Tyler Reddy edited this page May 5, 2015 · 2 revisions

The AMBER NetCDF binary trajectory reader (Issue 109) relies on the netcdf4-python package, which in turns depends on

  • hdf5 >= 1.8.7
  • netcdf4 (>4.1)

On modern versions of Ubuntu Linux (>= 11.04) one can install the prerequisite packages

apt-get install -y libhdf5-serial-dev libnetcdf-dev

and pip-install the netcdf4-python package

pip install netCDF4 

(See, for instance, the Install Recipe for Ubuntu 12.04.)

Older releases (such as 10.04) require you to build the libraries yourself as described below:

Installation Examples

Even if your specific operating system is not listed, read through the examples and you should be able to adapt them to your situation. Also note that the exact versions of libraries listed the examples are likely outdated: replace them with the current version!

Debian

For debian users getting the error: ValueError: did not find HDF5 headers, with the easy_install method for installing netcdf but having installed hdf5/netcdf from the official debian repositories, try:

export HDF5_LIBDIR=/usr/lib/x86_64-linux-gnu/hdf5/serial 
export HDF5_INCDIR=/usr/include/hdf5/serial

and then

easy_install netCDF4

Compiling on Ubuntu 10.04 Lucid Lynx

Download latest source for the HDF5 library from ftp://ftp.hdfgroup.org/HDF5/current/src

wget ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.9.tar.bz2
tar -jxvf hdf5-1.8.9.tar.bz2
cd hdf5-1.8.9

Install into /usr/local:

HDF5_DIR=/usr/local
./configure --prefix=$HDF5_DIR --enable-hl --enable-shared
make
sudo make install

Download latest source code for the netcdf4 library from ftp://ftp.unidata.ucar.edu/pub/netcdf/

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.2.0.tar.gz
cd netcdf-4.2
./configure --prefix=/usr/local --enable-netcdf-4 --enable-shared --enable-dap --disable-doxygen CPPFLAGS="-I$HDF5_DIR/include" LDFLAGS="-L$HDF5_DIR/lib"
make
sudo make install

This also installs into /usr/local.

After netcdf4 has been installed, MDAnalysis can be installed with python setup.py install and it will automatically install netcdf4-python in the process.

CentOS 5.8 as user

I am installing the HDF5 (from ftp://ftp.hdfgroup.org/HDF5/current/src) and netcdf (from ftp://ftp.unidata.ucar.edu/pub/netcdf/) libraries in my home directory under $HOME/Library. Because this is non-standard location I have to set two environment variables to make this work:

export HDF5_DIR=$HOME/Library
export NETCDF4_DIR=$HDF5_DIR 

# compile latest HDF5
wget ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.11.tar.bz2
tar xvf hdf5-1.8.11.tar.bz2  && cd hdf5-1.8.11
./configure --prefix=$HDF5_DIR --enable-hl --enable-shared
make && make install

cd ..

# compile latest netcdf4
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.0.tar.gz
tar xvf netcdf-4.3.0.tar.gz && cd netcdf-4.3.0
./configure --prefix=$NETCDF4_DIR --enable-netcdf-4 --enable-shared --enable-dap --disable-doxygen CPPFLAGS="-I$HDF5_DIR/include" LDFLAGS="-L$HDF5_DIR/lib"
make && make install

# install netcdf4-python
easy_install-2.6 --user netcdf4

Problems

error: 'H5F_LIBVER_18' undeclared (first use in this function)

As Re: netcdfgroup Trouble compiling netcdf 4.1.3 on Natty Narwhal says: Your HDF5 library is out of date. Upgrade to HDF5-1.8.7 and try again. Don't forget to do make clean first.

/usr/bin/Doxygen not found

Add the --disable-doxygen flag to netcdf's configure. Will omit generating doxygen docs.

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Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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