October 29, 2023
Environmental description
Operating system version: ubuntu 18.04
https://mirrors.aliyun.com/ubuntu-releases/bionic/ubuntu-18.04.6-live-server-amd64.iso
python version: 3.6.9
gcc version: 7.5.0
Compilation installation path:/usr/local
cmake: 3.10.2
I have packaged the required source code packages and put them in my resources.
In January 2021, I have already written a post about Ubuntu compilation and installation. FLEXPART installation and configuration notes (successful case) – The Road to Dreaming_The Blog of Building Dreams-CSDN Blog
I have also encountered a lot of netizens coming to inquire about problems during the compilation and installation process, so today I will sort out the compilation and installation process again, and by the way solve the things that were not very clear in what I wrote before. Welcome everyone to share and make corrections.
Preparing for compilation
# Update software source sudo apt-get update #Install compilation tools and dependency packages 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 #Install python related packages sudo apt-get install -y python3 python3-eccodes python3-genshi python3-numpy gfortran fftw3-dev libeccodes-dev libemos-dev # Configure the format displayed by pip sudo mkdir ~/.pip sudo cat > ~/.pip/pip.conf << EOF [list] format=columns EOF # Create soft link #sudo ln -sf /usr/bin/python3 /usr/bin/python #sudo ln -sf /usr/bin/pip3 /usr/bin/pip # examine #sudo python -V #sudo pip -V
Prepare python environment
# Install pip package
sudo pip3 install cdsapi ecmwf-api-client eccodes==1.6.1 -i https://pypi.douban.com/simple
#Check if the installation is successful
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 $2}'
sudo python3 -c "import ecmwfapi; print(ecmwfapi.__version__)"
Compile and install
1. Compile and install jasper
# Download source code package wget -c http://www.ece.uvic.ca/~mdadams/jasper/software/jasper-1.900.1.zip # Unzip the file to the specified directory unzip jasper-1.900.1.zip -d /usr/local/ # Create new directory mkdir -p /usr/local/jasper # Switch directory cd /usr/local/jasper-1.900.1 #Configuration CFLAGS="-fPIC" ./configure --prefix=/usr/local/jasper # compile make # Compilation check make check # Install make install
2. Compile and install grib_api
# Download source code wget -c https://people.freebsd.org/~sunpoet/sunpoet/grib_api-1.28.0-Source.tar.gz #Extract to the specified directory tar -zxvf grib_api-1.28.0-Source.tar.gz -C /usr/local/ # Create a directory mkdir -p /usr/local/grib_api # Switch directory cd /usr/local/grib_api-1.28.0-Source # Compile the trilogy ./configure --prefix=/usr/local/grib_api --with-jasper=/usr/local/jasper make make check make install
3. Compile and install eccodes
# Download source code wget -c https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.7.3-Source.tar.gz?api=v2 # Unzip the source code to the specified directory tar xvzf eccodes-2.7.3-Source.tar.gz -C /usr/local/ # Create a directory mkdir -p /usr/local/eccodes # Switch directory cd /usr/local/eccodes-2.7.3-Source # Compile the trilogy mkdir build & amp; & amp; cd build cmake -DCMAKE_INSTALL_PREFIX=/usr/local/eccodes /usr/local/eccodes-2.7.3-Source -DPYTHON_EXECUTABLE=/usr/bin/python3 make ctest make install # Configure environment variables cat >> /etc/profile << 'EOF' export ECCODES_SAMPLES_PATH=$PATH:/usr/local/eccodes/share/eccodes/samples export ECCODES_DEFINITION_PATH=$PATH:/usr/local/eccodes/share/eccodes/definitions EOF source /etc/profile # Check verification sudo apt-get install libeccodes-dev python3 -m eccodes selfcheck #Normal output is as follows: Found: ecCodes v2.6.0. Your system is ready.
4. Compile and install zlib
# Download source code
v=1.2.8
sudo wget http://www.zlib.net/fossils/zlib-${v}.tar.gz
#Extract to the specified directory
sudo tar -xf zlib-${v}.tar.gz -C /usr/local/ & amp; & amp; cd /usr/local/zlib-${v}
# Compile the trilogy
sudo ./configure --prefix=/usr/local
sudo make & amp; & amp; make install
5. Compile and install szlib
# Download source code
v=2.1
wget http://sources.buildroot.net/szip/szip-${v}.tar.gz
#Extract to the specified directory
tar -xf szip-${v}.tar.gz -C /usr/local/
cd /usr/local/szip-${v} & amp; & amp; mkdir -p /usr/local/szip
# Compile the trilogy
./configure --prefix=/usr/local/szip
make
make install
6. Compile and install hdf5
# Download source code
v=1.8.13
wget https://www.gfd-dennou.org/arch/ucar/netcdf/netcdf-4/hdf5-${v}.tar.gz
#Extract to the specified directory
tar -xf hdf5-${v}.tar.gz -C /usr/local/ & amp; & amp; cd /usr/local/hdf5-${v}
# Set variables
prefix="/usr/local/hdf5-$v"
echo "Add HDF5_DIR=$prefix to .bashrc"
echo "" >> ~/.bashrc
echo "# HDF5 libraries for python" >> ~/.bashrc
echo export HDF5_DIR=$prefix >> ~/.bashrc
# Compile the trilogy
./configure --enable-shared --enable-hl --prefix=$HDF5_DIR
make -j 2 # 2 for number of procs to be used
make install
7. Compile and install netcdf-c
# Download source code
v=4.1.3
wget https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/netcdf-${v}.tar.gz
#Extract to the specified directory
tar -xf netcdf-${v}.tar.gz -C /usr/local/ & amp; & amp; cd /usr/local/netcdf-${v}
# Set variables
prefix="/usr/local/"
echo "Add NETCDF4_DIR=$prefix to .bashrc"
echo "" >> ~/.bashrc
echo "#NETCDF4 libraries for python" >> ~/.bashrc
echo export NETCDF4_DIR=$prefix >> ~/.bashrc
# Compile the trilogy
CPPFLAGS=-I$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 installation
# 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. Compile and install FLEXPART10.4
# Download source code
wget -c https://www.flexpart.eu/downloads/66
#Extract to the specified directory
tar -xvf 66 -C /usr/local/
# Switch directory
cd /usr/local/flexpart_v10.4_3d7eebf
# Back up src directory
cp -r src src-backup-`date + %F`
cd src
# Modify the makefile
vim makefile
#### Modify the first part
#modified to lines 64-73
ROOT_DIR = /usr/local
F90 = /usr/bin/gfortran
MPIF90 = /usr/bin/mpifort
INCPATH1 = ${ROOT_DIR}/grib_api/include
INCPATH2 = ${ROOT_DIR}/jasper/include
INCPATH3 = ${ROOT_DIR}/include
LIBPATH1 = ${ROOT_DIR}/grib_api/lib
LIBPATH2 = ${ROOT_DIR}/jasper/lib
LIBPATH3 = ${ROOT_DIR}/lib
#### The second modification
### Enable netCDF output?
ifeq ($(ncf), yes)
NCOPT = -DUSE_NCF -lnetcdff -lnetcdf
else
NCOPT = -UUSE_NCF
endif
#### Modify the third part
## 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$(LIBPATH3)
# compile
make ncf=yes
# Configure environment variables
cat >> /etc/profile <<'EOF'
export LD_LIBRARY_PATH=/usr/local/grib_api/lib:$LD_LIBRARY_PATH
EOF
source /etc/profile
echo "/usr/local/lib" > /etc/ld.so.conf.d/test.conf
ldconfig
10. Prepare to install flex_extract
# Pull source code cd /usr/local git clone --single-branch --branch master https://www.flexpart.eu/gitmob/flex_extract
1) Compile and install zlib 1.2.9
# Download zlib 1.2.9 source code, compile and install zlib 1.2.9 version wget https://sourceforge.net/projects/libpng/files/zlib/1.2.9/zlib-1.2.9.tar.gz #Extract to the specified directory tar -zxvf zlib-1.2.9.tar.gz -C /usr/local cd /usr/local/zlib-1.2.9 # Compile the trilogy ./configure; make; make install #Create soft link ln -s -f /usr/local/lib/libz.so.1.2.9 /lib/x86_64-linux-gnu/libz.so.1
2) Compile and install emoslib
# Download source code wget https://confluence.ecmwf.int/download/attachments/3473472/libemos-4.5.9-Source.tar.gz # Create a directory mkdir /usr/local/emoslib #Extract to the specified directory tar -xzf libemos-4.5.9-Source.tar.gz -C /usr/local/ # Switch directory cd /usr/local/libemos-4.5.9-Source #Compile and install mkdir build; cd build cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/emoslib /usr/local/libemos-4.5.9-Source make make install
3) Install ECMWF and ERA5 installation permissions
cat > ~/.ecmwfapirc <<EOF
{
"url" : "https://api.ecmwf.int/v1",
"key" : "8fb37b516ba233bde068613a8f08c785",
"email" : "[email protected]"
}
EOF
cat > ~/.cdsapirc <<EOF
url: {api-url}
key: {uid}:{api-key}
EOF
4) Modify the makefile_local_gfortran file
# Switch directory cd /usr/local/flex_extract/Source/Fortran/ # Modify files vim makefile_local_gfortran # change the original path of ECCODES_INCLUDE_DIR to ECCODES_INCLUDE_DIR=/usr/include
5) Execute installation flex_extract
# Switch directory cd /usr/local/flex_extract # Execute installation ./setup_local.sh #The successful result output is as follows 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
6) Test flex_extract
# Test flex_extract cd Testing/Installation/Calc_etadot # execute the Fortran progam without arguments ../../../Source/Fortran/calc_etadot #Successful result display: STATISTICS: 98842.4598 98709.7359 5120.5385 STOP SUCCESSFULLY FINISHED calc_etadot: CONGRATULATIONS
At this point, all compilation and installation have been completed, and the test has been successful.
The version information of the python package is attached here for your reference:
# 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
If you don’t care about the version of flexpart, you can directly use the apt-get command to install it.
apt-get update & amp; & amp; apt-get install flexpart
The relevant source code package can be downloaded from my resources or through the link address in the article.
Note: The address of the source code package in this article will expire over time. If you cannot download it, please search for the relevant version file yourself.
https://v.youku.com/v_show/id_XNjEyOTMyMDc4NA==.html
View the python version in the source code flex_extract:
Check the python version in the flexpart source code:
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