[netCDF #QGV-335526]: Problem with netcdf and fortran 90

Delphine,

> many thanks for your help. I've made sure to build the library for a 64-bit.
> 
> I also corrected the links regarding the //
> 
> However, I've perform a make check and got one error.
> I'm attaching the result of this command.
> 
> Could this be the cause of the problem?

The error you are now seeing:

> *** Testing HDF5/NetCDF-4 interoperability...
> *** Creating a HDF5 file with one var with two dimension scales...ok.
> *** Checking that HDF5 file can be read by netCDF-4, and adding an att...ok.
> *** Checking that one var, two dimscales, one att file can still be read by 
> HDF5...ok.
> *** Creating a HDF5 file with one var and no dimension scales...ok.
> HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0:
>   #000: H5O.c line 717 in H5Oget_info_by_idx(): group not found
>     major: Symbol table
>     minor: Object not found

is the result of using the combination netCDF-4.1.1 and HDF5-1.8.6.
Here's a discussion of the problem and possible workarounds:

  http://www.unidata.ucar.edu/netcdf/docs/known_problems.html#incompat-411-186

--Russ

> On 15 Mar 2011, at 21:19, Unidata netCDF Support wrote:
> 
> > Hi Delphine ,
> >
> >> I'm trying to compile a fortran code but it seems my netcdf library is
> >> not referenced correctly. However, I can't find the reason why. I hope
> >> you could help me finding the source of the problem.
> >>
> >> My environment is Mac OS X 10.6.6.
> >> Fortran compiler is ifort 12.0.0
> >>
> >> I have installed the netcdf 4.1.1 library. See below the results of the
> >> command 'nc-config --all'
> >>
> >> I'm trying to compile a simple code requiring netcdf library. However,
> >> I'm getting this error message:
> >>
> >> Undefined symbols:
> >> "_nf_open_", referenced from:
> >> _wr4dnc_ in netcdf4d.o
> >> ld: symbol(s) not found
> >> make: *** [main] Error 1
> >
> > First, please check that the library was compiled for the same architecture
> > as your application program.  A common error on Mac's is to build a library
> > for a 64-bit x86_64 architecture and try to link a program compiled for a
> > 32-bit i386 architecture with that library (or vice versa).  The result is
> > that netCDF library functions won't be found.  You can check what
> > architectures your program and library are compiled for with the "file"
> > command, as in
> >
> >  $ file /opt/local/lib/netcdff.dylib
> >  /opt/local/lib/netcdff.dylib:  Mach-O 64-bit dynamically linked shared 
> > library x86_64
> >
> > If your Fortran and C compilers have different defaults for arcitectures,
> > you may have to use -m64 or -m32 CFLAGS or FCFLAGS explicitly to make sure
> > they match.
> >
> > That may not be the problem, because I see another possible symptom of
> > a problem in the nc-config output you sent:
> >
> >> --libs -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl -lhdf5 
> >> -L/opt/local//lib -lz -lm -L/opt/local//lib -lsz -L/opt/local/lib -lcurl 
> >> -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib -lidn -lssl -lcrypto 
> >> -lssl -lcrypto -lz -lz
> > ...
> >> --flibs -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl -lhdf5 
> >> -L/opt/local//lib -lz -lm -L/opt/local//lib -lsz -L/opt/local/lib -lcurl 
> >> -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib -lidn -lssl -lcrypto 
> >> -lssl -lcrypto -lz -lz
> >
> > Both of these have a double slash "//" in some -L options, as in
> > "-L/opt/local//lib".  That seems wrong, and may be the result of a typo
> > when the library was configured and built, or may be a bug in nc-config,
> > but I don't see such a double slash in the --libs or --flibs output of
> > the 4.1.1 nc-config here.
> >
> > Can you check if things work if you change this "//" to "/" in your link
> > command?
> >
> > --Russ
> >
> >> nc-config --all
> >>
> >> This netCDF 4.1.1 has been built with the following features:
> >>
> >> --cc        -> icc
> >> --cflags    ->  -I/opt/local/include
> >> --libs      -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl 
> >> -lhdf5  -L/opt/local//lib -lz -lm  -L/opt/local//lib -lsz  
> >> -L/opt/local/lib -lcurl -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib 
> >> -lidn -lssl -lcrypto -lssl -lcrypto -lz -lz
> >>
> >> --cxx       -> icpc
> >> --has-c++   -> yes
> >>
> >> --fc        -> ifort
> >> --fflags    -> -g -I/opt/local/include
> >> --flibs     -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl 
> >> -lhdf5  -L/opt/local//lib -lz -lm  -L/opt/local//lib -lsz  
> >> -L/opt/local/lib -lcurl -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib 
> >> -lidn -lssl -lcrypto -lssl -lcrypto -lz -lz
> >> --has-f77   -> yes
> >> --has-f90   -> yes
> >>
> >> --has-dap   -> yes
> >> --has-nc2   -> yes
> >> --has-nc4   -> yes
> >> --has-hdf5  -> yes
> >> --has-hdf4  -> no
> >> --has-szlib -> yes
> >>
> >> --prefix    -> /opt/local
> >> --includedir-> /opt/local/include
> >> --version   -> netCDF 4.1.1
> >>
> >>
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: QGV-335526
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> 
> 
> 

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



Ticket Details
===================
Ticket ID: QGV-335526
Department: Support netCDF
Priority: Normal
Status: Closed