574.html

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linux怎么自学（linux怎么学 知乎）

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