Re: octcdf-1.1.4 yields recompile with -fPIC

[Ismael Núñez-Riboni]

On 04/11/2012 06:58 PM, Ismael Núñez-Riboni wrote:
> Thanks for the amazingly quick answer!
>
> > > If for some reason you do need to build NetCDF yourself, then build a
> > > dynamic link of it.
>
> Indeed, I build Unidata NetCDF myself. I knew that Ubuntu includes a
> NetCDF library now, but I specifically need the Unidata library for
> another package. I believe thus I can do 2 things:
>
> 1) Perhaps I could link to the Ubuntu NetCDF library (and not the the
> Unidata one, which seems to be default) when I compile Octave? Do you
> know how to do this? (I think something like ./cofigure
> --with-netcdf=path2Ubuntu-netcdf).
>
> 2) I build now a shared library of the Unidata NetCDF (configure with
> --enable-shared) and I'm recompiling octave now, which takes some
> time... I can tell tomorrow if this worked but I guess 1) is the
> simplest solution...


Number 2 did not work. I successfully compiled netCDF with 
--enable-shared but Octave still cannot find the shared object:

octave:3> pkg([install_dir,'octcdf-1.1.4.tar.gz'],'install')
warning: X11 DISPLAY environment variable not set
warning: X11 DISPLAY environment variable not set
warning: X11 DISPLAY environment variable not set
warning: load_path: 
/home/ismael/octave/octcdf-1.1.4/x86_64-unknown-linux-gnu-api-v48+: No 
such file or directory
/home/ismael/octave/octcdf-1.1.4/x86_64-unknown-linux-gnu-api-v48+/netcdf.oct: 
failed to load: libnetcdf.so.4: cannot open shared object file: No such 
file or directory
error: called from `gen_doc_cache>create_cache' in file 
/usr/local/share/octave/3.6.1/m/help/gen_doc_cache.m near line 94, column 17
error: called from:
error:   /usr/local/share/octave/3.6.1/m/pkg/pkg.m at line 869, column 5
error:   /usr/local/share/octave/3.6.1/m/pkg/pkg.m at line 383, column 9

I tried then:

A) A soft link to the shared netCDF object:

sudo ln -s /usr/local/lib/libnetcdf.so.4.0.0 
/home/ismael/octave/octcdf-1.1.4/x86_64-unknown-linux-gnu-api-v48+/netcdf.oct

This fails because at the moment of installing the netCDF package inside 
Octave, pkg overwrites the target folder (and with it the soft link). At 
the end Octave tells again that the shared object does not exist.

B) Export the shared object:

export LD_LIBRARY_PATH=/usr/local/lib/libnetcdf.so.4

Which yields a similar error:

/home/ismael/octave/octcdf-1.1.4/x86_64-unknown-linux-gnu-api-v48+/netcdf.oct: 
failed to load: 
/home/ismael/octave/octcdf-1.1.4/x86_64-unknown-linux-gnu-api-v48+/netcdf.oct: 
undefined symbol: nc_put_att_double
error: called from `gen_doc_cache>create_cache' in file 
/usr/local/share/octave/3.6.1/m/help/gen_doc_cache.m near line 94, column 17
error: called from:
error:   /usr/local/share/octave/3.6.1/m/pkg/pkg.m at line 869, column 5
error:   /usr/local/share/octave/3.6.1/m/pkg/pkg.m at line 383, column 9

I think I need to configure octave with the path to the either the 
ubuntu netcdf library or to the unidata netcdf library, something like 
"./cofigure --with-netcdf=path2Ubuntu-netcdf" but I simply do not know 
how to do this...