[netCDF #UAT-411621]: getting undefined reference when compiling netCDF4.2 Fortran

Steve,

> When I set "--disable-fortran-type-check" as a compiler flag (found at
> http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg07203.html)
> and also set my LDFLAGS, I was finally able to get rid of the undefined
> references and "cannot execute" errors.  Thanks very much for your help.

Aha, thanks for pointing out that archived support response from 2008!

I've added advice about using the "disable-fortran-type-check" when
cross-compiling to our instructions for building netCDF-Fortran, at

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

--Russ

> address@hidden> wrote:
> 
> > Hi Steve,
> >
> > > I have attached my config.log file,  from running configure in netCDF
> > > Fortran 4.2. Perhaps you can detect something.
> > >
> > > I am still seeing errors like:
> > >
> > > libtool: link: /home/skirby/ANDROID19/bin/arm-linux-androideabi-gfortran
> > > -I.    ./fortran -I../f90 -g -O2 -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
> > > -L/home/skirby/NETCDF42-ANDROID/lib ../fortran/.libs/libnetcdff.so
> > > /home/skirby/NETCDF42-ANDROID/lib/libnetcdf.so -lm -Wl,-rpath
> > > -Wl,/home/skirby/NETCDF42-ANDROID/lib
> > > test_get.o: In function `test_nf_get_var1_int1_':
> > >
> > /home/skirby/ANDROID-NETCDF-FORTRAN-COMPILE/netcdf-fortran-4.2/nf_test/test_get.F:125:
> > > undefined reference to `nf_get_var1_int1_'
> > >
> > /home/skirby/ANDROID-NETCDF-FORTRAN-COMPILE/netcdf-fortran-4.2/nf_test/test_get.F:129:
> > > undefined reference to `nf_get_var1_int1_'
> > >
> > /home/skirby/ANDROID-NETCDF-FORTRAN-COMPILE/netcdf-fortran-4.2/nf_test/test_get.F:134:
> > > undefined reference to `nf_get_var1_int1_'
> > >
> > /home/skirby/ANDROID-NETCDF-FORTRAN-COMPILE/netcdf-fortran-4.2/nf_test/test_get.F:152:
> > > undefined reference to `nf_get_var1_int1_'
> > > test_get.o: In function `test_nf_get_var1_int2_':
> >
> > I don't think using netCDF-C version 4.3.1.1 rather than 4.2 is going
> > to fix the problem you are seeing with undefined references.
> >
> > It looks like you are cross-compiling and the gfortran you have
> > built for that purpose isn't working correctly as a loader in tests
> > run by the configure script.  As an example of this, the netCDF-Fortran
> > configure script tries to determine C types corresponding to various
> > Fortran types by compiling, linking, and running some programs at
> > configure time, resulting in these constants defined in a "confdefs.h"
> > file:
> >
> >  #define NF_INT1_IS_C_SIGNED_CHAR 1
> >  #define NF_INT2_IS_C_SHORT 1
> >  #define NF_INT_IS_C_INT 1
> >  #define NF_REAL_IS_C_FLOAT 1
> >  #define NF_DOUBLEPRECISION_IS_C_DOUBLE 1
> >
> > When you run configure, all those constants are left undefined in
> > confdefs.h.  The reason they are not defined is due to failures such
> > as this, from the config.log you sent (absolute paths elided or
> > simplified for clarity):
> >
> >     configure: checking if Fortran "byte" is C "signed char"
> >     configure: gcc -c -I${NCDIR}/include -g -O2 conftest.c
> >     conftest.c: In function 'sub_':
> >     conftest.c:4:3: warning: incompatible implicit declaration of built-in
> > function 'exit' [enabled by default]
> >        exit(values[1] != -2 || values[2] != -3);
> >        ^
> >     configure: $? = 0
> >     configure: gfortran -g -O2 -c conftestf.f
> >     configure: $? = 0
> >     configure: gfortran -o conftest -g -O2 -L${NCDIR}/lib conftestf.o
> > conftest.o  -lnetcdf
> >     configure: $? = 0
> >     configure: ./conftest
> >     ./configure: line 17846: ./conftest: cannot execute binary file
> >     configure: $? = 126
> >     configure: result: no
> >
> > When I run configure for netCDF Fortran 4.2 using an installed netCDF C
> > 4.3.1.1, the config.log output from this test is:
> >
> >     configure: checking if Fortran "byte" is C "signed char"
> >     configure: gcc -c -I${NCDIR}/include -g -O2 conftest.c
> >     conftest.c: In function 'sub_':
> >     conftest.c:4:3: warning: incompatible implicit declaration of built-in
> > function 'exit'
> >     configure: $? = 0
> >     configure: gfortran -g -O2 -c conftestf.f
> >     configure: $? = 0
> >     configure: gfortran -o conftest -g -O2 -L${NCDIR}/lib conftestf.o
> > conftest.o  -lnetcdf
> >     configure: $? = 0
> >     configure: ./conftest
> >     configure: $? = 0
> >     configure: result: yes
> >
> > The compiler warning is irrelevant, the important failure is "cannot
> > execute binary file", from which an error status 126 is returned on
> > your system.  Maybe your gfortran used as a cross-compiler is not
> > linking correctly on the 32-bit arm-linux platform that's your target,
> > or maybe our configure script is not working correctly for
> > cross-compiling, which we don't test.  This may be difficult to fix ...
> >
> > --Russ
> >
> > >
> > > etc.
> > >
> > > I have not built the netCDF C 4.3.1.1 code yet. These results are still
> > > based on netCDF C 4.2.
> > >
> > > I set these environment variables:
> > > CPPFLAGS=-I/home/skirby/NETCDF42-ANDROID/include
> > > LDFLAGS=-L/home/skirby/NETCDF42-ANDROID/lib
> > > LIBS=-lnetcdf
> > > LD_LIBRARY_PATH=/home/skirby/NETCDF42-ANDROID/lib
> > >
> > >
> > > --Steve
> > >
> > >
> > >
> > >
> > >
> > >
> > > address@hidden> wrote:
> > >
> > > > Hi Steve,
> > > >
> > > > Rather than using compiler flags related to underscores, I recommend
> > > > following the steps here, which work with many compiler combinations
> > > > without messing with underscores in function names:
> > > >
> > > >   http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html
> > > >
> > > > The instructions above explain when LD_LIBRARY_PATH may be required in
> > > > addition to LD_FLAGS and CPPFLAGS settings.  If this doesn't work for
> > > > you, we might be able to provide more help if you send the config.log
> > > > file generated by the configure script when you start building the
> > > > netCDF Fortran API from source.
> > > >
> > > > Also, it would be better to use the most recent netCDF C release,
> > version
> > > > 4.3.1.1, with netCDF Fortran 4.2.  It has various bug fixes and
> > > > other improvements since netCDF C 4.2 was released, and it's compatible
> > > > with netCDF-Fortran version 4.2.
> > > >
> > > > --Russ
> > > >
> > > > > I have successfully cross-compiled netcdf C 4.2, i.e., build it on a
> > > > x86_64
> > > > > linux box to run on a android ARM.
> > > > >
> > > > > Now I'm trying to cross-compile netcdf fortran 4.2.  But I'm getting
> > > > > undefined references like the one I show below, when I run "gmake
> > check".
> > > > >
> > > > >
> > > > > libtool: link: /home/me/ANDROID19/bin/arm-linux-androideabi-gfortran
> > -l
> > > > > ./fortran -I../f90 -g -O2 -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 -Wl,-rpath
> > > > -Wl,/home/me/NETCDF42-ANDROID/lib
> > > > > test_get.o: In function `test_nf_get_var1_int1_':
> > > > >
> > > >
> > /home/me/ANDROID-NETCDF-FORTRAN-COMPILE/netcdf-fortran-4.2/nf_test/test_get.F:125:
> > > > > undefined reference to `nf_get_var1_int1_'
> > > > >
> > > > > and lots more very similar to this.
> > > > >
> > > > > Prior to this I compiled the netCDF C code, version 4.2.  Then I
> > point
> > > > > CPPFLAGS=-I/path/to/netCDF-C-compile/include and
> > > > > LD_LIBRARY_PATH=/path/to/netCDF-C-compile/lib.
> > > > >
> > > > > If anybody could point me toward how to fix this or give me some
> > ideas
> > > > that
> > > > > would be great.  If it helps at all, I have attached the config log
> > file.
> > > > >
> > > > > TIA,
> > > > > SK
> > > > >
> > > > >
> > > >
> > > > Russ Rew                                         UCAR Unidata Program
> > > > address@hidden                      http://www.unidata.ucar.edu
> > > >
> > > >
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: UAT-411621
> > > > Department: Support netCDF
> > > > Priority: Normal
> > > > Status: Closed
> > > >
> > > >
> > >
> > >
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: UAT-411621
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: UAT-411621
Department: Support netCDF
Priority: Normal
Status: Closed