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[netCDF #IYN-849218]: FAIL: nc_test

Konrad,

> Another chapter of my adventure with netcdf:
> This time I tried to build netcdf-fortran-4.2 on another computer using pgi
> compiler, but I've discovered that it is impossible. This time, whether I
> compiled it with pgi or gcc, i have similar errors - there was same vague
> undefined reference to the gfortran (if I used FC=pgf90 and F77=pgi90) or
> undefined reference to the pgf90 (when I used gfortran). For example with
> pgi, this massage shown on the screen after typing 'make check':
> 
> /bin/sh ../libtool --tag=F77 --mode=link pgf90 -I../fortran -I../f90 -g -o
> nf_test test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o
> util.o fortlib.o ../fortran/libnetcdff.la -lnetcdf
> libtool: link: pgf90 -I../fortran -I../f90 -g -o .libs/nf_test test_get.o
> test_put.o nf_error.o nf_test.o test_read.o test_write.o util.o fortlib.o
> ../fortran/.libs/libnetcdff.so -lnetcdf
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_internal_unpack'

This looks like you have first tried unsuccessfully to build the netCDF 
Fortran library with gfortran, then tried to build with pgf90 instead,
without running "make clean" first.  Remnants of the unsuccessful 
attempt to build with gfortran are left in the build directory and pgf90
can't use those to finish the build.

After an unsuccessful build, you should either start over from a clean
source directory or make sure you run "make clean" and run the configure
script again with new compiler settings before trying to build with
"make" or "make check".

I recommend following these instructions:

  http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html

--Russ

> ../fortran/.libs/libnetcdff.so: undefined reference to `_gfortran_size0'
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_string_len_trim'
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_string_trim'
> ../fortran/.libs/libnetcdff.so: undefined reference to `_gfortran_reshape_4'
> ../fortran/.libs/libnetcdff.so: undefined reference to `_gfortran_shape_4'
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_internal_pack'
> make[2]: *** [nf_test] Error 2
> make[2]: Leaving directory `/work/kwisniew/netcdf-fortran-4.2/nf_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/work/kwisniew/netcdf-fortran-4.2/nf_test'
> make: *** [check-recursive] Error 1
> I attached config.log, which was created after this 'make check'
> I will be very grateful for your help!
> 
> 
> 2013/9/3 Unidata netCDF Support <address@hidden>
> 
> > > Ok, I realize that I can live without HDF5, so I just used
> > > --disable-netcdf-4 option, and everything went fine. But now I'm having a
> > > problem building the Fortran version 4.2. I installed C libraries in
> > > default location /usr/local, but I still have this problem:
> > >
> > > checking size of off_t... configure: error: in
> > > `/home/kon/source/netCDF/netcdf-fortran-4.2':
> > > configure: error: cannot compute sizeof (off_t)
> > >
> > > I've attached the config.log file. Any help would be greatly appreciated!
> >
> > The config.log file shows this:
> >
> >   configure:19798: checking size of off_t
> >   configure:19803: gcc -o conftest -g -O2 -I/usr/local/include
> > -L/usr/local/lib conftest.c -lnetcdf  >&5
> >   configure:19803: $? = 0
> >   configure:19803: ./conftest
> >   ./conftest: error while loading shared libraries: libnetcdf.so.7: cannot
> > open shared object file: No such file or directory
> >
> > which looks like not setting
> >
> >   LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib
> >
> > before running the configure script.  For more about the reasons
> > this is sometimes required, see:
> >
> >    http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html
> >
> > --Russ
> >
> > > 2013/9/3 Unidata netCDF Support <address@hidden>
> > >
> > > > Hi Konrad,
> > > >
> > > > > I'm trying to build netcdf-4.3.0 on openSUSE 11.3, and I have some
> > > > problems
> > > > > with it. An error occurred while 'make check' is running. This is
> > what I
> > > > > see in terminal:
> > > > >
> > > > >
> > > >
> > ============================================================================
> > > > > Testsuite summary for netCDF 4.3.0
> > > > >
> > > >
> > ============================================================================
> > > > > # TOTAL: 12
> > > > > # PASS:  11
> > > > > # SKIP:  0
> > > > > # XFAIL: 0
> > > > > # FAIL:  1
> > > > > # XPASS: 0
> > > > > # ERROR: 0
> > > > >
> > > >
> > ============================================================================
> > > > > See nc_test/test-suite.log
> > > > >
> > > > > make[3]: *** [test-suite.log] Error 1
> > > > > make[3]: Leaving directory
> > > > > `/work/kwisniew/netcdf-4.3.0/netcdf-4.3.0/nc_test'
> > > > > make[2]: *** [check-TESTS] Error 2
> > > > > make[2]: Leaving directory
> > > > > `/work/kwisniew/netcdf-4.3.0/netcdf-4.3.0/nc_test'
> > > > > make[1]: *** [check-am] Error 2
> > > > > make[1]: Leaving directory
> > > > > `/work/kwisniew/netcdf-4.3.0/netcdf-4.3.0/nc_test'
> > > > > make: *** [check-recursive] Error 1
> > > > >
> > > > > I'm trying to build it with gcc compiler. I have reinstalled the hdf5
> > > > > libraries, but I still got the same result.
> > > > > I attached test-suite.log to this mail. I have no idea how to solve
> > this
> > > > > problem, so I will be grateful for any help.
> > > >
> > > > What version of HDF5 were you linking against?  It looks like the
> > problem
> > > > may
> > > > be with HDF5.  You can tell the HDF5 version by looking at the
> > > > "libhdf5.settings"
> > > > file in the directory where libhdf5 is installed.
> > > >
> > > > We tested netCDF-4.3.0 against HDF5-1.8.10 and HDF5-1.8.11
> > successfully,
> > > > but
> > > > there may be problems with earlier versions.
> > > >
> > > > If that's not the problem, could you please send us the config.log you
> > get
> > > > from running the netCDF configure script?
> > > >
> > > > --Russ
> > > >
> > > > Russ Rew                                         UCAR Unidata Program
> > > > address@hidden                      http://www.unidata.ucar.edu
> > > >
> > > >
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: IYN-849218
> > > > Department: Support netCDF
> > > > Priority: Normal
> > > > Status: Closed
> > > >
> > > >
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: IYN-849218
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
> Another chapter of my adventure with netcdf:
> This time I tried to build netcdf-fortran-4.2 on another computer using pgi
> compiler, but I've discovered that it is impossible. This time, whether I
> compiled it with pgi or gcc, i have similar errors - there was same vague
> undefined reference to the gfortran (if I used FC=pgf90 and F77=pgi90) or
> undefined reference to the pgf90 (when I used gfortran). For example with
> pgi, this massage shown on the screen after typing 'make check':
> 
> /bin/sh ../libtool --tag=F77 --mode=link pgf90 -I../fortran -I../f90 -g -o
> nf_test test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o
> util.o fortlib.o ../fortran/libnetcdff.la -lnetcdf
> libtool: link: pgf90 -I../fortran -I../f90 -g -o .libs/nf_test test_get.o
> test_put.o nf_error.o nf_test.o test_read.o test_write.o util.o fortlib.o
> ../fortran/.libs/libnetcdff.so -lnetcdf
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_internal_unpack'
> ../fortran/.libs/libnetcdff.so: undefined reference to `_gfortran_size0'
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_string_len_trim'
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_string_trim'
> ../fortran/.libs/libnetcdff.so: undefined reference to `_gfortran_reshape_4'
> ../fortran/.libs/libnetcdff.so: undefined reference to `_gfortran_shape_4'
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `_gfortran_internal_pack'
> make[2]: *** [nf_test] Error 2
> make[2]: Leaving directory `/work/kwisniew/netcdf-fortran-4.2/nf_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/work/kwisniew/netcdf-fortran-4.2/nf_test'
> make: *** [check-recursive] Error 1
> I attached config.log, which was created after this 'make check'
> I will be very grateful for your help!
> 
> 
> 2013/9/3 Unidata netCDF Support <address@hidden>
> 
> > > Ok, I realize that I can live without HDF5, so I just used
> > > --disable-netcdf-4 option, and everything went fine. But now I'm having a
> > > problem building the Fortran version 4.2. I installed C libraries in
> > > default location /usr/local, but I still have this problem:
> > >
> > > checking size of off_t... configure: error: in
> > > `/home/kon/source/netCDF/netcdf-fortran-4.2':
> > > configure: error: cannot compute sizeof (off_t)
> > >
> > > I've attached the config.log file. Any help would be greatly appreciated!
> >
> > The config.log file shows this:
> >
> >   configure:19798: checking size of off_t
> >   configure:19803: gcc -o conftest -g -O2 -I/usr/local/include
> > -L/usr/local/lib conftest.c -lnetcdf  >&5
> >   configure:19803: $? = 0
> >   configure:19803: ./conftest
> >   ./conftest: error while loading shared libraries: libnetcdf.so.7: cannot
> > open shared object file: No such file or directory
> >
> > which looks like not setting
> >
> >   LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib
> >
> > before running the configure script.  For more about the reasons
> > this is sometimes required, see:
> >
> >    http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html
> >
> > --Russ
> >
> > > 2013/9/3 Unidata netCDF Support <address@hidden>
> > >
> > > > Hi Konrad,
> > > >
> > > > > I'm trying to build netcdf-4.3.0 on openSUSE 11.3, and I have some
> > > > problems
> > > > > with it. An error occurred while 'make check' is running. This is
> > what I
> > > > > see in terminal:
> > > > >
> > > > >
> > > >
> > ============================================================================
> > > > > Testsuite summary for netCDF 4.3.0
> > > > >
> > > >
> > ============================================================================
> > > > > # TOTAL: 12
> > > > > # PASS:  11
> > > > > # SKIP:  0
> > > > > # XFAIL: 0
> > > > > # FAIL:  1
> > > > > # XPASS: 0
> > > > > # ERROR: 0
> > > > >
> > > >
> > ============================================================================
> > > > > See nc_test/test-suite.log
> > > > >
> > > > > make[3]: *** [test-suite.log] Error 1
> > > > > make[3]: Leaving directory
> > > > > `/work/kwisniew/netcdf-4.3.0/netcdf-4.3.0/nc_test'
> > > > > make[2]: *** [check-TESTS] Error 2
> > > > > make[2]: Leaving directory
> > > > > `/work/kwisniew/netcdf-4.3.0/netcdf-4.3.0/nc_test'
> > > > > make[1]: *** [check-am] Error 2
> > > > > make[1]: Leaving directory
> > > > > `/work/kwisniew/netcdf-4.3.0/netcdf-4.3.0/nc_test'
> > > > > make: *** [check-recursive] Error 1
> > > > >
> > > > > I'm trying to build it with gcc compiler. I have reinstalled the hdf5
> > > > > libraries, but I still got the same result.
> > > > > I attached test-suite.log to this mail. I have no idea how to solve
> > this
> > > > > problem, so I will be grateful for any help.
> > > >
> > > > What version of HDF5 were you linking against?  It looks like the
> > problem
> > > > may
> > > > be with HDF5.  You can tell the HDF5 version by looking at the
> > > > "libhdf5.settings"
> > > > file in the directory where libhdf5 is installed.
> > > >
> > > > We tested netCDF-4.3.0 against HDF5-1.8.10 and HDF5-1.8.11
> > successfully,
> > > > but
> > > > there may be problems with earlier versions.
> > > >
> > > > If that's not the problem, could you please send us the config.log you
> > get
> > > > from running the netCDF configure script?
> > > >
> > > > --Russ
> > > >
> > > > Russ Rew                                         UCAR Unidata Program
> > > > address@hidden                      http://www.unidata.ucar.edu
> > > >
> > > >
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: IYN-849218
> > > > Department: Support netCDF
> > > > Priority: Normal
> > > > Status: Closed
> > > >
> > > >
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: IYN-849218
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: IYN-849218
Department: Support netCDF
Priority: Normal
Status: Closed