install cdo with eccodes, hdf5, netcdf4

installcdo.sh

#!/bin/bash

#   This installs CDO with ecCodes, netCDF and HDF5 support. Uses standard locations, with binaries landing in /usr/local/bin
#   Forked from https://gist.github.com/mainvoid007/e5f1c82f50eb0459a55dfc4a0953a08e
#   Updated to latest versions
#   The only “breaking” change for JasPer is the maintainer switched from make to cmake for its build

cdo_path=/opt/cdo-install
apt-get update && apt-get install -y wget build-essential checkinstall unzip m4 curl libcurl4-gnutls-dev

#   download, compile and install --> zlib
cd $cdo_path
wget https://zlib.net/zlib-1.2.11.tar.gz
tar -xzvf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure
make && sudo make install

#   download, compile and install --> hdf5
cd $cdo_path
wget https://www.hdfgroup.org/package/source-gzip-2/?wpdmdl=11810&refresh=5ac7c53570acd1523041589 -O hdf5-1.10.2.tar.gz
tar -xzvf hdf5-1.10.2.tar.gz
cd hdf5-1.10.2
./configure --prefix=/usr/local
make && sudo make install

sudo apt install libcurl4-gnutls-dev -y

#   download, compile and install --> netCDF
cd $cdo_path
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.6.1.tar.gz
tar -xzvf netcdf-4.6.1.tar.gz 
cd netcdf-4.6.1/
./configure
make && sudo make install

#   download, compile and install --> jasper
cd $cdo_path
wget http://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz
tar -xzvf jasper-2.0.14.tar.gz
cd jasper-2.0.14
mkdir release
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release ../
cd release
make && sudo make install

#   download, compile and install --> eccodes
cd $cdo_path
wget https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.7.0-Source.tar.gz?api=v2 -O eccodes-2.7.0-Source.tar.gz
tar -xzvf eccodes-2.7.0-Source.tar.gz
cd eccodes-2.7.0-Source
mkdir build
cd build
cmake ../
make && sudo make install

#   download, compile and install --> cdo
cd $cdo_path
wget https://code.mpimet.mpg.de/attachments/download/16435/cdo-1.9.3.tar.gz
tar -xvzf cdo-1.9.3.tar.gz
cd cdo-1.9.3
./configure --with-netcdf=yes --with-hdf5=yes --with-eccodes=yes
make && sudo make install

# Ensure shared libraries are wired up
sudo ldconfig

hi, i just followed your code with small changes as I am Fedora user. everything went fine, without any problem, but when I tried make check while installing CDO it cant find libeccodes. I installed to the same cdo-folder, from the same sources, using the same instalation commands...but it just cant load eccodes lib even though it is installed properly and eccodes test passed. I just dont know what happened, I even set the directory to eccodes lib while configuration process,but it didnt help. :( please help,thanks

@dasa-chmi I’m not familiar with Fedora, but generally speaking, the sudo make install should install ecCodes to the appropriate shared library path, and ldconfig should refresh things so all these newly-installed libraries are available for use.

You may wish to review the install instructions for ecCodes on their wiki, but unfortunately, I won’t be able to help beyond that.

Thanks a lot for this gist. Without it, it would have taken me ages to install CDO correctly.

for linux there are some alternatives:

• conda: cdo is available in the conda-forge channel in the latest release (pre-built)
• spack: conda replacement, but everything is built from source

Thanks a lot for this gist. Without it, it would have taken me ages to install CDO correctly.

You’re welcome @pjpetersik!