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CESM2.1.3 移植记录_cesm移植记录

作者：小丑西瓜9 | 2024-05-31 22:38:26

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cesm移植记录

前言

这次是在学院超算上配置cesm的运行环境，由于有上一次的记录：CESM移植记录 可以参考，同时由于多次安装相比以前对cesm需求的环境又有了更深的认识，因此更新一下之前的记录，补充之前比较模糊的一些细节。

这次用到的编译器的并行运算是超算上自带的，因此直接导入就行，不需要自己安装。
编译器：intel编译器
并行运算：mpi

module load compiler/2021.3.0
module load mpi/2021.3.0

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安装包存放路径是 /share/home/dq060/install_software/install_cesm/
安装目录是 /share/home/dq060/software/libcesm/
源代码存放目录是 /share/home/dq060/model/cesm
其中，/share/home/dq060 是我账号的home目录，请自行进行替换。

软件安装

注意：在安装之前可能需要退出anaconda的虚拟环境，我在安装时遇到过由于（似乎）存在python3的问题导致perl的一些模块和cmake的安装失败
另注：以前安装时以为git和svn是必须的，因此花了很多时间安装svn，但后来发现git和svn只是用来下载cesm的源码的，如果已经有完整源码了，就无需安装这两个软件了，在最后把我下载好的4个版本的cesm源码打包分享出来，只要直接解压就可以用了。

1. perl5

perl5 这次的安装与之前有较多的补充，为了区分，把 perl5 的版本升级成了 5.36.1，安装包可以自行在GitHub下载，或者用回之前的版本也行，改改脚本里的版本号就可以了。

01_perl5.sh

export CC=icc
export CXX=icpc
export CPP='icc -E'
export CXXCPP='icpc -E'
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPPFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=ifort
export FC=ifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export FCLAGS='-O3 -xHost -ip -no-prec-div -static-intel'

DIR=/share/home/dq060/software/libcesm/perl5

tar -xvf perl-5.36.1.tar.gz
cd perl-5.36.1
./Configure -des -Dusethreads -Dprefix=${DIR}
make
make test
make install

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安装好了之后在 ~/.bashrc 中直接配置包括perl5在内的环境变量，这样之后安装完其他软件之后就无需重复 source ~/.bashrc 了，环境变量可参考最后的 env_cesm.sh 。不提前配置是因为安装perl5时如果存在 CPATH 变量会导致循环include带来的异常

# perl5
export PATH=/share/home/dq060/software/libcesm/perl5/bin:$PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/perl5/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/perl5/lib:$LD_LIBRARY_PATH

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用 perl --version 验证

This is perl 5, version 36, subversion 1 (v5.36.1) built for x86_64-linux-thread-multi

Copyright 1987-2023, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at https://www.perl.org/, the Perl Home Page.

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相比上次的补充
cesm 运行必须的perl模块有 Alien::LibXML、 Alien::Libxml2、 XML::LibXML，需要提前装好，否则之后开始编译 cesm 的 case 时，会报perl找不到某些模块的错。
以下过程需要网络连接，不需要网络的安装过程我自己试了一半就放弃了，太麻烦了

# 以下命令查看安装了哪些模块，可用来前后对照
# find `perl -e 'print "@INC"'` -name '*.pm' -print
# find `perl -e 'print "@INC"'` -name '*.pm' -print | grep XML
##############能联网情况
# 利用cpan直接安装Alien::LibXML，会自动下载安装所有依赖模块
cpan install Alien::LibXML
cpan install Alien::Libxml2
# XML::LibXML依赖于 XML::SAX
cpan install XML::SAX
# 手动安装XML::LibXML，因为我这里35huge_mode的test不通过，通过修改35huge_mode.t使其跳过该项测试，最终编译结果不影响使用，或者在make之后直接make install
tar -xvf XML-LibXML-2.0208.tar.gz
cd XML-LibXML-2.0208
perl Makefile.PL
make
# 修改35huge_mode.t
# 把其中
# if (XML::LibXML::LIBXML_VERSION() < 20700) {
#     plan skip_all => "XML_PARSE_HUGE option not supported for libxml2 < 2.7.0";
# }
# else {
#     plan tests => 5;
# }
# 改为
# plan skip_all => "skip this test";
# 继续进行test和install
make test
make install

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如果不联网，需要自己在cpan官网下对应模块的安装包，再一个个手动编译安装，折腾了一下午，发现才只装了一半，而且发现中途某个包的 make test 似乎仍然需要联网，所以直接放弃了，不过大致需要的前置模块如下所示，可以参考一下：

##############不能联网情况
# 依次安装
# inc::latest
cd ..
tar -xvf inc-latest-0.500.tar.gz
cd inc-latest-0.500
perl Makefile.PL
make
make test
make install
# MRO::Compat
cd ..
tar -xvf MRO-Compat-0.15.tar.gz
cd MRO-Compat-0.15
perl Makefile.PL
make
make test
make install
# Params::Util
cd ..
tar -xvf Params-Util-1.102.tar.gz
cd Params-Util-1.102
perl Makefile.PL
make
make test
make install
# Sub::Install
cd ..
tar -xvf Sub-Install-0.929.tar.gz
cd Sub-Install-0.929
perl Makefile.PL
make
make test
make install
# Data::OptList
cd ..
tar -xvf Data-OptList-0.114.tar.gz
cd Data-OptList-0.114
perl Makefile.PL
make
make test
make install
# Sub::Exporter
cd ..
tar -xvf Sub-Exporter-0.989.tar.gz
cd Sub-Exporter-0.989
perl Makefile.PL
make
make test
make install
# Capture::Tiny
cd ..
tar -xvf Capture-Tiny-0.48.tar.gz
cd Capture-Tiny-0.48
perl Makefile.PL
make
make test
make install
# Test::FailWarnings
cd ..
tar -xvf Test-FailWarnings-0.008.tar.gz
cd Test-FailWarnings-0.008
perl Makefile.PL
make
make test
make install
# Data::Section
cd ..
tar -xvf Data-Section-0.200008.tar.gz
cd Data-Section-0.200008
perl Makefile.PL
make
make test
make install
# Test::More::UTF8
cd ..
tar -xvf Test-More-UTF8-0.05.tar.gz
cd Test-More-UTF8-0.05
perl Makefile.PL
make
make test
make install
# Test::Warnings
cd ..
tar -xvf Test-Warnings-0.031.tar.gz
cd Test-Warnings-0.031
perl Makefile.PL
make
make test
make install
# Text::Template
cd ..
tar -xvf Text-Template-1.61.tar.gz
cd Text-Template-1.61
perl Makefile.PL
make
make test
make install
# Try::Tiny
cd ..
tar -xvf Try-Tiny-0.31.tar.gz
cd Try-Tiny-0.31
perl Makefile.PL
make
make test
make install
# Software::License
cd ..
tar -xvf Software-License-0.104004.tar.gz
cd Software-License-0.104004
perl Makefile.PL
make
make test
make install
# Module::Build
cd ..
perl Makefile.PL
make
make test
make install
# Importer
cd ..
tar -xvf Importer-0.026.tar.gz
cd Importer-0.026
perl Makefile.PL
make
make test
make install
# Term::Table
cd ..
tar -xvf Term-Table-0.016.tar.gz
cd Term-Table-0.016
perl Makefile.PL
make
make test
make install
# Test2::V0
cd ..
tar -xvf Test2-Suite-0.000155.tar.gz
cd Test2-Suite-0.000155
perl Makefile.PL
make
make test
make install
# Test::Fatal
cd ..
tar -xvf Test-Fatal-0.017.tar.gz 
cd Test-Fatal-0.017
perl Makefile.PL
make
make test
make install
# Test::Needs
cd ..
tar -xvf Test-Needs-0.002010.tar.gz
cd Test-Needs-0.002010
perl Makefile.PL
make
make test
make install
# URI::file
cd ..
tar -xvf URI-5.19.tar.gz
cd URI-5.19
perl Makefile.PL
make
make test
make install
# File::chdir
cd ..
tar -xvf File-chdir-0.1011.tar.gz
cd File-chdir-0.1011
perl Makefile.PL
make
make test
make install
# Sort::Versions
tar -xvf Sort-Versions-1.62.tar.gz
cd Sort-Versions-1.62
perl Makefile.PL
make
make test
make install
# Path::Tiny
cd ..
tar -xvf Path-Tiny-0.144.tar.gz
cd Path-Tiny-0.144
perl Makefile.PL
make
make test
make install
# Archive::Extract
cd ..
tar -xvf Archive-Extract-0.88.tar.gz
cd Archive-Extract-0.88
perl Makefile.PL
make
make test
make install
# File::Which
cd ..
tar -xvf File-Which-1.27.tar.gz
cd File-Which-1.27
perl Makefile.PL
make
make test
make install
# FFI::CheckLib
cd ..
tar -xvf FFI-CheckLib-0.31.tar.gz
cd FFI-CheckLib-0.31
perl Makefile.PL
make
make test
make install
# Alien::Base
cd ..
tar -xvf Alien-Build-2.80.tar.gz 
cd Alien-Build-2.80
perl Makefile.PL
make
make test
make install
# Shell::Guess
cd ..
tar -xvf Shell-Guess-0.09.tar.gz 
cd Shell-Guess-0.09
perl Makefile.PL
make
make test
make install
# Shell::Config::Generate
cd ..
tar -xvf Shell-Config-Generate-0.34.tar.gz 
cd Shell-Config-Generate-0.34
perl Makefile.PL
make
make test
make install
# Alien::Base::ModuleBuild
cd ..
tar -xvf Alien-Base-ModuleBuild-1.17.tar.gz
cd Alien-Base-ModuleBuild-1.17
perl Build.PL
./Build
./Build test
./Build install
# Alien:LibXML
tar -xvf Alien-LibXML-0.004.tar.gz
cd Alien-LibXML-0.004
perl Build.PL
./Build # 这一步似乎要联网下载libxml2,看看后续怎么改
./Build test
./Build install
# Alien::Build::Plugin::Download::GitLab
cd ..
tar -xvf Alien-Build-Plugin-Download-GitLab-0.01.tar.gz
cd Alien-Build-Plugin-Download-GitLab-0.01
perl Makefile.PL
make
make test
make install
# Mozilla::CA
cd ..
tar -xvf Mozilla-CA-20221114.tar.gz
cd Mozilla-CA-20221114
perl Makefile.PL
make
make test
make install
# Net::SSLeay
cd ..
tar -xvf Net-SSLeay-1.92.tar.gz 
cd Net-SSLeay-1.92

# IO::Socket::SSL
cd ..
tar -xvf IO-Socket-SSL-2.083.tar.gz 
cd IO-Socket-SSL-2.083


# Alien::Libxml2
cd ..
tar -xvf Alien-Libxml2-0.19.tar.gz
cd Alien-Libxml2-0.19


# XML::LibXML，修改35huge_mode.t使其跳过该项测试
cd ..
tar -xvf XML-LibXML-2.0208.tar.gz
cd XML-LibXML-2.0208

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==下面的软件安装均和以前一样，不展开了，细节可参考 CESM移植记录 ==

2. cmake

02_cmake.sh

export CC=icc
export CXX=icpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPP='icc -E'
export CXXCPP='icpc -E'

DIR=/share/home/dq060/software/libcesm/cmake

tar -xvf cmake-2.8.12.2.tar.gz
cd cmake-2.8.12.2
./bootstrap --prefix=${DIR}
make
make install

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配置cmake环境变量。

# cmake
export PATH=/share/home/dq060/software/libcesm/cmake/bin:$PATH

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用 cmake --version 验证

cmake version 2.8.12.2

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4. zlib

04_zlib.sh

export CC=icc
export CXX=icpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPP='icc -E'
export CXXCPP='icpc -E'

DIR=/share/home/dq060/software/libcesm/zlib

tar -xvf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure --prefix=${DIR}
make
make check
make install

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配置 zlib 环境变量。

# zlib
export CPATH=/share/home/dq060/software/libcesm/zlib/include:$CPATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/zlib/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/zlib/lib:$LD_LIBRARY_PATH

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5. hdf5

05_hdf5.sh

export CC=mpiicc
export CXX=mpiicpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=mpiifort
export FC=mpiifort
export F90=mpiifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPP='icc -E'
export CXXCPP='icpc -E'

DIR=/share/home/dq060/software/libcesm/hdf5

tar -xvf hdf5-1.10.4.tar.gz
cd hdf5-1.10.4
./configure --with-zlib=/share/home/dq060/software/libcesm/zlib --prefix=${DIR} --enable-fortran --enable-fortran2003 -enable-parallel --with-pic
make
make check
make install

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配置 hdf5 环境变量。

# hdf5
export PATH=/share/home/dq060/software/libcesm/hdf5/bin:$PATH
export CPATH=/share/home/dq060/software/libcesm/hdf5/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/hdf5/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/hdf5/lib:$LIBRARY_PATH

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6. pnetcdf

06_pnetcdf.sh

export CC=mpiicc
export CXX=mpiicpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel -fPIC'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel -fPIC'
export F77=mpiifort
export FC=mpiifort
export F90=mpiifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel -fPIC'
export CPP='mpiicc -E'
export CXXCPP='mpiicpc -E'

DIR=/share/home/dq060/software/libcesm/pnetcdf

tar -xvf pnetcdf-1.12.0.tar.gz
cd pnetcdf-1.12.0
./configure --prefix=${DIR} --enable-relax-coord-bound

make
make check
make install

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配置 pnetcdf 环境变量

# pnetcdf
export PATH=/share/home/dq060/software/libcesm/pnetcdf/bin:$PATH
export CPATH=/share/home/dq060/software/libcesm/pnetcdf/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/pnetcdf/lib:$LD_LIBRARY_PATH
export MANPATH=/share/home/dq060/software/libcesm/pnetcdf/share/man:$MANPATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/pnetcdf/lib:$LIBRARY_PATH

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7. netcdf-c

07_netcdf_c.sh

export CC=mpiicc
export CXX=mpiicpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=mpiifort
export FC=mpiifort
export F90=mpiifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPP='icc -E'
export CXXCPP='icpc -E'
export CPPFLAGS='-I/share/home/dq060/software/libcesm/hdf5/include -I/share/home/dq060/software/libcesm/pnetcdf/include'
export LDFLAGS='-L/share/home/dq060/software/libcesm/hdf5/lib -L/share/home/dq060/software/libcesm/pnetcdf/lib'

DIR=/share/home/dq060/software/libcesm/netcdf

tar -xvf netcdf-c-4.7.4.tar.gz
cd netcdf-c-4.7.4

./configure --prefix=${DIR} --enable-pnetcdf --disable-dap
make
make check
make install

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配置 netcdf 环境变量。

# netcdf
export PATH=/share/home/dq060/software/libcesm/netcdf/bin:$PATH
export CPATH=/share/home/dq060/software/libcesm/netcdf/include:$CPATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/netcdf/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/netcdf/lib:$LD_LIBRARY_PATH
export MANPATH=/share/home/dq060/software/libcesm/netcdf/share/man:$MANPATH

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用 nc-config --all 验证

This netCDF 4.7.4 has been built with the following features: 

  --cc            -> mpiicc
  --cflags        -> -I/share/home/dq060/software/libcesm/netcdf/include -I/share/home/dq060/software/libcesm/hdf5/include -I/share/home/dq060/software/libcesm/pnetcdf/include
  --libs          -> -L/share/home/dq060/software/libcesm/netcdf/lib -lnetcdf
  --static        -> -lpnetcdf -lhdf5_hl -lhdf5 -lm -lz 

  --has-c++       -> no
  --cxx           -> 

  --has-c++4      -> no
  --cxx4          -> 

  --has-fortran   -> yes
  --fc            -> mpiifort
  --fflags        -> -I/share/home/dq060/software/libcesm/netcdf/include -I/share/home/dq060/software/libcesm/netcdf/include
  --flibs         -> -L/share/home/dq060/software/libcesm/netcdf/lib -lnetcdff
  --has-f90       -> 
  --has-f03       -> yes

  --has-dap       -> no
  --has-dap2      -> no
  --has-dap4      -> no
  --has-nc2       -> yes
  --has-nc4       -> yes
  --has-hdf5      -> yes
  --has-hdf4      -> no
  --has-logging   -> no
  --has-pnetcdf   -> yes
  --has-szlib     -> no
  --has-cdf5      -> yes
  --has-parallel4 -> yes
  --has-parallel  -> yes

  --prefix        -> /share/home/dq060/software/libcesm/netcdf
  --includedir    -> /share/home/dq060/software/libcesm/netcdf/include
  --libdir        -> /share/home/dq060/software/libcesm/netcdf/lib
  --version       -> netCDF 4.7.4


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8. netcdf-fortran

注意，两个要装在同一目录下
参数中除了之前的 hdf5 和 pnetcdf 外，还要带上上一步的 netcdf-c。

08_netcdf_f.sh

export CC=mpiicc
export CXX=mpiicpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=mpiifort
export FC=mpiifort
export F90=mpiifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPP='icc -E'
export CXXCPP='icpc -E'
export CFLAGS=$(nc-config --cflags)
export CPPFLAGS='-I/share/home/dq060/software/libcesm/netcdf/include -I/share/home/dq060/software/libcesm/hdf5/include -I/share/home/dq060/software/libcesm/pnetcdf/include'
export LDFLAGS='-L/share/home/dq060/software/libcesm/netcdf/lib -L/share/home/dq060/software/libcesm/hdf5/lib -L/share/home/dq060/software/libcesm/pnetcdf/lib'

DIR=/share/home/dq060/software/libcesm/netcdf

tar -xvf netcdf-fortran-4.5.3.tar.gz
cd netcdf-fortran-4.5.3
./configure --prefix=${DIR} --enable-pnetcdf
make
make check
make install

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验证 nf-config --all

This netCDF-Fortran 4.5.3 has been built with the following features: 

  --cc        -> mpiicc
  --cflags    -> -I/share/home/dq060/software/libcesm/netcdf/include -I/share/home/dq060/software/libcesm/netcdf/include -I/share/home/dq060/software/libcesm/hdf5/include -I/share/home/dq060/software/libcesm/pnetcdf/include

  --fc        -> mpiifort
  --fflags    -> -I/share/home/dq060/software/libcesm/netcdf/include -I/share/home/dq060/software/libcesm/netcdf/include
  --flibs     -> -L/share/home/dq060/software/libcesm/netcdf/lib -lnetcdff 
  --has-f90   -> 
  --has-f03   -> yes

  --has-nc2   -> yes
  --has-nc4   -> yes

  --prefix    -> /share/home/dq060/software/libcesm/netcdf
  --includedir-> /share/home/dq060/software/libcesm/netcdf/include
  --version   -> netCDF-Fortran 4.5.3


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9. lapack blas

这两个是线性代数的计算包。
blas包含在lapack的安装包内，但默认不编译，所以要修改 Makefile 文件让它编译。
如下面注释所示，然后通过 make 安装，再进入到LAPACKE文件夹中再 make 一次，最后把产生的 .h 文件和 .a 文件都放到安装目录里面就可以了。

09_lapack_blas.sh

export CC=icc
export CXX=icpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPP='icc -E'
export CXXCPP='icpc -E'

DIR=/share/home/dq060/software/libcesm/lapack

tar -xvf lapack-3.10.1.tar.gz
cd lapack-3.10.1
cp INSTALL/make.inc.ifort make.inc

# 修改Makefile文件使其编译blas
sed -i '12s/^/#/g'  Makefile
sed -i '13s/#//g'  Makefile
# /*******************************************************************
# .PHONY: lib
# lib: lapacklib tmglib
# #lib: blaslib variants lapacklib tmglib
# 变成
# .PHONY: lib
# #lib: lapacklib tmglib
# lib: blaslib variants lapacklib tmglib
# *******************************************************************/

make
cd LAPACKE
make

mkdir ${DIR}
mkdir ${DIR}/include
mkdir ${DIR}/lib

cp include/*.h ${DIR}/include/

cd ..
cp *.a ${DIR}/lib/
make
cd LAPACKE
make

mkdir ${DIR}
mkdir ${DIR}/include
mkdir ${DIR}/lib

cp include/*.h ${DIR}/include/

cd ..
cp *.a ${DIR}/lib/

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配置环境变量

# lapack
export CPATH=/share/home/dq060/software/libcesm/lapack/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/lapack/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/lapack/lib:$LIBRARY_PATH

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10. esmf
同以前一样，不过因为对比了两个版本 esmf 的不同而修改了下安装路径，参考了许多帖子之后还是选择了比较旧的 esmf 7.1.0

10_esmf.sh

ESMF_HOME=/share/home/dq060/software/libcesm/esmf_7_1_0/esmf-ESMF_7_1_0r
export ESMF_DIR=$ESMF_HOME
export ESMF_COMM=intelmpi
export ESMF_COMPILER=intel
export ESMF_ABI=64
export ESMF_INSTALL_PREFIX=/share/home/dq060/software/libcesm/esmf_7_1_0/install
export ESMF_NETCDF_INCLUDE=/share/home/dq060/software/libcesm/netcdf/include
export ESMF_NETCDF_LIBPATH=/share/home/dq060/software/libcesm/netcdf/lib
export ESMF_NETCDF_LIBS="-lnetcdf -lnetcdff"

export ESMF_CCOMPILER="mpiicc -cc=icc"
export ESMF_CXXCOMPILER=mpiicpc
export ESMF_CXXLINKER=mpiicpc
export ESMF_F90COMPILER=mpiifort
export ESMF_F90LINKER=mpiifort

unzip esmf-ESMF_7_1_0r.zip -d /share/home/dq060/software/libcesm/esmf_7_1_0/
cd $ESMF_DIR
make
make check 
make install 

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配置环境变量

# esmf
export PATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/bin/binO/Linux.intel.64.intelmpi.default:$PATH
export CPATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/lib/libO/Linux.intel.64.intelmpi.default:$LD_LIBRARY_PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/lib/libO/Linux.intel.64.intelmpi.default:$LIBRARY_PATH

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cesm环境

我把 cesm 的运行环境的环境变量放在软件安装目录下的一个shell脚本里面，这样只要每次登录后 source 一下该脚本即可。
位置： /share/home/dq060/software/libcesm/env_cesm.sh

env_cesm.sh

# compiler and mpi
module load compiler/2021.3.0
module load mpi/2021.3.0

# perl5
export PATH=/share/home/dq060/software/libcesm/perl5/bin:$PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/perl5/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/perl5/lib:$LD_LIBRARY_PATH

# cmake
export PATH=/share/home/dq060/software/libcesm/cmake/bin:$PATH

# zlib
export CPATH=/share/home/dq060/software/libcesm/zlib/include:$CPATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/zlib/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/zlib/lib:$LD_LIBRARY_PATH

# hdf5
export PATH=/share/home/dq060/software/libcesm/hdf5/bin:$PATH
export CPATH=/share/home/dq060/software/libcesm/hdf5/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/hdf5/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/hdf5/lib:$LIBRARY_PATH

# pnetcdf
export PATH=/share/home/dq060/software/libcesm/pnetcdf/bin:$PATH
export CPATH=/share/home/dq060/software/libcesm/pnetcdf/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/pnetcdf/lib:$LD_LIBRARY_PATH
export MANPATH=/share/home/dq060/software/libcesm/pnetcdf/share/man:$MANPATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/pnetcdf/lib:$LIBRARY_PATH

# netcdf
export PATH=/share/home/dq060/software/libcesm/netcdf/bin:$PATH
export CPATH=/share/home/dq060/software/libcesm/netcdf/include:$CPATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/netcdf/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/netcdf/lib:$LD_LIBRARY_PATH
export MANPATH=/share/home/dq060/software/libcesm/netcdf/share/man:/$MANPATH

# lapack
export CPATH=/share/home/dq060/software/libcesm/lapack/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/lapack/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/lapack/lib:$LIBRARY_PATH

# esmf
export PATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/bin/binO/Linux.intel.64.intelmpi.default:$PATH
export CPATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/include:$CPATH
export LD_LIBRARY_PATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/lib/libO/Linux.intel.64.intelmpi.default:$LD_LIBRARY_PATH
export LIBRARY_PATH=/share/home/dq060/software/libcesm/esmf_7_1_0/install/lib/libO/Linux.intel.64.intelmpi.default:$LIBRARY_PATH

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cesm源代码移植

源代码

我目前使用的cesm版本为 2.1.3，这个是目前比较稳定的版本，注意，某些 compset 和 res 的搭配可能在某个版本上是可以的，但在更新版本中则要加上 --run-unsupported 这个标签才能创建 case。

源码在超算上的路径： /share/home/dq060/model/cesm/cesm_2.1.3
输入数据在超算上的路径： /share/home/dq060/model/cesm/inputdata
cesm输出在超算上的路径：/share/home/dq060/model/cesm/scratch

cesm下载好全部组件的源代码链接：

链接：https://pan.baidu.com/s/1M6l-trumaqswWw3JwSs3nA?pwd=aqyj 
提取码：aqyj

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配置

然后在自己 home 目录下新建文件夹 .cime ，将以下三个配置文件放到这个目录下，用来覆盖cesm原有的配置，配置文件的含义可以参考上一篇博客，这里只指出一些新的修改和细节。

  1. config_machines.xml
<?xml version="1.0"?> 
<config_machines version="2.0">
  <machine MACH="daqi">
    <DESC>test</DESC>
    <NODENAME_REGEX>ln9.*</NODENAME_REGEX>
    <OS>LINUX</OS>
    <COMPILERS>intel</COMPILERS>
    <MPILIBS>intelmpi</MPILIBS>
    <PROJECT>none</PROJECT>
    <CIME_OUTPUT_ROOT>$ENV{HOME}/model/cesm/scratch</CIME_OUTPUT_ROOT>
    <DIN_LOC_ROOT>$ENV{HOME}/model/cesm/inputdata</DIN_LOC_ROOT>
	<DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/model/cesm/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
    <DOUT_S_ROOT>$ENV{HOME}/model/cesm/scratch/$CASE</DOUT_S_ROOT>
    <BASELINE_ROOT>$ENV{HOME}/model/cesm/baselines</BASELINE_ROOT>
    <CCSM_CPRNC>$ENV{HOME}/model/cesm/cesm_2.1.3/cime/tools/cprnc</CCSM_CPRNC>

    <GMAKE>make</GMAKE>
    <GMAKE_J>8</GMAKE_J>
    <BATCH_SYSTEM>none</BATCH_SYSTEM>
    <SUPPORTED_BY>ouzhliang@mail2.sysu.edu.cn</SUPPORTED_BY>
    <MAX_TASKS_PER_NODE>48</MAX_TASKS_PER_NODE>
    <MAX_MPITASKS_PER_NODE>48</MAX_MPITASKS_PER_NODE>
    <PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
    <mpirun mpilib="default">
      <executable>mpirun</executable>
        <arguments>
          <arg name="num_tasks" > -n {{ total_tasks }}</arg>
        </arguments>
    </mpirun>
    <module_system type="none"></module_system>
    <environment_variables>
      <env name="OMP_STACKSIZE">256M</env>
    </environment_variables>
    <resource_limits>
      <resource name="RLIMIT_STACK">-1</resource>
    </resource_limits>
  </machine>
</config_machines>


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其中，
<machine> 是机器的名称，可以理解为方便模式识别的id，主要用于创建case时指定某种配置。

<CIME_OUTPUT_ROOT> 就是模式输出的数据的存放目录，这里统一将所有输出放在 $ENV{HOME}/model/cesm/scratch 这个目录下，这里的 $ENV{HOME} 是自适应的写法，会根据自己的用户目录进行替换，以前以为是不能这样用的，但看了别人的配置文件后学会了这么写，当然更简单的是直接用绝对路径。

<DIN_LOC_ROOT> 就是模式输入数据的存放目录，这里统一将所有输入文件放在 $ENV{HOME}/model/cesm/inputdata 方便不同版本的cesm共同调用。

<DOUT_S_ROOT> 就是模式最终输出数据的存放目录，这里统一将所有输出放在 $ENV{HOME}/model/cesm/scratch/$CASE 中，$CASE 是创建case时的名字，模式的输出会归档到每个case下面。再详细点其实就是，在模式运行过程中的中间输出会暂时存放在该目录下的 run 文件夹，一旦运行完成，就会把所有输出分门别类地移动到其他文件夹，如 atm 表示大气模块相关的输出的存放位置； rest 表示模式重启所需的重启动文件的存放位置。

<MAX_TASKS_PER_NODE> 和<MAX_MPITASKS_PER_NODE> 就是模式在单个节点使用的最大核数，按照超算的数据填写即可。

  1. config_compilers.xml
<?xml version="1.0"?>
<config_compilers version="2.0">
  <compiler COMPILER="intel" MACH="daqi">
    <CPPDEFS>
      <append>-DLINUX</append>
    </CPPDEFS>
    <LDFLAGS>
      <append compile_threaded="TRUE"> -fopenmp </append>
      <!-- <append> -mkl </append> -->
    </LDFLAGS>
    <CFLAGS>
      <append DEBUG="FALSE"> -O2 </append>
    </CFLAGS>
    <CONFIG_ARGS>
      <base> --host=Linux </base>
    </CONFIG_ARGS>
    <FFLAGS>
      <append DEBUG="FALSE"> -O2 </append>
    </FFLAGS>
    <SCC>/share/apps/lico/intel/oneapi/compiler/2021.3.0/linux/bin/intel64/icc</SCC>
    <SCXX>/share/apps/lico/intel/oneapi/compiler/2021.3.0/linux/bin/intel64/icpc</SCXX>
    <SFC>/share/apps/lico/intel/oneapi/compiler/2021.3.0/linux/bin/intel64/ifort</SFC>
    <MPICC>/share/apps/lico/intel/oneapi/mpi/2021.3.0/bin/mpiicc</MPICC>
    <MPICXX>/share/apps/lico/intel/oneapi/mpi/2021.3.0/bin/mpiicpc</MPICXX>
    <MPIFC>/share/apps/lico/intel/oneapi/mpi/2021.3.0/bin/mpiifort</MPIFC>

    <ESMF_LIBDIR>/share/home/dq060/software/libcesm/esmf_7_1_0/install/lib/libO/Linux.intel.64.intelmpi.default</ESMF_LIBDIR>
    <MPI_PATH>/share/apps/lico/intel/oneapi/mpi/2021.3.0/bin</MPI_PATH>
    <NETCDF_PATH>/share/home/dq060/software/libcesm/netcdf</NETCDF_PATH>
    <PNETCDF_PATH>/share/home/dq060/software/libcesm/pnetcdf</PNETCDF_PATH>

    <SLIBS>
      <append>-L/share/home/dq060/software/libcesm/netcdf/lib -lnetcdf -lnetcdff -L/share/home/dq060/software/libcesm/hdf5/lib -lhdf5 -lhdf5_hl -L/share/home/dq060/software/libcesm/zlib/lib -lz -L/share/home/dq060/software/libcesm/lapack/lib -llapack</append>
    </SLIBS>
  </compiler>
</config_compilers>

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其中，
<SCC> 至 <MPIFC> 的这些标签分别指各编译器的执行路径，这里可以直接用命令而不用给出完整路径，不过我为了稳妥一点还是用完整路径了。

ESMF_LIBDIR 指 esmf 的动态链接库的目录，这个标签十分重要，错误的话会导致cesm运行时报错。

<SLIBS> 里相比上次删掉了 -mkl 因为发现超算上的intel编译器似乎没有 mkl 这个功能（我也不是很动这个），报错了好几次，所以直接删掉不添加了。

注意：以上<SCC> 等标签不要分行写，即，不要写成

<SCC>
/share/apps/lico/intel/oneapi/compiler/2021.3.0/linux/bin/intel64/icc
</SCC>

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不然会在编译过程中会报错在make文件里发现了不合适的分隔符，原因就是这里的换行符也会被直接传进去make文件里

  1. config_batchs.xml
    自己用命令提交超算作业，所以这里设置为空白。
<?xml version="1.0"?>
<config_batch version="2.0">
  <batch_system MACH="daqi" type="none" >
  </batch_system>
</config_batch>

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结语

因为最近在跑 WACCM-X 的原因，重装了cesm很多次来排查问题，所以安装基本上能碰到的坑都踩了一遍了，这次也正好记录下来供大家参考一下。csdn的私信我不是经常看，如果文中有错误的地方或者有写不清楚的地方的话，可以发邮件给我大家一起讨论~
我的邮箱：ouzhliang@mail2.sysu.edu.cn

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