[netCDF #FUW-295578]: netcdf Make check error

Alex,

> Thank you for your help with the previous 2 problems. I sorry, but I've
> managed to have another issue now. As before, I have successfully installed
> the netcdf C library (4.3.1) already, and now I'm trying to install the
> fortran library (4.2). I have exported the env variable $LD_LIBRARY_PATH
> that points to the lib directory of the netcdf C installation as you
> suggested, which allowed the `configure` step to complete without errors.
> 
> However, after I call `configure` on the fortran library as below:
> 
> CC=$HOME/apps/gcc/gcc/bin/gcc CXX=$HOME/apps/gcc/gcc/bin/g++
> FC=$HOME/apps/gcc/gcc/bin/gfortran
> CPPFLAGS=-I$HOME/apps/netcdf/4.3.1/include
> LDFLAGS=-L$HOME/apps/netcdf/4.3.1/lib ./configure
> --prefix=$HOME/apps/netcdf/4.3.1
> 
> I then get the following error when I call `make check`:
> 
> libtool: compile:  /home/fispalma25/apps/gcc/gcc/bin/gcc -DHAVE_CONFIG_H
> -I. -I.. -DDLL_EXPORT -I/home/fispalma25/apps/netcdf/4.3.1/include -g -O2
> -MT fort-attio.lo -MD -MP -MF .deps/fort-attio.Tpo -c fort-attio.c  -fPIC
> -DPIC -o .libs/fort-attio.o
> In file included from fort-attio.c:8:0:
> *ncfortran.h:24:42: fatal error: NF_INT_IS_C_... not defined: No such file
> or directory*
> * #   include "NF_INT_IS_C_... not defined"*
> *                                          ^*
> compilation terminated.
> 
> Once again, I'd be grateful for any help you could give me. I've never had
> these problems installing netcdf before. I suppose I have overlooked some
> detail again. The config.log and fortran/nfconfig.in, fortran/nfconfig.inc
> files are attached if they help.

I've seen this problem before in config.log, here's the description:

  http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11949.html

The solution explained there is:

   You either need to rebuild your gfortran configured with 
   --disable-libquadmath (which means it won't support REAL(16) 
   or COMPLEX(16) types, not required by the Fortran standards 
   as far as I know, or you'll have to install libquadmath to 
   make such support available.

You might find it easier to just install a gcc and gfortran
compiler pair that are known to have been built compatibly.
There is no need to have the very latest gcc/gfortran.  I'd
recommend just getting the compilers from a package management
system that makes binaries available, such as "yum".

--Russ

> address@hidden> wrote:
> 
> > Hi Alex,
> >
> > > Thanks for the help. I recompiled hdf5 with zlib enabled and now the all
> > > the tests for the netcdf c library have been passed, and I installed
> > > successfully.
> > >
> > > However, now I am not able to successfully install the fortran
> > > (netcdf-fortran-4.2) library. I get the following error:
> > >
> > > checking size of off_t... configure: error: in
> > > `/home/fispalma25/apps/netcdf/netcdf-fortran-4.2':
> > > configure: error: cannot compute sizeof (off_t)
> > > See `config.log' for more details
> > >
> > > I have attached `config.log` in case that helps. I would appreciate any
> > > advice you can provide.
> >
> > Since you installed the netCDF C library as a shared library in a location
> > that is
> > not searched by default, you need to set the LD_LIBRARY_PATH environment
> > variable (or the equivalent DYLD_LIBRARY_PATH for OSX) , as described here:
> >
> >   http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html
> >
> > This is in addition to the LDFLAGS you are giving the compiler, because the
> > LD_LIBRARY_PATH is used by the loader to find shared libraries.
> >
> > --Russ
> >
> > > Cheers,
> > > Alex
> > >
> > >
> > >
> > >
> > >
> > > address@hidden> wrote:
> > >
> > > > On 1/23/14, 9:27 AM, Alex Robinson wrote:
> > > > > New Ticket: netcdf Make check error
> > > > >
> > > > > This test failed during `Make check`:
> > > > >
> > > > > *** Checking HDF5 variable functions.
> > > > > *** Checking HDF5 boolen variables...ok.
> > > > > *** Checking HDF5 variable with unlimited dimension...ok.
> > > > > *** Checking HDF5 deflate filter setting and getting...Sorry!
> > Unexpected
> > > > > result, tst_h_vars.c, line: 230
> > > > > FAIL: tst_h_vars
> > > > >
> > > > > I am installing netCDF version 4.3.1 with HDF5 version 1.8.12.
> > > > >
> > > > > Am I doing something wrong?
> > > > >
> > > > > Thanks,
> > > > > Alex
> > > > >
> > > > >
> > > > Frequently this is caused by an HDF5 install that was not compiled
> > > > with zlib compression enabled.  It may also be caused if HDF5 was
> > > > compiled with SZIP support but if netCDF was not.  If you provide
> > > > the config.log file, I will be happy to take a look, but the first step
> > > > will be to ensure that you are using an HDF5 compiled with zlib
> > > > support.
> > > >
> > > > Thanks!
> > > >
> > > > -Ward
> > > >
> > > >
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: FUW-295578
> > > > Department: Support netCDF
> > > > Priority: Normal
> > > > Status: Open
> > > >
> > > >
> > >
> > >
> > > --
> > > Alexander Robinson
> > > Dpto. Astrofísica y CC de la Atmósfera
> > > Facultad de CC Físicas
> > > Universidad Complutense de Madrid
> > > 28040 Madrid, Spain
> > > ---------------------------------
> > > Tel (Fax): +34 91 394 4457 (4635)
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: FUW-295578
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
> --
> Alexander Robinson
> Dpto. Astrofísica y CC de la Atmósfera
> Facultad de CC Físicas
> Universidad Complutense de Madrid
> 28040 Madrid, Spain
> ---------------------------------
> Tel (Fax): +34 91 394 4457 (4635)
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: FUW-295578
Department: Support netCDF
Priority: Normal
Status: Closed