UsingNetCDF

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Using NetCDF files for your data

Introduction

Software Installation

On Ubuntu

The Ubuntu package manager makes this very easy. Go to System->Administration->Synaptic Package Manager (you will need to enter your password) and select the packages:

  • python-scientific (this provides a python interface for reading/writing NetCDF files)

along with:

  • python-tk
  • python-matplotlib) (these provide a means to view your data graphically)

Compiling from Source

This is not as convenient as using a package manager and is a bit messy!

Compiling the NetCDF Libraries from Unidata

The source code can be downloaded from Unidata:

wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.0.tar.gz

Now, unpack the tarball and build the libraries:

tar -xzf netcdf-4.0.tar.gz
cd netcdf-4.0
./configure --prefix=/opt/netcdf/netcdf-4.0 --enable-shared FC=ifort CC=gcc CXX=g++ CPPFLAGS="-DpgiFortran" \
FCFLAGS="-fpic" CFLAGS="-fPIC" CXXFLAGS="-fPIC"
make
make check
make install

Note that we need to build the shared libraries. Hence the addition of the -fPIC flags

Installing the Python Interface

wget http://sourcesup.cru.fr/frs/download.php/1833/Numeric-23.8.2.tar.gz
tar -xzf ...
cd Numeric...
python setup.py install
wget http://sourcesup.cru.fr/frs/download.php/2309/ScientificPython-2.8.tar.gz
cd ..
tar ...

but now need to hack setup.py for:

  • netcdf path
  • problems with /usr/lib and /usr/lib64

perhaps easiest to just patch with a symbolic link:

cd /usr/lib/python2.4/site-packages
ln -s /usr/lib64/python2.4/site-packages/Scientific

An Example Session