ubuntu 18.04 编译安装flexpart 10.4(2023年) —— 筑梦之路

2023年10月29日

环境说明

操作系统版本:ubuntu  18.04

python版本:3.6.9

gcc版本:7.5.0

编译安装路径:/usr/local

cmake: 3.10.2

所需要的源码包我已经打包放到我的资源。

2021年1月份已经写过一篇Ubuntu 编译安装的帖子FLEXPART安装配置笔记(成功案例)——筑梦之路_筑梦之路的博客-CSDN博客

也遇到比较多的网友来咨询在编译安装过程中的问题,因此今天再次整理一下编译安装的过程,顺便解决之前写的不是很明确的地方,欢迎大家交流指正。

准备编译工作

# 更新软件源
sudo apt-get update

# 安装编译工具和依赖包
sudo apt-get install -y g++ gfortran autoconf libtool automake flex bison cmake python3-dev python3-pip git vim curl unzip build-essential libbz2-dev libssl-dev libreadline-dev libsqlite3-dev tk-dev ruby


# 安装python相关包

sudo apt-get install -y python3 python3-eccodes python3-genshi python3-numpy gfortran fftw3-dev libeccodes-dev libemos-dev


# 配置pip显示的格式

sudo mkdir ~/.pip

sudo cat > ~/.pip/pip.conf << EOF
[list]
format=columns
EOF

# 建立软链接

sudo ln -sf /usr/bin/python3 /usr/bin/python
sudo ln -sf /usr/bin/pip3 /usr/bin/pip

# 检查

sudo python -V
sudo pip -V

ubuntu 18.04 编译安装flexpart 10.4(2023年) —— 筑梦之路_第1张图片

 准备python环境

# 安装pip的包

sudo pip3 install cdsapi ecmwf-api-client eccodes==1.6.1 -i https://pypi.douban.com/simple
 
#检查是否安装成功

sudo python3 -c "import eccodes; print(eccodes.__version__)"
sudo python3 -c "import genshi; print(genshi.__version__)"
sudo python3 -c "import numpy; print(numpy.__version__)"
sudo pip3 list | grep cdsapi | awk '{print $2}'
sudo python3 -c "import ecmwfapi; print(ecmwfapi.__version__)"

ubuntu 18.04 编译安装flexpart 10.4(2023年) —— 筑梦之路_第2张图片

编译安装

1. 编译安装jasper

# 下载源码包

wget -c http://www.ece.uvic.ca/~mdadams/jasper/software/jasper-1.900.1.zip

# 解压文件到指定目录

unzip jasper-1.900.1.zip -d /usr/local/

# 新建目录

mkdir -p /usr/local/jasper

# 切换目录

cd /usr/local/jasper-1.900.1

# 配置

CFLAGS="-fPIC" ./configure --prefix=/usr/local/jasper

# 编译
make

# 编译检查
make check

# 安装
make install

2. 编译安装grib_api

# 下载源码

wget -c https://people.freebsd.org/~sunpoet/sunpoet/grib_api-1.28.0-Source.tar.gz

# 解压到指定目录

tar -zxvf grib_api-1.28.0-Source.tar.gz -C /usr/local/

# 创建目录

mkdir -p /usr/local/grib_api

# 切换目录

cd /usr/local/grib_api-1.28.0-Source

# 编译三部曲

./configure --prefix=/usr/local/grib_api --with-jasper=/usr/local/jasper

make

make check

make install

3. 编译安装eccodes

# 下载源码

wget -c  https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.7.3-Source.tar.gz?api=v2

# 解压源码到指定目录

tar xvzf eccodes-2.7.3-Source.tar.gz -C /usr/local/

# 创建目录

mkdir -p /usr/local/eccodes

# 切换目录

cd /usr/local/eccodes-2.7.3-Source

# 编译三部曲

mkdir build && cd build

cmake -DCMAKE_INSTALL_PREFIX=/usr/local/eccodes /usr/local/eccodes-2.7.3-Source -DPYTHON_EXECUTABLE=/usr/bin/python3

make

ctest

make install

# 配置环境变量

cat >> /etc/profile << 'EOF'
export ECCODES_SAMPLES_PATH=$PATH:/usr/local/eccodes/share/eccodes/samples
export ECCODES_DEFINITION_PATH=$PATH:/usr/local/eccodes/share/eccodes/definitions
EOF

source /etc/profile

# 检查验证

sudo apt-get install libeccodes-dev
python3 -m eccodes selfcheck

# 正常输出如下:
Found: ecCodes v2.6.0.
Your system is ready.

ubuntu 18.04 编译安装flexpart 10.4(2023年) —— 筑梦之路_第3张图片

4. 编译安装zlib

# 下载源码

v=1.2.8  

sudo wget http://www.zlib.net/fossils/zlib-${v}.tar.gz

# 解压到指定目录

sudo tar -xf zlib-${v}.tar.gz -C /usr/local/ && cd /usr/local/zlib-${v}

# 编译三部曲

sudo ./configure --prefix=/usr/local

sudo make && make install

5. 编译安装 szlib

# 下载源码

v=2.1
wget http://sources.buildroot.net/szip/szip-${v}.tar.gz

# 解压到指定目录

tar -xf szip-${v}.tar.gz -C /usr/local/

cd /usr/local/szip-${v} && mkdir -p /usr/local/szip

# 编译三部曲

./configure --prefix=/usr/local/szip
make
make install

6. 编译安装hdf5

# 下载源码

v=1.8.13

wget https://www.gfd-dennou.org/arch/ucar/netcdf/netcdf-4/hdf5-${v}.tar.gz

# 解压到指定目录

tar -xf hdf5-${v}.tar.gz -C /usr/local/ && cd /usr/local/hdf5-${v}

# 设置变量

prefix="/usr/local/hdf5-$v"
 
echo "Add HDF5_DIR=$prefix to .bashrc"

echo "" >> ~/.bashrc

echo "# HDF5 libraries for python" >> ~/.bashrc

echo export HDF5_DIR=$prefix  >> ~/.bashrc

# 编译三部曲
 
./configure --enable-shared --enable-hl --prefix=$HDF5_DIR

make -j 2              # 2 for number of procs to be used

make install

7. 编译安装netcdf-c

# 下载源码

v=4.1.3

wget https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/netcdf-${v}.tar.gz

# 解压到指定目录

tar -xf netcdf-${v}.tar.gz -C /usr/local/ && cd /usr/local/netcdf-${v}

# 设置变量

prefix="/usr/local/"
 
echo "Add NETCDF4_DIR=$prefix to .bashrc"
echo "" >> ~/.bashrc
echo "# NETCDF4 libraries for python" >> ~/.bashrc
echo export NETCDF4_DIR=$prefix  >> ~/.bashrc

# 编译三部曲

CPPFLAGS=-I$HDF5_DIR/include LDFLAGS=-L$HDF5_DIR/lib ./configure --enable-netcdf-4 --enable-shared --enable-dap --prefix=$NETCDF4_DIR

make 
make install

8. python Netcdf4 安装

# install python's netCDF4

sudo pip3 install cftime==1.3.1 -i https://pypi.douban.com/simple

sudo pip3 install numpy==1.19.4 -i https://pypi.douban.com/simple

sudo pip3 install netCDF4==1.5.5.1 -i https://pypi.douban.com/simple

sudo python3 -c "import netCDF4;print(netCDF4.__version__)"
 

9. 编译安装FLEXPART10.4

# 下载源码

wget -c https://www.flexpart.eu/downloads/66

# 解压到指定目录

tar -xvf 66 -C /usr/local/ 

# 切换目录

cd /usr/local/flexpart_v10.4_3d7eebf

# 备份src目录

cp -r src src-backup-`date +%F`

# 修改makefile文件

vim makefile

#### 修改第一处

#modified to 64-73行
        ROOT_DIR = /usr/local
 
        F90       = /usr/bin/gfortran
        MPIF90    = /usr/bin/mpifort
         
        INCPATH1  = ${ROOT_DIR}/grib_api/include
        INCPATH2  = ${ROOT_DIR}/jasper/include
        INCPATH3 = /include
        LIBPATH1 = ${ROOT_DIR}/grib_api/lib
        LIBPATH2 = ${ROOT_DIR}/jasper/lib
        LIBPATH3 = /lib

#### 修改第二处

### Enable netCDF output?
ifeq ($(ncf), yes)
        NCOPT = -DUSE_NCF -lnetcdff -lnetcdf
else
        NCOPT = -UUSE_NCF
endif

#### 修改第三处

## LIBRARIES
LIBS = -lgrib_api_f90 -lgrib_api -lm -ljasper $(NCOPT) -lnetcdff
 
FFLAGS   = -I$(INCPATH1) -I$(INCPATH2) -I$(INCPATH3) -O$(O_LEV) -g -cpp -m64 -mcmodel=medium -fconvert=little-endian -frecord-marker=4 -fmessage-length=0 -flto=jobserver -O$(O_LEV) $(NCOPT) $(FUSER)  #-Warray-bounds -fcheck=all # -march=native
 
DBGFLAGS = -I$(INCPATH1) -I$(INCPATH2) -I$(INCPATH3) -O$(O_LEV_DBG) -g3 -ggdb3 -cpp -m64 -mcmodel=medium -fconvert=little-endian -frecord-marker=4 -fmessage-length=0 -flto=jobserver -O$(O_LEV_DBG) $(NCOPT) -fbacktrace   -Wall  -fdump-core $(FUSER)  #  -ffpe-trap=invalid,overflow,denormal,underflow,zero  -Warray-bounds -fcheck=all
 
LDFLAGS  = $(FFLAGS) -L$(LIBPATH1) -Wl,-rpath,$(LIBPATH1) $(LIBS) -L$(LIBPATH2) -L$(LIBPATH3)
LDDEBUG  = $(DBGFLAGS) -L$(LIBPATH1) $(LIBS) -L$(LIBPATH2) -L$(LIBPATH3)


# 编译

make ncf=yes

# 配置环境变量
cat >> /etc/profile <<'EOF'
export LD_LIBRARY_PATH=/usr/local/grib_api/lib:$LD_LIBRARY_PATH
EOF

source /etc/profile

10. 准备安装flex_extract

# 拉取源码

cd /usr/local

git clone --single-branch --branch master https://www.flexpart.eu/gitmob/flex_extract

1)编译安装zlib 1.2.9


# 下载zlib 1.2.9源码,编译安装zlib 1.2.9版本

wget https://sourceforge.net/projects/libpng/files/zlib/1.2.9/zlib-1.2.9.tar.gz

# 解压到指定目录

tar -zxvf zlib-1.2.9.tar.gz -C /usr/local

cd /usr/local/zlib-1.2.9

# 编译三部曲

./configure; make; make install

# 创建软链接

ln -s -f /usr/local/lib/libz.so.1.2.9 /lib/x86_64-linux-gnu/libz.so.1

2) 编译安装emoslib

# 下载源码

wget https://confluence.ecmwf.int/download/attachments/3473472/libemos-4.5.9-Source.tar.gz

# 创建目录

mkdir /usr/local/emoslib

# 解压到指定目录

tar -xzf libemos-4.5.9-Source.tar.gz -C /usr/local/

# 切换目录

cd /usr/local/libemos-4.5.9-Source

# 编译安装

mkdir build ; cd build 
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/emoslib /usr/local/libemos-4.5.9-Source
make
make install

3)安装ECMWF 与ERA5安装权限

cat > ~/.ecmwfapirc < ~/.cdsapirc <

4) 修改makefile_local_gfortran文件

# 切换目录

cd /usr/local/flex_extract/Source/Fortran/

# 修改文件

vim makefile_local_gfortran

# change the original path of ECCODES_INCLUDE_DIR to 
ECCODES_INCLUDE_DIR=/usr/include

5) 执行安装flex_extract

# 切换目录

cd /usr/local/flex_extract

# 执行安装

./setup_local.sh

#成功结果输出如下内容

WARNING: installdir has not been specified
flex_extract will be installed in here by compiling the Fortran source in /usr/local/flex_extract/Source/Fortran
Install flex_extract_v7.1.2 software at local in directory /usr/local/flex_extract

Using makefile: makefile_local_gfortran
gfortran   -O3  -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm  -lemosR64 -I. -I/usr/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./rwgrib2.f90
gfortran   -O3  -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm  -lemosR64 -I. -I/usr/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./phgrreal.f90
gfortran   -O3  -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm  -lemosR64 -I. -I/usr/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./grphreal.f90
gfortran   -O3  -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm  -lemosR64 -I. -I/usr/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./ftrafo.f90
gfortran   -O3  -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm  -lemosR64 -I. -I/usr/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./calc_etadot.f90
gfortran   -O3  -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm  -lemosR64 -I. -I/usr/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./posnam.f90
gfortran  rwgrib2.o calc_etadot.o ftrafo.o grphreal.o posnam.o phgrreal.o -o calc_etadot_fast.out  -O3  -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm  -lemosR64 -fopenmp
ln -sf calc_etadot_fast.out calc_etadot

lrwxrwxrwx 1 root root 20 Oct 29 06:30 ./calc_etadot -> calc_etadot_fast.out

ubuntu 18.04 编译安装flexpart 10.4(2023年) —— 筑梦之路_第4张图片

6)测试flex_extract 

# 测试flex_extract

cd Testing/Installation/Calc_etadot
# execute the Fortran progam without arguments
../../../Source/Fortran/calc_etadot
 
#成功结果展示:
STATISTICS:          98842.4598  98709.7359   5120.5385
STOP SUCCESSFULLY FINISHED calc_etadot: CONGRATULATIONS

至此,已经全部编译安装完成,并测试成功。

这里附上python包的版本信息,以供各位参考:

# pip list
Package                Version            
---------------------- -------------------
asn1crypto             0.24.0             
attrs                  17.4.0             
Automat                0.6.0              
blinker                1.4                
cdsapi                 0.6.1              
certifi                2018.1.18          
cffi                   1.15.1             
cftime                 1.3.1              
chardet                3.0.4              
click                  6.7                
cloud-init             23.1.2             
colorama               0.3.7              
command-not-found      0.3                
configobj              5.0.6              
constantly             15.1.0             
cryptography           2.1.4              
distro-info            0.18ubuntu0.18.04.1
eccodes                1.6.1              
ecmwf-api-client       1.6.3              
findlibs               0.0.5              
Genshi                 0.7                
httplib2               0.9.2              
hyperlink              17.3.1             
idna                   2.6                
importlib-resources    5.4.0              
incremental            16.10.1            
Jinja2                 2.10               
jsonpatch              1.16               
jsonpointer            1.10               
jsonschema             2.6.0              
keyring                10.6.0             
keyrings.alt           3.0                
language-selector      0.1                
MarkupSafe             1.0                
netCDF4                1.5.5.1            
netifaces              0.10.4             
numpy                  1.19.5             
oauthlib               2.0.6              
PAM                    0.4.2              
pexpect                4.2.1              
pip                    9.0.1              
pyasn1                 0.4.2              
pyasn1-modules         0.2.1              
pycparser              2.21               
pycrypto               2.6.1              
pygobject              3.26.1             
PyJWT                  1.5.3              
pyOpenSSL              17.5.0             
pyserial               3.4                
python-apt             1.6.5+ubuntu0.7    
python-debian          0.1.32             
pyxdg                  0.25               
PyYAML                 3.12               
requests               2.18.4             
requests-unixsocket    0.1.5              
SecretStorage          2.3.1              
service-identity       16.0.0             
setuptools             39.0.1             
six                    1.11.0             
sos                    4.3                
ssh-import-id          5.7                
systemd-python         234                
tqdm                   4.64.1             
Twisted                17.9.0             
ubuntu-advantage-tools 27.2               
ufw                    0.36               
unattended-upgrades    0.1                
urllib3                1.22               
wheel                  0.30.0             
zipp                   3.6.0              
zope.interface         4.3.2

如果不关心flexpart的版本,可以直接使用apt-get命令安装

apt-get update  && apt-get install flexpart

ubuntu 18.04 编译安装flexpart 10.4(2023年) —— 筑梦之路_第5张图片 

相关源码包在我的资源或者通过文中链接地址下载。

注意事项:文中源码包的地址会随着时间过期,若不能下载请自行搜索相关版本文件。 

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