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 <PACKAGE>

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