Editing Software Development Platforms (section)

===HDF5 and netCDF===

Get HDF5 from http://www.hdfgroup.org/downloads/index.html .

I used the CMake build for HDF5, instead of the automake build.  Note that for version 1.8.9 you have to apply a patch (or edit by hand one file) as described here: http://www.hdfgroup.org/ftp/HDF5/current/src/ .

Here are some interesting cmake options:

{| border="1" cellpadding="2" cellspacing="0"
|-
! option
! Setting
|- valign="top"
| BUILD_SHARED_LIBS ||               ON                                           
|- valign="top"
| CMAKE_BUILD_TYPE || Release
|- valign="top"
| CMAKE_INSTALL_PREFIX ||            /opt/hdf5-1.8.9
|- valign="top"
| HDF5_BUILD_CPP_LIB || OFF
|- valign="top"
| HDF5_BUILD_FORTRAN || OFF
|- valign="top"
| HDF5_BUILD_HL_LIB || ON
|- valign="top"
| HDF5_BUILD_TOOLS || ON
|- valign="top"
| HDF5_ENABLE_Z_LIB_SUPPORT || ON
|}

Build in the usual way for CMake.

Note that the automake build has all the defaults as above anyway, so it is just

 ./configure --prefix=/Users/Shared/install/hdf5-1.8.9

Here's a setenv script for setting environment variables:

<source lang=bash>
#!/bin/bash

source /usr/local/bin/setenv_functions.sh

remove_path PATH '/.*/hdf5(-[^/]+)?/bin/?'
remove_path DYLD_LIBRARY_PATH '/.*/hdf5(-[^/]+)?/lib/?'

SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

export HDF5_DIR="${SCRIPT_DIR}"
export HDF5_ROOT="${HDF5_DIR}"
add_path PATH "${HDF5_DIR}/bin"
add_path DYLD_LIBRARY_PATH "${HDF5_DIR}/lib"
</source>

Now for netCDF, which you can get from ftp://ftp.unidata.ucar.edu/pub/netcdf . The standard package builds only the C interface:

 tar xvzf netcdf-4.2.1.tar.g
 cd netcdf-4.2.1
 source /opt/hdf5-1.8.9/setenv.sh
 export CPPFLAGS="-I$HDF5_DIR/include"
 export LDFLAGS="-L$HDF5_DIR/lib"
 ./configure --prefix=/opt/netcdf-4.2.1 --disable-dap --disable-doxygen 
 make -j 4
 make check
 sudo make install

Here is a setenv.sh script:

<source lang=bash>
#!/bin/bash
 
source /opt/hdf5-1.8.9/setenv.sh

remove_path PATH '/.*/netcdf(-[^/]+)?/bin/?'
remove_path DYLD_LIBRARY_PATH '/.*/netcdf(-[^/]+)?/lib/?'
remove_path PYTHONPATH '/.*/netcdf(-[^/]+)?/lib/?'

SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
export NETCDF4_DIR="${SCRIPT_DIR}"
add_path PATH "${NETCDF4_DIR}/bin"
add_path DYLD_LIBRARY_PATH "${NETCDF4_DIR}/lib"
add_path PYTHONPATH "${NETCDF4_DIR}/lib/python2.7/site-packages"
</source>

Now for the fortran interface:

 tar xvzf netcdf-fortran-4.2.tar.gz
 cd netcdf-fortran-4.2
 source /opt/netcdf-4.2.1/setenv.sh
 export FC=/opt/local/bin/gfortran-mp-4.4
 export CPPFLAGS="-I$NETCDF4_DIR/include -I$HDF5_DIR/include -DgFortran"

Note that the  -DgFortran part is to ensure correct name mangling in Fortran.  See http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg09206.html .  A future version may not require this.

 export LDFLAGS="-L$NETCDF4_DIR/lib -L$HDF5_DIR/lib"
 ./configure --prefix=/opt/netcdf-4.2.1
 make -j 4
 make check
 sudo make install

For the python module netcdf4-python from http://code.google.com/p/netcdf4-python/ , I needed to make a link gcc-4.2 as follows (OS-X 10.7 only):

 cd /usr/bin
 sudo ln -s gcc-4.2 llvm-gcc-4.2

Then some usual stuff:

 tar xvzf netCDF4-1.0fix1.tar.gz
 mv netCDF4-1.0 netCDF4-python-1.0    # Rename to something more informative
 cd netCDF4-python-1.0
 source /opt/netcdf-4.2.1/setenv.sh

Now it turns out that with HDF 1.8.9 and python netCDF 1.0 we need to fix up the setup.py script a bit:

<source lang=diff>
*** setup.py.old	2012-07-11 09:40:08.603064046 -0700
--- setup.py	2012-07-11 09:40:17.566869824 -0700
***************
*** 21,26 ****
--- 21,28 ----
      for line in f:
          if line.startswith('#define H5_VERSION'):
              hdf5_version = line.split()[2]
+         elif line.startswith('#define VERSION'):
+             hdf5_version = line.split()[2]
      return hdf5_version
  
  def check_ifnetcdf4(netcdf4_includedir):
</source>

The build continues:

 python setup.py build
 sudo bash
 source /opt/netcdf-4.2.1/setenv.sh
 python setup.py install --prefix=/opt/netcdf-4.2.1
 exit