2020-03-16solps安装流程

作者: 锅炉工的自我修养 | 来源:发表于2020-03-17 22:38 被阅读0次

将最新把版本的solps repository clone to 本地

1. 选择branch

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2. 选择clone 地址

获得ssh协议地址

3. 配置ssh密钥

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复制公钥内容

4. clone repository到本地

clone repository

由于仓库位置恒定，可以把这个仓库设置成远端

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失败

下载成功，会在当前目录下生成 solps-iter文件夹

5. pro git 中文版

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共享空间，没有操作权限

git submodule init # 初始化本地配置文件
git submodule update # 从该项目中抓取所有数据并检出父项目中列出的合适提交

5. 编译solps

runoob 命令查询工具网站

- 1. cd solps.iter

- 2. git submodule init

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初始化本地配置文件

-3. git submodule update

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从project中抓取对应的数据

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此时module中内容已经被下载

-4.开始编译

whereami

1. tr：装换或删除文件中的字符
  
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1. nslookup
  
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1. grep -m
  
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grep 命令

1. hostname
  
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1. set:

set machine_location=`hostname`

将hostname 置零的输出结果赋值给machine_location

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csh 基本命令

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set fullhost=`nslookup $machine_location | grep -m 1 Name | awk '/Name:/{print $2}' | tr 'A-Z' 'a-z'`

查询machine_location 对应变量的DNS信息，匹配第一个是含有 Name的行，打印改行的第二个字段，将第二个四段的大写字母全部换成小写。把结果复制给fullhost

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$HOST_NAME 是自己设置的？

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1. if ... endif

if ("$fullhost" == "") then
  set fullhost=`hostname -f`
endif

如果fullhost的值为空，则将其赋值为 hostname -f 对应的结果（本测试为 sms）,即简略的hostname

1. cut

set mephi_check=`echo $machine_location | cut -c1-4`

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截取变量machine_location按字符计算的1-4个字节（machine_location对应'sms'，只有三个字符），把结果赋值给mephi_check

1. switch

set mephi_check=`echo $machine_location | cut -c1-4`
if ("$mephi_check" == "head" || "$mephi_check" == "node") then
  switch ($fullhost)
  case "*.cm.cluster":
    breaksw
  default:
    echo "mephi_check = $mephi_check - special mephi cluster treatment applies"
    set machine_location="cluster21.mephi.ru"
    set fullhost=$machine_location
  endsw
endif

如果mephi_check对应值为‘head’或者‘node’,则switch fullhost（本测试 fullhostname为‘sms.hlsm.local’）

1. [ -d /af ] : 如果文件存在

 [ -d /afs ] && echo ITM || echo MARCONI

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小结：

whereami脚本通过查询hostname，判断本地集群所在的位置。并将结果打印到屏幕

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解决办法：直接输出你的集群名字，把这个脚本替换掉

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- 1. 修改文件的过程脚本化

#!/bin/bash

# =================== 修改whereami 脚本 ===================== #
# 第二次运行该脚本，保留原始的whereami
if [ -f whereami_orgin ]
then
        mv whereami_orgin whereami
fi
mv whereami whereami_orgin
# 将需要修改的内容重定向到whereami 文件
`echo -e "#!/bin/csh\n echo DUT-PSI"| cat > whereami`
# 给whereami文件加可执行权限
chmod u+x whereami

default_compiler

if (! $?HOST_NAME ) then
  if (-e whereami) then
    set HOST_NAME=`./whereami|tail -1`
  else
    set HOST_NAME="UNKNOWN"
  endif

  if ( $HOST_NAME == "*UNKNOWN*" ) then
    set HOST_NAME=default
  endif
  echo "Using HOST_NAME = $HOST_NAME"
endif

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1. $?HOST_NAME
  
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如果 HOST_NAME的返回值为零，即HOST_NAME没有出错（正常退出的返回值为0）

1. （ - e whereami ）
  
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如果whereami 当前目录存在，执行脚本 whereami,把输出结果的最后一行赋值给HOST_NAME

1. 将DUT-PSI 添加到对应的位置
sed 方法

sed -i '/CCFE/a\case "DUT-PSI"' default_compiler

在 “CCFE”行后添加本课题组的host_name，使编译器默认为 ifort64

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awk方法

# 获取CCFE所在行号
nt=`awk '$2 ~ "CCFE" {print NR} ' default_compiler`
# 在指定的行后添加内容
sed -i "${nt}a\case \"DUT-PSI\"" default_compiler

判断default_compiler中是否存在“DUT-PSI”

# 在指定的行后添加内容,如果不存在DUT-PSI,则添加
flag=`grep DUT-PSI default_compiler`
if [[ !${flag} ]]
then
sed -i "${nt}a\case \"DUT-PSI\"" default_compiler
fi

 [: case: unary operator expected 错误

[ ** ] 表达式为空，通过[[ ** ]] ，可以消除错误

判断变量是否存在
 指定行前后插入行

复制配置文件到lib

初始的lib/目录

目前未知DUT.ifort64如何编译，使用编译好的库

1. 指定源文件位置

用户指定

1. 指定destination

full_path="${base_path}/lib"
# copy the completed lib to new solps package
if [ ! -d "${full_path}/DUT-PSI.ifort64" ]
then
        cp -r ${lib_source} ${full_path}
else
        echo "DUT-PSI.ifrot64 has existed"
fi

如果已经存在，则不复制

在bash脚本中启动 tcsh

1. 不可用
1. 可能的解决方案
  
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不经济，暂停

解决方案——通过bash 产生tcsh脚本，通过bash,调用产生的tcsh脚本

#!/bin/bash

`echo -e "#!/bin/tcsh\n source setup.csh"| cat > start_solps_tcsh`
# 给whereami文件加可执行权限
chmod u+x start_solps_tcsh
./start_solps_tcsh

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通过bash写一个tcsh 文件，重定向，加权限，在bash 中调入用tcsh

scr/first_setup

#! /usr/bin/env ksh
OLD_PWD=$PWD
filename=setup.csh.${HOST_NAME}.${COMPILER}
echo ${filename}
cd $SOLPSTOP/SETUP
[ -s ${filename} ] && {
  echo "Non-empty ${filename} already present in $PWD: nothing done"
} || {
  cp setup.csh.default.default ${filename}
  echo "Created ${filename} from setup.csh.default.default in $PWD: please modify if needed"
}
filename=config.${HOST_NAME}.${COMPILER}
echo ${filename}
[ -s ${filename} ] && {
  echo "Non-empty ${filename} already present in $PWD: nothing done"
} || {
  cp config.default.default ${filename}
  echo "Created ${filename} from config.default.default in $PWD: please modify if needed"
}

如果文件名存在，提示文件已存在，否则根据默认文件产生出示文件，以供修改。
操作的文件包括SETUP和modules的所有子文件夹

小结

通过bash，写文件，写脚本，加权限，然后调用。（终极套娃）；通过bash写tcsh脚本，调用tcsh脚本从而实现，跨shell协作。

修改SETUP/config.DUT-PSI.ifort64

1. 检查NCARG_ROOT 是否设置正确

awk 'BEGIN{FS = "/"} /NCARG_ROOT \?=/ {print $2}' config.DUT-PSI.ifort64

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运行 first_setup,通过lib/DUT-PSI生成对应的modules&SETUP config 文件。

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1. 修改setup.csh.DUT-PSI.ifort64
在指定行之后添加多行文本

sed -i '/# Set/a\i am first\n   i am second\n        i am last!' cong

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1. awk 添加缺省项

 sed 's/?=/& ${SOLPSLIB}/g' config.DUT-PSI.ifort64

awk修改文件

在匹配行的末尾添加文件

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脚本迁移

1. 给一个问价下所有脚本加权限

chmod -R u+x dir

1. 添加快捷方式
  定义群组 user defined

今日成果

完成编译配置文件自动修改脚本
编译成功solps-iter
关闭b2plot自动弹窗
通过编写脚本，熟悉awk命令，以及程序编写的渐进过程
实现在bash中调用tcsh

以下是脚本代码

input: lib/DUT-PSI.ifort64 dir's path
output: compeleted modified configuration file

#!/bin/bash

# =================== 修改whereami 脚本 ===================== #
# 第二次运行该脚本，保留原始的whereami
echo -e  "==================== Modify whereami & default_compiler ======================\n "
if [ -f whereami_orgin ]
then
    mv whereami_orgin whereami
fi
mv whereami whereami_orgin 
# 将需要修改的内容重定向到whereami 文件
`echo -e "#!/bin/csh\n echo DUT-PSI"| cat > whereami`
# 给whereami文件加可执行权限
chmod u+x whereami

# =================== 修改default_complier ================== # 

# sed 方法
#sed -i '/CCFE/a\case "DUT-PSI"' default_compiler

# awk 方法
nt=`awk '$2 ~ "CCFE" {print NR} ' default_compiler`
# 在指定的行后添加内容,如果不存在DUT-PSI,则添加
flag=`grep DUT-PSI default_compiler`
if [[ ! ${flag} ]]
then
    sed -i "${nt}a\case \"DUT-PSI\"" default_compiler
else
    echo "DUT-PSI has existed!"
fi
# =================== 复制编译好的库文件到 lib/ ============= #

# specify the source path (user sepcify)
echo -e  "==================== Specify the lib/DUT-PSI source path ======================\n "
stop_source='/home/zhangyanjie/SOLPS_newest_bak/solps-iter'


lib_source="${stop_source}/lib/DUT-PSI.ifort64"
# get the destination path
base_path=`pwd`
full_path="${base_path}/lib"
# copy the completed lib to new solps package
if [ ! -d "${full_path}/DUT-PSI.ifort64" ] 
then
    cp -r ${lib_source} ${full_path}
    echo "copy DUT-PSI.ifort64 success!"
else    
    echo "DUT-PSI.ifrot64 has existed."
fi 


# ==================== 启动solps ============================= #
echo -e  "==================== Start solps success! ==== ======================\n "
`echo -e "#!/bin/tcsh\n source setup.csh\n first_setup | cat > /dev/null"| cat > start_solps_tcsh`
# 给whereami文件加可执行权限
chmod u+x start_solps_tcsh
./start_solps_tcsh

echo -e  "\n==================== Start modify SETUP config files ===============\n "
# ========================= modify the SETUP/ configuration files =============== #
# 获得SETUP/ path
setup_path="${base_path}/SETUP"

# modify the setup.DUT-PSI.ifort64
flag=`grep HL-2M "${setup_path}/setup.csh.DUT-PSI.ifort64"`

if [[ ! ${flag} ]]
then
    sed -i '/# Set/a\if ( ! $?DEVICE) then\n   setenv DEVICE HL-2M\nendif\nsetenv GLI_HOME ${SOLPSTOP}/{HOST_NAME}.${COMPILER}\nsetenv NCARG_ROOT ${SOLPSTOP}/lib/${HOST_NAME}.${COMPILER}/NCARG' "${setup_path}/setup.csh.DUT-PSI.ifort64"
    echo "Modify setup.csh.DUT-PSI.ifort64 success!"
else 
    echo "setup.csh.DUT-PSI.ifort64 has changed."
fi

echo "SETUP/setup.csh.DUT-PSI.ifort64 change information."
sed -n '/DEVICE/,/NCARG/p' "${setup_path}/setup.csh.DUT-PSI.ifort64"

echo -e "===================================================================\n"



# modify the config.DUT-OSI.ifort64

# 注释掉第一行
sed -i 's/\$(error/#\$(error/' "${setup_path}/config.DUT-PSI.ifort64"

flag=`awk '/?=/ {print NF}' "${setup_path}/config.DUT-PSI.ifort64" | tail -n1`
if [ ${flag} -eq 2 ]
then
    sed -i 's/?=/& ${SOLPSLIB}/g' "${setup_path}/config.DUT-PSI.ifort64" 
    sed -i '/NCARG_ROOT ?=/s/${SOLPSLIB}/${SOLPSLIB}\/NCARG/' "${setup_path}/config.DUT-PSI.ifort64"
    sed -i '/MDSPLUS_DIR ?=/s/${SOLPSLIB}/${SOLPSLIB}\/MDSPLUS/' "${setup_path}/config.DUT-PSI.ifort64"
    echo "Modify config.DUT-PSI.fort64 success!"
else
    echo "config.DUT-PSI.ifort64 has changed."
fi

# add "#" for LD_MPI,delete /lib except for NCARG & MDSPLUS
flag=`awk '/^#L/ {print $1}' "${setup_path}/config.DUT-PSI.ifort64"  `
if [[ ! ${flag} ]]
then
    sed -i '/lmpi/s/LD_MPI/#LD_MPI/' "${setup_path}/config.DUT-PSI.ifort64"
    echo "Modify the #LD_MPI success!"
else
    echo "#LD_MPI has changed."
fi

sed -i '/LD_NETCDF/s/\/lib//' "${setup_path}/config.DUT-PSI.ifort64"
sed -i '/LD_MSCL/s/\/lib//' "${setup_path}/config.DUT-PSI.ifort64"
sed -i '/LD_GR/s/\/lib//' "${setup_path}/config.DUT-PSI.ifort64"
sed -i '/LD_NAG/s/\/lib//' "${setup_path}/config.DUT-PSI.ifort64"
grep error "${setup_path}/config.DUT-PSI.ifort64"
grep NCARG_ROOT "${setup_path}/config.DUT-PSI.ifort64" | head -n1
grep MDSPLUS_DIR "${setup_path}/config.DUT-PSI.ifort64" | head -n1
grep 'L\$' "${setup_path}/config.DUT-PSI.ifort64"
echo "Modify config.DUT-PSI.ifort64 successs!"

# ========================= modify modules configuration files ================== #
echo -e "========================= modify modules configuration files ==================="
module_path="${base_path}/modules" # modules path

# modify B2.5
flag=`grep ffreestanding "${module_path}/B2.5/config/config.DUT-PSI.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/B2.5/config/config.DUT-PSI.ifort64"
    echo "Modify the B2.5 configuration file success!"
else
    echo "B2.5 ffreestranding has changed."
fi

# modify the mpiifort
nr=`awk '/USE_MPI/ {print NR}' "${module_path}/B2.5/config/config.DUT-PSI.ifort64" | head -n 1`
nt=`echo "${nr} + 1"|bc `
#echo ${nt}
sed -i "${nt}s/mpif90/mpiifort/" "${module_path}/B2.5/config/config.DUT-PSI.ifort64"

nr=`awk '/IMPG/ {print NR}' "${module_path}/B2.5/config/config.DUT-PSI.ifort64" | head -n 1`
nt1=`echo "${nr} + 1"|bc `
#echo ${nt}
sed -i  "${nt1}s/mpif90/mpiifort/" "${module_path}/B2.5/config/config.DUT-PSI.ifort64"

# changed information
grep ffree "${module_path}/B2.5/config/config.DUT-PSI.ifort64"

echo "B2.5 mpiifort has changed."
grep mpiifort "${module_path}/B2.5/config/config.DUT-PSI.ifort64"

echo -e "===================================================================\n"


# modify Eirene
flag=`grep ffreestanding "${module_path}/Eirene/config/config.DUT-PSI.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/Eirene/config/config.DUT-PSI.ifort64"
    echo "Modify the Eirene configuration file success!"
else
    echo "Eirene ffreestranding has changed."
fi

# modify the mpiifort
nr=`awk '/USE_MPI/ {print NR}' "${module_path}/Eirene/config/config.DUT-PSI.ifort64" | head -n 1`
nt=`echo "${nr} + 1"|bc `
#echo ${nt}
sed -i "${nt}s/mpif90/mpiifort/" "${module_path}/Eirene/config/config.DUT-PSI.ifort64"

nr=`awk '/IMPG/ {print NR}' "${module_path}/Eirene/config/config.DUT-PSI.ifort64" | head -n 1`
nt1=`echo "${nr} + 1"|bc `
#echo ${nt}
sed -i  "${nt1}s/mpif90/mpiifort/" "${module_path}/Eirene/config/config.DUT-PSI.ifort64"

# changed information
grep ffree "${module_path}/Eirene/config/config.DUT-PSI.ifort64"

echo "Eirene mpiifort has changed."
grep mpiifort "${module_path}/Eirene/config/config.DUT-PSI.ifort64"

echo -e "===================================================================\n"


# modify Uinp
flag=`grep ffreestanding "${module_path}/Uinp/config/config.DUT-PSI.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/Uinp/config/config.DUT-PSI.ifort64"
    echo "Modify the Uinp configuration file success!"
else
    echo "Uinp ffreestranding has changed."
fi

# modify the mpiifort
nr=`awk '/USE_MPI/ {print NR}' "${module_path}/Uinp/config/config.DUT-PSI.ifort64" | head -n 1`
nt=`echo "${nr} + 1"|bc `
#echo ${nt}
sed -i "${nt}s/mpif90/mpiifort/" "${module_path}/Uinp/config/config.DUT-PSI.ifort64"


# changed information
grep ffree "${module_path}/Uinp/config/config.DUT-PSI.ifort64"

echo "Uinp mpiifort has changed."
grep mpiifort "${module_path}/Uinp/config/config.DUT-PSI.ifort64"


echo -e "===================================================================\n"


# modify fxdr
flag=`grep ffreestanding "${module_path}/fxdr/config/config.default.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/fxdr/config/config.default.ifort64"
    echo "Modify the fxdr configuration file success!"
else
    echo "Fxdr ffreestranding has changed."
fi

# delete the -vec_report0
sed -i 's/-vec_report0//' "${module_path}/fxdr/config/config.default.ifort64"

# changed information
grep ffree "${module_path}/fxdr/config/config.default.ifort64"

echo "Fxdr FFLAGS has changed."
grep FFLAGS "${module_path}/fxdr/config/config.default.ifort64" | awk 'NR==2 {print}'



echo -e "===================================================================\n"

# modify Carre
flag=`grep ffreestanding "${module_path}/Carre/config/config.DUT-PSI.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/Carre/config/config.DUT-PSI.ifort64"
    echo "Modify the Carre configuration file success!"
else
    echo "Carre ffreestranding has changed."
fi

# delete the -vec_report0
sed -i 's/-vec_report0//' "${module_path}/Carre/config/config.DUT-PSI.ifort64"

# changed information
grep ffree "${module_path}/Carre/config/config.DUT-PSI.ifort64"

echo "Carre FFLAGS has changed."
grep FFLAGS "${module_path}/Carre/config/config.DUT-PSI.ifort64" | awk 'NR==2 {print}'


echo -e "===================================================================\n"

# modify Triang
flag=`grep ffreestanding "${module_path}/Triang/config/config.DUT-PSI.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/Triang/config/config.DUT-PSI.ifort64"
    echo "Modify the Triang configuration file success!"
else
    echo "Triang ffreestranding has changed."
fi

# delete the -vec_report0
sed -i 's/-vec_report0//' "${module_path}/Triang/config/config.DUT-PSI.ifort64"

# changed information
grep ffree "${module_path}/Triang/config/config.DUT-PSI.ifort64"

echo "Triang vec_report has deleted."
grep FCOPTS "${module_path}/Triang/config/config.DUT-PSI.ifort64" | tail -n1


echo -e "===================================================================\n"

# modify Divgeo equtrn
flag=`grep ffreestanding "${module_path}/DivGeo/equtrn/config/config.DUT-PSI.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/DivGeo/equtrn/config/config.DUT-PSI.ifort64"
    echo "Modify the DG equtrn configuration file success!"
else
    echo "DG equtrn ffreestranding has changed."
fi


# changed information
grep ffree "${module_path}/DivGeo/equtrn/config/config.DUT-PSI.ifort64"

echo -e "===================================================================\n"

# modify Divgeo convert
flag=`grep ffreestanding "${module_path}/DivGeo/convert/config/config.DUT-PSI.ifort64"`
if [[ ! ${flag} ]]
then
    sed -i 's/traditional/& -ffreestanding/g' "${module_path}/DivGeo/convert/config/config.DUT-PSI.ifort64"
    echo "Modify the DG convert configuration file success!"
else
    echo "DG convert ffreestranding has changed."
fi


# changed information
grep ffree "${module_path}/DivGeo/convert/config/config.DUT-PSI.ifort64"

echo -e "========================================= start to compiler ======================================"

























# ==================== 复制setup.csh到SETUP/ ================ #
#setup_path="${base_path}/SETUP"
#setup_source="${stop_source}/SETUP/setup.csh.DUT-PSI.ifort64"
#config_source="${stop_source}/SETUP/config.DUT-PSI.ifort64"

# copy setup.csh.DUT-PSI.ifort64
#if [ ! -f "${setup_path}/SETUP/setup.csh.DUT-PSI.ifort64" ]
#then
#   cp ${setup_source} ${setup_path}
#   echo "copy setup.csh success!"
#else
#   echo "setup.csh.DUT-PSI.ifort64 has existed."
#fi

# copy config.DUT-PSI.ifort64
#if [ ! -f "${setup_path}/SETUP/config.DUT-PSI.ifort64" ]
#then
#   cp ${config_source} ${setup_path}
#   echo "copy config success!"
#else
#   echo "config.DUT-PSI.ifort64 has existed."
#fi

# =================== modify the config.DUT-PSI.ifort64 =========== #
# check the NCARG,MDSPLUS ROOT

#echo -e "Begin check the config.DUT-PSI.ifort64!\n"

#ncarg_root=`awk 'BEGIN{FS = "/"} /NCARG_ROOT \?=/ {print $2}' "${setup_path}/config.DUT-PSI.ifort64"`
#if [ ${ncarg_root} == "NCARG" ]
#then
#   echo "NCARG_ROOT is ok!"
#else
#   echo "please check the NCARG_ROOT."
#fi

#mdsplus_root=`awk 'BEGIN{FS = "/"} /MDSPLUS_DIR \?=/ {print $2}' "${setup_path}/config.DUT-PSI.ifort64"`
#if [ ${mdsplus_root} == "MDSPLUS" ]
#then
#   echo "MDSPLUS_DIR is ok!"
#else
#   echo "please check the MDSPLUS_DIR."
#fi

#grep -m 2 "LD_NETCDF" "${setup_path}/config.DUT-PSI.ifort64" | tail -n 1
#grep -m 2 "LD_MSCL" "${setup_path}/config.DUT-PSI.ifort64" | tail -n 1
#grep -m 2 "LD_GR" "${setup_path}/config.DUT-PSI.ifort64" | tail -n 1
#grep -m 2 "LD_GKS" "${setup_path}/config.DUT-PSI.ifort64" | head -n 1
#grep -m 2 "LD_NCARG" "${setup_path}/config.DUT-PSI.ifort64" | head -n 1
#grep -m 2 "LD_NAG" "${setup_path}/config.DUT-PSI.ifort64" | tail -n 1
##grep -m 2 "LD_MDSPLUS" "${setup_path}/config.DUT-PSI.ifort64" | head -n 1
#grep -m 2 "LD_SONNET" "${setup_path}/config.DUT-PSI.ifort64" | head -n 1
#grep -m 2 "#LD_MPI" "${setup_path}/config.DUT-PSI.ifort64" | tail -n 1

# ==================== modify the modules config files ================== #
#modules_path="${base_path}/modules"

# copy the B2.5 config/ to new solps-iter




# modify the B2.5 config


















#`echo tcsh` # 启动tcsh
#`echo source setup.csh`
#echo "test tcsh & source"

2020-03-16solps安装流程

将最新把版本的solps repository clone to 本地

1. 选择branch

2. 选择clone 地址

3. 配置ssh密钥

4. clone repository到本地

下载成功，会在当前目录下生成 solps-iter文件夹

5. pro git 中文版

5. 编译solps

- 1. cd solps.iter

- 2. git submodule init

-3. git submodule update

-4.开始编译

whereami

小结：

- 1. 修改文件的过程脚本化

default_compiler

复制配置文件到lib

在bash脚本中启动 tcsh

scr/first_setup

小结

修改SETUP/config.DUT-PSI.ifort64

image.png

脚本迁移

今日成果

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