https://github.com/mcuntz/install_netcdf
Install open source packages to work with netCDF and openMPI on Mac OS X and Linux.
https://github.com/mcuntz/install_netcdf
cdo command-line install linux macos mpi netcdf
Last synced: 5 months ago
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Install open source packages to work with netCDF and openMPI on Mac OS X and Linux.
- Host: GitHub
- URL: https://github.com/mcuntz/install_netcdf
- Owner: mcuntz
- License: mit
- Created: 2019-05-15T22:07:17.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2025-01-10T23:39:01.000Z (over 1 year ago)
- Last Synced: 2025-01-11T00:29:06.832Z (over 1 year ago)
- Topics: cdo, command-line, install, linux, macos, mpi, netcdf
- Language: Shell
- Homepage:
- Size: 213 KB
- Stars: 2
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# install_netcdf
Install open source packages to work with netCDF and openMPI on Mac OS X and Linux.
The script was initially written to install netCDF4 (hence its name) and all its
dependencies to be used with different Fortran compilers, as well as
some netCDF tools such as cdo, nco and ncview.
It is also used to install missing packages locally on computing
clusters. For example, a cluster might have the netCDF C-library
installed but not the Fortran version.
Set parameters in Setup section, as well as directories to packages that are already installed.
Prerequisites: curl, c and c++ compilers, pkg-config for nco.
Optional prerequisites: fortran compiler (e.g. gfortran) for netcdf3 and netcdf4-fortran
java compiler for antlr2, i.e. ncap2 of nco
The script was tested on Mac OS X 10.9 through 10.11 (Mavericks, Yosemite, El Capitan).
It was not tested on Ubuntu for quite a while.
#### Dependencies are:
| | |
| --- | --- |
| hdf5 | <- zlib, szip |
| netcdf4 | <- hdf5 |
| netcdf4\_fortran | <- netcdf4 |
| grib\_api | <- netcdf4, jasper, libpng |
| or | |
| eccodes | <- netcdf4, jasper, libpng |
| cdo | <- netcdf4, proj4, grib_api or eccodes, udunits |
| nco | <- netcdf4, gsl, udunits, pkg-config, antlr v2 (not v3/4) for ncap2 |
| ncview | <- netcdf4, udunits |
| tiff | <- jpeg |
| ffmpeg | <- yasm |
#### The websites to check for the latest versions are:
| | |
| --- | --- |
| zlib | http://zlib.net |
| openssl | https://www.openssl.org/source/ |
| szip | http://www.hdfgroup.org/ftp/lib-external/szip/ |
| hdf5 | http://www.hdfgroup.org/ftp/HDF5/releases/ |
| netcdf4/\_fortran | https://www.unidata.ucar.edu/downloads/netcdf |
| netcdf3 | http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3\_6\_3 |
| udunits | ftp://ftp.unidata.ucar.edu/pub/udunits/ |
| libpng | http://sourceforge.net/projects/libpng/files/ |
| libjpeg | http://www.ijg.org/files/ |
| tiff | https://download.osgeo.org/libtiff/ |
| proj4 | https://download.osgeo.org/proj/ |
| jasper | http://www.ece.uvic.ca/~frodo/jasper/ |
| grib\_api | https://software.ecmwf.int/wiki/display/GRIB/Releases |
| eccodes | https://software.ecmwf.int/wiki/display/ECC/Releases |
| cdo | https://code.zmaw.de/projects/cdo/files |
| ncview | ftp://cirrus.ucsd.edu/pub/ncview/ |
| gsl | ftp://ftp.gnu.org/gnu/gsl/ |
| antlr | http://www.antlr2.org/download.html |
| nco | http://nco.sourceforge.net/src/ |
| openmpi | http://www.open-mpi.org |
| mpich | http://www.mpich.org/downloads/ |
| geos | https://download.osgeo.org/geos |
| gdal | https://trac.osgeo.org/gdal/wiki/DownloadSource |
| yasm | http://yasm.tortall.net/Download.html |
| ffmpeg | http://ffmpeg.org/releases/ |
| p7zip | http://sourceforge.net/projects/p7zip/ |
| hdf4 | http://www.hdfgroup.org/release4/obtain.html |
| enscript | http://ftp.gnu.org/gnu/enscript |
| htop | http://hisham.hm/htop/ |
#### Check for all latest versions by copying the following to open/xdg-open:
http://zlib.net https://www.openssl.org/source/ http://www.hdfgroup.org/ftp/lib-external/szip/ http://www.hdfgroup.org/ftp/HDF5/releases/ https://www.unidata.ucar.edu/downloads/netcdf http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3\_6\_3 ftp://ftp.unidata.ucar.edu/pub/udunits/ http://sourceforge.net/projects/libpng/files/ http://www.ijg.org/files/ https://download.osgeo.org/libtiff/ https://download.osgeo.org/proj/ http://www.ece.uvic.ca/~frodo/jasper/ https://software.ecmwf.int/wiki/display/GRIB/Releases https://software.ecmwf.int/wiki/display/ECC/Releases https://code.zmaw.de/projects/cdo/files ftp://cirrus.ucsd.edu/pub/ncview/ ftp://ftp.gnu.org/gnu/gsl/ http://www.antlr2.org/download.html http://nco.sourceforge.net/src/ http://www.open-mpi.org http://www.mpich.org/downloads/ https://download.osgeo.org/geos https://trac.osgeo.org/gdal/wiki/DownloadSource http://yasm.tortall.net/Download.html http://ffmpeg.org/releases/ http://sourceforge.net/projects/p7zip/ http://www.hdfgroup.org/release4/obtain.html http://ftp.gnu.org/gnu/enscript http://hisham.hm/htop/releases/
#### Note
- Do not untabify the script because the netcdf_fortran libtool patch will not work anymore.
- If some libraries are already installed such as png, set dolibpng=0 below.
- One can set EXTRA_CPPFLAGS and EXTRA_LDFLAGS if the compilers do not find it automatically, for example:
EXTRA_LDFLAGS='-L/opt/local'
#### Note on Mac OS X using homebrew
install homebrew with
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
install the following packages via homebrew by typing: brew install
brew install gcc netcdf cmake udunits proj jasper gsl
brew cask install java
brew install antlr@2 geos gdal ffmpeg enscript htop
brew install nco
brew install ncview
Set CMAKE below to cmake.
All libraries should link into /usr/local. If a package cannot link properly then try
brew link
This normally shows a directory which cannot be written. Set owner to username, e.g.
sudo chown ${USER} /usr/local/share/man/man3
Then, do not select the instaled packages below
dozlib=0
doszip=0
dohdf5=0
donetcdf4=0
doudunits=0
dolibpng=0
dolibjpeg=0
dotiff=0
doproj4=0
dojasper=0
dogsl=0
doantlr=0
donco=0
doncview=0
Then use the script to install all libraries that provide Fortran interfaces with all your Fortran compilers,
such as netcdf4-fortran, netcdf3, openmpi, mpich, giving the list of your Fortran compilers below, e.g.
fortran_compilers="gfortran nagfor pgfortran ifort"
Also install cdo with the script because of the dropped science support of homebrew.
Homebrew can also be used exclusivley for the additional packages:
geos
gdal
ffmpeg
enscript
htop
#### Note on (Scientific) Linux
zlib installed by default.
Install antlr-C++ bindings from paket manager.
#### Note on Ubuntu
install the following software from package management via the command line
by typing sudo apt install
zlib [installed by default on Ubuntu]
or
libz-mingw-w64 [on Ubuntu on Windows]
libpng-dev
libtiff-dev [installs libjpeg-dev]
libantlr-dev
libexpat-dev
libcurl4-openssl-dev
xorg-dev
cmake
bison
Therefore do not select the packages below
dozlib=0
dolibpng=0
dolibjpeg=0
dotiff=0
doantlr=0
Authors: Matthias Cuntz, Stephan Thober
Created: Oct 2014
**Copyright (c) 2014-2019 Matthias Cuntz - mc (at) macu (dot) de**