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 ~/.pipsudo 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

 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__)"

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/jaspermakemake checkmake 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 buildcmake -DCMAKE_INSTALL_PREFIX=/usr/local/eccodes /usr/local/eccodes-2.7.3-Source -DPYTHON_EXECUTABLE=/usr/bin/python3makectestmake 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
EOFsource /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.

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/localsudo 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=1.8.13wget 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=$prefix to .bashrc"echo "" >> ~/.bashrcecho "# HDF5 libraries for python" >> ~/.bashrcecho export HDF5_DIR=$prefix  >> ~/.bashrc# 编译三部曲./configure --enable-shared --enable-hl --prefix=$HDF5_DIRmake -j 2              # 2 for number of procs to be usedmake install

7. 编译安装netcdf-c

# 下载源码v=4.1.3wget 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_DIRmake 
make install

8. python Netcdf4 安装

# install python's netCDF4sudo pip3 install cftime==1.3.1 -i https://pypi.douban.com/simplesudo pip3 install numpy==1.19.4 -i https://pypi.douban.com/simplesudo pip3 install netCDF4==1.5.5.1 -i https://pypi.douban.com/simplesudo 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/localF90       = /usr/bin/gfortranMPIF90    = /usr/bin/mpifortINCPATH1  = ${ROOT_DIR}/grib_api/includeINCPATH2  = ${ROOT_DIR}/jasper/includeINCPATH3 = /includeLIBPATH1 = ${ROOT_DIR}/grib_api/libLIBPATH2 = ${ROOT_DIR}/jasper/libLIBPATH3 = /lib#### 修改第二处### Enable netCDF output?
ifeq ($(ncf), yes)NCOPT = -DUSE_NCF -lnetcdff -lnetcdf
elseNCOPT = -UUSE_NCF
endif#### 修改第三处## LIBRARIES
LIBS = -lgrib_api_f90 -lgrib_api -lm -ljasper $(NCOPT) -lnetcdffFFLAGS   = -I$(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) $(FUSER)  #-Warray-bounds -fcheck=all # -march=nativeDBGFLAGS = -I$(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=allLDFLAGS  = $(FFLAGS) -L$(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
EOFsource /etc/profile

10. 准备安装flex_extract

# 拉取源码cd /usr/localgit 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/localcd /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 <<EOF
{"url"   : "https://api.ecmwf.int/v1","key"   : "8fb37b516ba233bde068613a8f08c785","email" : "[e-mail]"
}
EOFcat > ~/.cdsapirc <<EOF
url: {api-url}
key: {uid}:{api-key}
EOF

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

6）测试flex_extract 

# 测试flex_extractcd 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

 

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。