[netCDF #UYL-334118]: FAIL: run_tests.sh

> So I ignore this -lsz and tried to again.
> The config seemed to work (again attached).

Yes, sorry about that, the "-lsz" should not have been included in LIBS
if the HDF5 library was not built with szlib, and that's not needed for
netCDF-4.

> Compilation failed though with this error msg:
> libtool: link: gcc -shared  -fPIC -DPIC  .libs/libnetcdf_la-stub.o
> -Wl,--whole-archive ../libdispatch/.libs/libnetcdf2.a
> ../libdispatch/.libs/libdispatch.a ../libsrc/.libs/libnetcdf3.a
> ../libdap2/.libs/libdap2.a ../oc/.libs/liboc.a
> ../libsrc4/.libs/libnetcdf4.a -Wl,--no-whole-archive  -Wl,-rpath
> -Wl,/usr/local/hdf5/lib -Wl,-rpath -Wl,/usr/local/hdf5/lib
> -L/usr/local/hdf5/lib -L/usr/local/hdf4/lib -L/usr/lib/x86_64-linux-gnu
> /usr/local/hdf4/lib/libmfhdf.a /usr/local/hdf4/lib/libdf.a -ljpeg
> /usr/local/hdf5/lib/libhdf5_hl.so /usr/local/hdf5/lib/libhdf5.so -lrt -lm
> -lz /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so  -O2   -Wl,-soname
> -Wl,libnetcdf.so.7 -o .libs/libnetcdf.so.7.2.0
> /usr/bin/ld: /usr/local/hdf4/lib/libmfhdf.a(mfsd.o): relocation R_X86_64_32
> against `.rodata.str1.1' can not be used when making a shared object;
> recompile with -fPIC
> /usr/local/hdf4/lib/libmfhdf.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[1]: *** [libnetcdf.la] Error 1
> make[1]: Leaving directory
> `/home/saulo/extra_software/netcdf-4.2.1.1/liblib'
> make: *** [check-recursive] Error 1
> 
> Any idea how can I fix this?

You could try including "-fPIC" in CFLAGS before running configure when
compiling HDF4.  Alternatively, building HDF4 as a shared library may work.

Sorry we don't have a definitive answer for this.  Currently our test build
with HDF4 is not working on our snapshot release, although I believe it was
working with 4.2.1.1.

Of course another solution would be to build without --enable-hdf4, but I'm
assuming you have a need for the limited HDF4 reading capabilities in the
netCDF-4 C libraries.

--Russ

> On Mon, Sep 24, 2012 at 2:06 PM, Saulo Soares <address@hidden> wrote:
> 
> > Hi Russ,
> >
> > Thanks for looking into this.
> > I had tried the HDF4 with --disable-netcdf before and it didn't work but I
> > rebuilt it again with --disable-netcdf anyway.
> > I tried your LIBS choice but now the configure fails:
> >
> > checking whether the C compiler works... no
> > configure: error: in `/home/saulo/extra_software/netcdf-4.2.1.1':
> > configure: error: C compiler cannot create executables
> > See `config.log' for more details
> >
> > Atthached is the log, it seems I don't have this -lsz lib.
> >
> > Thanks
> > Saulo
> >
> >
> > address@hidden> wrote:
> >
> >> Saulo,
> >>
> >> I also see a presentation on using HDF4 with netCDF from several years ago
> >> that had slide 19 with the following bullet text:
> >>
> >>   - This feature cannot be used at the same time as
> >>     HDF4's netCDF v2 API, because HDF4 steals
> >>     the netCDF v2 API function names. So you
> >>     must use --disable-netcdf when building HDF4.
> >>     (It might also work to –disable-v2 for the
> >>     netCDF build.)
> >>
> >> I don't know if the problem you are seeing is related to this, but it may
> >> be a good idea to build the HDF4 library using the --disable-netcdf option
> >> to the configure script.
> >>
> >> --Russ
> >>
> >> > Hi Saulo,
> >> >
> >> > Sorry to have taken so long to respond to your question ...
> >> > > I've attached my config log in case it may help.
> >> >
> >> > Yes, it looks like the hdf4 library, which you have installed in
> >> /usr/local/hdf4/lib/,
> >> > is not being searched.  Could you try running the configure script
> >> again with the
> >> > CPPFLAGS and LDFLAGS you used, but also adding the definition
> >> >
> >> > LIBS='-lmfhdf -ldf -lhdf5_hl -lhdf5 -lsz -lm -lz -lcurl'
> >> >
> >> > The "-lmfhdf -ldf" tell the linker to explicitly search the HDF4
> >> libraries in the
> >> > directories you specified in LDFLAGS.  I don't know whether the
> >> configure script is
> >> > supposed to do this automatically, but if so, it appears to have a bug .
> >> >
> >> > --Russ
> >> >
> >> > > address@hidden> wrote:
> >> > >
> >> > > >
> >> > > > Saulo Soares,
> >> > > >
> >> > > > Your Ticket has been received, and a Unidata staff member will
> >> review it
> >> > > > and reply accordingly. Listed below are details of this new Ticket .
> >> Please
> >> > > > make sure the Ticket ID remains in the Subject: line on all
> >> correspondence
> >> > > > related to this Ticket.
> >> > > >
> >> > > >     Ticket ID: UYL-334118
> >> > > >     Subject: FAIL: run_tests.sh
> >> > > >     Department: Support netCDF
> >> > > >     Priority: Normal
> >> > > >     Status: Open
> >> > > >
> >> > > >
> >> > > >
> >> > > > The NetCDF libraries are developed at the Unidata Program Center,
> >> > > > in Boulder, Colorado, funded primarily by the National Science
> >> Foundation.
> >> > > >
> >> > > > All support requests are handled by the development team. No
> >> dedicated
> >> > > > support staff are funded at this time. For this reason we cannot
> >> guarantee
> >> > > > response times, nor that we can resolve every support issue,
> >> although we
> >> > > > do our best to respond within 72 hours.
> >> > > >
> >> > > > It is in the nature of support requests that the same question is
> >> asked
> >> > > > many
> >> > > > times. We urge you to search the support archives for material
> >> relating to
> >> > > > your support request:
> >> > > >
> >> > > > http://www.unidata.ucar.edu/search.jsp?support&netcdf
> >> > > >
> >> > > > If you are having trouble building netCDF, please take a look at the
> >> > > > "Building NetCDF" page:
> >> > > >
> >> > > > http://www.unidata.ucar.edu/software/netcdf/docs/building.html
> >> > > >
> >> > > > or the (unfortunately somewhat out-of-date) NetCDF Build
> >> Troubleshooter
> >> > > > page:
> >> > > >
> >> > > > http://www.unidata.ucar.edu/software/netcdf/docs/troubleshoot.html
> >> > > >
> >> > > > Windows users should see the FAQ list:
> >> > > >
> >> > > >
> >> http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#windows_netcdf4_2
> >> > > >
> >> > > > Complete documentation (including a tutorial, and sample programs
> >> in C,
> >> > > > Fortran,
> >> > > > Java, and other programming languages) can be found on the netCDF
> >> > > > Documentation page:
> >> > > >
> >> > > > http://www.unidata.ucar.edu/software/netcdf/docs/
> >> > > > http://www.unidata.ucar.edu/software/netcdf/examples/programs/
> >> > > >
> >> > > > If you resolve your issue through one of these methods, please send
> >> a
> >> > > > reply to
> >> > > > this email, letting us know that you no longer need support. This
> >> will help
> >> > > > us spend more time on netCDF development.
> >> > > >
> >> > > > Best regards,
> >> > > >
> >> > > > Unidata User Support
> >> > > >
> >> > > >
> >> > >
> >> > >
> >> > Russ Rew                                         UCAR Unidata Program
> >> > address@hidden                      http://www.unidata.ucar.edu
> >> >
> >> >
> >> Russ Rew                                         UCAR Unidata Program
> >> address@hidden                      http://www.unidata.ucar.edu
> >>
> >>
> >>
> >> Ticket Details
> >> ===================
> >> Ticket ID: UYL-334118
> >> Department: Support netCDF
> >> Priority: Normal
> >> Status: Closed
> >>
> >>
> >
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: UYL-334118
Department: Support netCDF
Priority: Normal
Status: Closed