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[netCDF #PSS-815442]: error building netcdf 4.3.0 with gfortran 4.7.2
- Subject: [netCDF #PSS-815442]: error building netcdf 4.3.0 with gfortran 4.7.2
- Date: Thu, 27 Jun 2013 11:05:37 -0600
> So here the config.log from running the netcdf-fortran-4.2 configure script.
Thanks, I see what the problem is, and it's not really related to netCDF.
When your gfortran was built, it was apparently configured to support 128-bit
precision complex numbers and functions, from libquadmath software. The netCDF
libraries never use or require libquadmath. I know this because it's not
installed on my Linux system, but I've never gotten an error message that it's
missing in all the testing I do for netCDF, HDF5, OPeNDAP, etc.
The error message in your netcdf-fortran config.log says it can't be found:
configure:17817: checking if Fortran "byte" is C "signed char"
configure:17827: gcc -c -Dgfortran -I/opt/netcdf-4.3.0-gf/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]
configure:17830: $? = 0
configure:17833: gfortran -g -O2 -c conftestf.f
configure:17836: $? = 0
configure:17839: gfortran -o conftest -g -O2 -L/opt/netcdf-4.3.0-gf/lib
conftestf.o conftest.o
configure:17842: $? = 0
configure:17845: ./conftest
./conftest: error while loading shared libraries: libquadmath.so.0: cannot
open shared object file: No such file or directory
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.
The reason you're seeing the error message even though no libquadmath functions
are used
by netCDF is "explained" here:
http://gcc.gnu.org/ml/fortran/2011-01/msg00040.html
Please let me know if you come up with a better solution for this problem. It
may have
just been the result of a bad gfortran build/installation ...
--Russ
> -----Original Message-----
> From: Unidata netCDF Support [mailto:address@hidden]
> Sent: Thursday, June 27, 2013 4:41 PM
> To: Hans Malschaert
> Cc: address@hidden
> Subject: [netCDF #PSS-815442]: error building netcdf 4.3.0 with gfortran 4.7.2
>
> Hans,
>
> > Hereby I send you the requested log files, config.log and
> > fortran/nfconfig.inc.
>
> Oops, I wasn't clear enough. I need the config.log from running the
> netcdf-fortran-4.2 configure script, which should be in the top-level of the
> netcdf-fortran-4.2 directory.
>
> The one you sent was from the netcdf-4.3.0 C library build, which seemed to
> have been successful.
>
> --Russ
>
> > Regards,
> > Hans Malschaert
> >
> > -----Original Message-----
> > From: Unidata netCDF Support [mailto:address@hidden]
> > Sent: Wednesday, June 26, 2013 4:44 PM
> > To: Hans Malschaert
> > Cc: address@hidden
> > Subject: [netCDF #PSS-815442]: error building netcdf 4.3.0 with
> > gfortran 4.7.2
> >
> > Hans,
> >
> > > Thank you for your response. We followed the instructions you described
> > > with as result the same error as mentioned before.
> > > I also noticed that I sent you the wrong definitions of the
> > > environmental variables but hereby I sent you in detail the steps we
> > > followed; 1. First the gcc build.
> > >
> > > cd /opt/netcdf-work/netcdf-4.3.0
> > > make distclean
> > > ./configure --prefix=/opt/netcdf-4.3.0-gf --disable-netcdf-4
> > > --disable-dap make check make install
> > >
> > > The result is successfull. The following files are now created;
> > >
> > > /opt/netcdf-4.3.0-gf/bin:
> > > drwxr-xr-x. 2 root root 4096 Jun 26 15:13 .
> > > drwxr-xr-x. 6 root root 4096 Jun 26 15:13 ..
> > > -rwxr-xr-x. 1 root root 5006 Jun 26 15:13 nc-config
> > > -rwxr-xr-x. 1 root root 118026 Jun 26 15:13 nccopy -rwxr-xr-x. 1
> > > root root 221658 Jun 26 15:13 ncdump -rwxr-xr-x. 1 root root 679918
> > > Jun 26
> > > 15:13 ncgen -rwxr-xr-x. 1 root root 204029 Jun 26 15:13 ncgen3
> > >
> > > /opt/netcdf-4.3.0-gf/include:
> > > total 68
> > > drwxr-xr-x. 2 root root 4096 Jun 26 15:13 .
> > > drwxr-xr-x. 6 root root 4096 Jun 26 15:13 ..
> > > -rw-r--r--. 1 root root 58489 Jun 26 15:13 netcdf.h
> > >
> > > /opt/netcdf-4.3.0-gf/lib:
> > > total 4732
> > > drwxr-xr-x. 3 root root 4096 Jun 26 15:13 .
> > > drwxr-xr-x. 6 root root 4096 Jun 26 15:13 ..
> > > -rw-r--r--. 1 root root 2799068 Jun 26 15:13 libnetcdf.a
> > > -rwxr-xr-x. 1 root root 945 Jun 26 15:13 libnetcdf.la
> > > lrwxrwxrwx. 1 root root 18 Jun 26 15:13 libnetcdf.so ->
> > > libnetcdf.so.7.2.0
> > > lrwxrwxrwx. 1 root root 18 Jun 26 15:13 libnetcdf.so.7 ->
> > > libnetcdf.so.7.2.0
> > > -rwxr-xr-x. 1 root root 2026296 Jun 26 15:13 libnetcdf.so.7.2.0
> > > drwxr-xr-x. 2 root root 4096 Jun 26 15:13 pkgconfig
> > >
> > >
> > > 2. The fortran build
> > >
> > > CPPFLAGS=-I/opt/netcdf-4.3.0-gf/include;export CPPFLAGS
> > > LDFLAGS=-L/opt/netcdf-4.3.0-gf/lib;export LDFLAGS export
> > > LD_LIBRARY_PATH=/opt/netcdf-4.3.0-gf/lib:${LD_LIBRARY_PATH}
> > >
> > > cd netcdf-fortran-4.2
> > > make distclean
> > > ./configure --prefix=/opt/netcdf-4.3.0-gf make check
> > >
> > > which results in the error :
> > > ncfortran.h:24:42: fatal error: NF_INT_IS_C_... not defined: No such
> > >
> > > We would really appreciate your advice in this case.
> >
> > I don't see the cause of the error, so will need more information. Could
> > you please send the complete config.log file, as well as the file
> > fortran/nfconfig.inc that was generated when the configure script was run?
> >
> > Thanks!
> >
> > --Russ
> >
> > > -----Original Message-----
> > > From: Unidata netCDF Support
> > > [mailto:address@hidden]
> > > Sent: Tuesday, June 25, 2013 9:26 PM
> > > To: Hans Malschaert
> > > Cc: address@hidden
> > > Subject: [netCDF #PSS-815442]: error building netcdf 4.3.0 with
> > > gfortran 4.7.2
> > >
> > > Hi Hans,
> > >
> > >
> > > > We met an error message building netcdf 4.3.0 in a Centos 6.2
> > > > environment with a gfortran 4.7.2 compiler.
> > > >
> > > > Could you give some advice to solve the problem?
> > >
> > > First, you'll have trouble building netCDF 4.3.0 with a Fortran compiler,
> > > as it is only a C library. You should be building it with gcc rather
> > > than gfortran, for example, according to these instructions:
> > >
> > > http://www.unidata.ucar.edu/netcdf/docs/building.html
> > >
> > > Once you have the netCDF C library built and installed, you can get and
> > > build the separate netCDF Fortran 4.2 libraries by following these
> > > instructions:
> > >
> > > http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html
> > >
> > > --Russ
> > >
> > > > The environment variables are set as follows ;
> > > > LDFLAGS=-L/opt/shared/tools/gcc/4.7.2/rtf/lib
> > > > CPPFLAGS=-I/opt/shared/tools/gcc/4.7.2/rtf/include
> > > > -I/opt/netcdf-4.3.0-gf/include
> > > > LD_LIBRARY_PATH=/opt/shared/tools/gcc/4.7.2/rtf/lib
> > > >
> > > > ./configure --prefix=/opt/netcdf-4.3.0-gf make check
> > > >
> > > > which generate the following error..
> > > > Making check in fortran
> > > > make[1]: Entering directory `/opt/netcdf-4.1.3/fortran'
> > > > echo '! NetCDF-3.' > netcdf.inc
> > > > cat ../fortran/netcdf3.inc >> netcdf.inc echo >> netcdf.inc
> > > > echo '! NetCDF-2.' >> netcdf.inc
> > > > cat ../fortran/netcdf2.inc >> netcdf.inc make check-am
> > > > make[2]: Entering directory `/opt/netcdf-4.1.3/fortran'
> > > > depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
> > > > /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
> > > > -I.. -I../include -g -O2 -MT fort-attio.lo -MD -MP -MF
> > > > $depbase.Tpo -c -o fort-attio.lo fort-attio.c &&\
> > > > mv -f $depbase.Tpo $depbase.Plo
> > > > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../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 compilation terminated.
> > > > make[2]: *** [fort-attio.lo] Error 1
> > > > make[2]: Leaving directory `/opt/netcdf-4.1.3/fortran'
> > > > make[1]: *** [check] Error 2
> > > > make[1]: Leaving directory `/opt/netcdf-4.1.3/fortran'
> > > > make: *** [check-recursive] Error 1
> > > >
> > > >
> > > > Best regards,
> > > > Hans Malschaert
> > > > System/Network administrator
> > > >
> > > > Information and Presentation Centre (IPC) Royal Netherlands
> > > > Institute for Sea Research (Koninklijk Nederlands Instituut voor
> > > > Zeeonderzoek) Landsdiep 4 - 1797 SZ Den Hoorn - Netherlands
> > > > * mailto: address@hidden<mailto:address@hidden>
> > > > ? tel : +31 222 369377
> > > > ? fax : +31 222 319674
> > > > * ftp : http://nioz.wetransfer.com<http://nioz.wetransfer.com/>
> > > > * web : http://www.nioz.nl<http://www.nioz.nl/>
> > > > [Description: cid:image001.gif@01CBEAF1.BA49FCA0]
> > > >
> > > >
> > > >
> > > Russ Rew UCAR Unidata Program
> > > address@hidden http://www.unidata.ucar.edu
> > >
> > >
> > >
> > > Ticket Details
> > > ===================
> > > Ticket ID: PSS-815442
> > > Department: Support netCDF
> > > Priority: Normal
> > > Status: Closed
> > >
> > >
> >
> > Russ Rew UCAR Unidata Program
> > address@hidden http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: PSS-815442
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
>
> Russ Rew UCAR Unidata Program
> address@hidden http://www.unidata.ucar.edu
>
>
>
> Ticket Details
> ===================
> Ticket ID: PSS-815442
> Department: Support netCDF
> Priority: Normal
> Status: Closed
>
>
Russ Rew UCAR Unidata Program
address@hidden http://www.unidata.ucar.edu
Ticket Details
===================
Ticket ID: PSS-815442
Department: Support netCDF
Priority: Normal
Status: Closed