NetCDF format

From GHER

NetCDF stands for Network Common Data Form. It is self-describing, machine-independent data format, frequently used in ocean and atmospheric sciences.

Contents 1 General 2 Visualization of NetCDF files 3 Installation of the NetCDF library 3.1 Use a package manager to download libraries 3.2 Download the sources if you do not find libraries 3.2.1 Compilation with Intel Compilers 3.2.2 Install HDF5 and zlib packages 3.2.3 Compile 3.2.4 Compilation with gcc 3.2.5 Failed options 4 Operations on NetCDF files 4.1 ncdump 4.1.1 Display header information 4.1.2 Display a given variable 4.2 netCDF Operator (NCO) 4.3 Ncclamp 4.4 CDO

General

• Home page: http://www.unidata.ucar.edu/software/netcdf/
• What is NetCDF: http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#whatisit

Visualization of NetCDF files

There are several ways to have a quick view of the content of a NetCDF file:

• ncBrowse (very easy to install on any platform)
• Ncview (easy on Linux, tricky on Windows), installation detailed here
• Ferret: an interactive computer visualization and analysis environment.
• ODV: lets you explore and visualize CF, COARDS, GDT and CDC compliant netCDF datasets.
• Panoply: the NASA data viewer for netCDF, HDF and GRIB data.

Installation of the NetCDF library

Use a package manager to download libraries

This approach is generally the easiest one provided you find a library which was compiled with the same compile you plan to use (gnu gfortran for example). Make sure you install development libraries and Fortran interface libraries. If this approach does not work you will need to compile netCDF yourself as explained in the following

Download the sources if you do not find libraries

The following instructions describe the installation of the NetCDF 4 library, with the HDF5 storage format.

The installation of the packages and libraries was performed on nic3 in the directory /u/mc and on the computer gher01 in the directory /usr/local.

• Download the NetCDF sources from Unidata webpage:

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf.tar.gz

• Extract the archive:

tar -xvf netcdf.tar.gz

Compilation with Intel Compilers

Intel compilers are available for free non-commercial download at http://software.intel.com/en-us/articles/non-commercial-software-download/

Install HDF5 and zlib packages

• Download:

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/hdf5-1.8.2.tar.gz
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/zlib-1.2.3.tar.gz

• Extract the archives:

tar -xvf hdf5-1.8.2.tar.gz
tar -xvf zlib-1.2.3.tar.gz

• Install zlib first

cd /u/mc/zlib-1.2.3
./configure --prefix=/u/mc
make
make install

• Install HDF5

cd /u/mc/hdf5-1.8.2
./configure --prefix=/u/mc
make
make check
make install

Notes:

1. if you want to be sure to have the last version of zlib and hdf5, check ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4/
2. that the make operation can take quite a long time.
3. replace /u/mc by /usr/local (or something else) for an installation on you machine

Compile

• Specify the compilation options you want:

export CC=icc
export FC=ifort

• Launch the configuration

./configure --enable-netcdf-4 --with-hdf5=/u/mc/ --with-zlib=/u/mc/ --prefix=/u/mc/

where /u/mc can be replaced by the location you want.

• Run the tests

make check

Note that some of the tests may fail, but usually that is not a problem.

• Perform the installation

make install

Once the installation is performed, new directories will appear in /u/mc:

• bin/
• include/
• lib/
• share/

In particular, the netcdf library is located in lib:

nick3:/u/mc$ ls lib/
libhdf5.a      libhdf5_hl.so        libhdf5.la        libhdf5.so.6      libnetcdf_c++.a   libz.a
libhdf5_hl.a   libhdf5_hl.so.0      libhdf5.settings  libhdf5.so.6.0.1  libnetcdf_c++.la  pkgconfig
libhdf5_hl.la  libhdf5_hl.so.0.0.0  libhdf5.so        libnetcdf.a       libnetcdf.la

Compilation with gcc

sudo aptitude install libhdf4-dev libhdf5-serial-dev 
./configure --enable-hdf4  --enable-cxx-4  --with-udunits --with-pic
make 
sudo make install

Failed options

--with-libcf

*** No rule to make target `../../libsrc/libnetcdf.la', needed by `cfcheck'.  Stop.

--enable-netcdf4

*** Testing HDF4/NetCDF-4 interoperability...
/bin/bash: line 5: 28738 Segmentation fault      ${dir}$tst
FAIL: tst_interops2
================================================
1 of 60 tests failed
================================================

Operations on NetCDF files

ncdump

The command ncdump allows the user to examine the content of a NetCDF file.

Examples are available here: http://www.unidata.ucar.edu/software/netcdf/workshops/2011/utilities/NcdumpExamples.html

Display header information

ncdump -h time file.nc

Display a given variable

ncdump -v time file.nc

netCDF Operator (NCO)

NetCDF Operator (NCO) is a set of command-line programs that take netCDF files as input and perform operations on their content.

Ncclamp

ncclamp is another command-line tool for the replacement of values in files.

Note that you may have to modify the makefile before compilation of the code.

ncclamp northsea_TSM.nc TSM nan -999 eq

replaces all the NaN's by -999

CDO

CDO stands for Climate Data Operator. A collection of command line Operators to manipulate and analyse Climate and NWP model Data.