Re: Octcdf package installation with NetCDF4

[E. Joshua Rigler]

OK, it might be bad form to reply to my own post, but I just realized
something.  NetCDF 3.6 (the current version) does not actually link to
either of the HDF5libraries, so it's entirely possible that what I
said about HDF5 v1.8 having once had all of its functions in a single
library file (libhdf5.so) was completely wrong.  It is still necessary
to link to both libhdf5.so and libhdf5_hl.so in order to compile a
function that calls nc_open however, and to get Octcdf to compile
properly using the new NetCDF 4 (the new version) libraries.

-EJR


On Tue, May 6, 2008 at 3:58 PM, E. Joshua Rigler <address@hidden> wrote:
> Hopefully Alexander Barth is paying attention, so he might incorporate
>  a small fix into his Octcdf package that anticipates certain changes
>  in the upcoming NetCDF 4 release, but here's what I did to get Octcdf
>  working with a development snapshot of NetCDF 4:
>
>  For starters, while I leave most of the compilation and installation
>  of NetCDF4 as an exercise for the reader, note that this is a
>  substantial deviation from the current 'mature' version, namely NetCDF
>  v3.6.  As I understand it, NetCDF 4 relies heavily on the recently
>  released HDF5 v1.8 for its low-level data model.  HDF5 v1.8, in turn,
>  now seems to have two important libraries instead of one, these being
>  libhdf5.so and libhdf5_hl.so.
>
>  Why is this relevant for Octave?  The Octcdf package Autoconf
>  configure script currently tests for the function nc_open to see if
>  the libnetcdf.so library is suitable for compiling the netcdf.oct
>  file.  nc_open in turn relies on functions that originally all resided
>  in libhdf5.so, but some of which now apparently reside inside
>  libhdf5_hl.so.  So, if one simply tries to type 'pkg install
>  octcdf-1.0.9.tar.gz', it will fail when the configure script fails to
>  ascertain that suitable NetCDF libraries exist, since its attempt to
>  compile a test function that calls nc_open will fail due to 'undefined
>  reference' errors.
>
>  My Solution:  start Octave and run the pkg install script in the
>  following manner:
>
>   $> LDFLAGS=-L/path/to/libs CPPFLAGS=-I/path/to/headers LIBS='-lhdf5
>  -lhdf5_hl' octave -q
>   octave:1> pkg install -verbose octcdf-1.0.9.tar.gz
>
>  I'm not sure if a more 'permanent' solution lies with the NetCDF
>  maintainers (can they fix libnetcdf.so to automatically link to both
>  HDF5 libraries?), or is it up to A. Barth to modify his Octcdf
>  package's Autoconf script to check for, and link to, both required
>  HDF5 libraries in a manner similar to my somewhat ad hoc solution?
>  BTW, I have not tested Octcdf extensively with the new NetCDF 4
>  libraries, but the Octcdf package's built-in test suite passed.
>
>  -EJR
>