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[netCDF #ASX-279014]: Building netcdf-fortran-4.2 on 64-bit CentOS 5.6

Jennifer,

> I found an error in my LDFLAGS environment variable, I had put -I instead of 
> -L. Oops! I made that change, reran configure, make, and then tried 'make 
> check'. Here's the result:
> 
> is6[root]:/opt/netcdf/4.2/intel/11.1.064/src # make check
> Making check in f90
> make[1]: Entering directory `/opt/netcdf/4.2/intel/11.1.064/src/f90'
> make  check-am
> make[2]: Entering directory `/opt/netcdf/4.2/intel/11.1.064/src/f90'
> make[2]: Nothing to be done for `check-am'.
> make[2]: Leaving directory `/opt/netcdf/4.2/intel/11.1.064/src/f90'
> make[1]: Leaving directory `/opt/netcdf/4.2/intel/11.1.064/src/f90'
> Making check in fortran
> make[1]: Entering directory `/opt/netcdf/4.2/intel/11.1.064/src/fortran'
> make  check-am
> make[2]: Entering directory `/opt/netcdf/4.2/intel/11.1.064/src/fortran'
> make[2]: Nothing to be done for `check-am'.
> make[2]: Leaving directory `/opt/netcdf/4.2/intel/11.1.064/src/fortran'
> make[1]: Leaving directory `/opt/netcdf/4.2/intel/11.1.064/src/fortran'
> Making check in nf_test
> make[1]: Entering directory `/opt/netcdf/4.2/intel/11.1.064/src/nf_test'
> make  nf_test          tst_f90
> make[2]: Entering directory `/opt/netcdf/4.2/intel/11.1.064/src/nf_test'
> ifort -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include -I../fortran  -I../f90 -g -c -o 
> test_get.o test_get.F
> ifort -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include -I../fortran  -I../f90 -g -c -o 
> test_put.o test_put.F
> ifort -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include -I../fortran  -I../f90 -g -c -o 
> nf_error.o nf_error.F
> ifort -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include -I../fortran  -I../f90 -g -c -o nf_test.o 
> nf_test.F
> ifort -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include -I../fortran  -I../f90 -g -c -o 
> test_read.o test_read.F
> ifort -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include -I../fortran  -I../f90 -g -c -o 
> test_write.o test_write.F
> ifort -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include -I../fortran  -I../f90 -g -c -o util.o 
> util.F
> depbase=`echo fortlib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
> /usr/bin/gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran   
> -I/opt/netcdf/4.2/gnu/4.1.2/include  -g -O1 -fPIC  -MT fortlib.o -MD -MP -MF 
> $depbase.Tpo -c -o fortlib.o fortlib.c &&\
> mv -f $depbase.Tpo $depbase.Po
> /bin/sh ../libtool --tag=F77   --mode=link ifort -I../fortran  -I../f90 -g  
> -L/opt/netcdf/4.2/gnu/4.1.2/lib -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
> libtool: link: ifort -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  
> -L/opt/netcdf/4.2/gnu/4.1.2/lib ../fortran/.libs/libnetcdff.so -Wl,-rpath 
> -Wl,/opt/netcdf/4.2/intel/11.1.064/lib
> /opt/intel/compiler/11.1.064/lib/intel64/libimf.so: warning: warning: 
> feupdateenv is not implemented and will always fail
> ../fortran/.libs/libnetcdff.so: undefined reference to `nc_put_vara_short'
> ../fortran/.libs/libnetcdff.so: undefined reference to `nc_get_vara_short'

It looks like ifort is not finding the C library in the 
/opt/netcdf/4.2/intel/11.1.064/lib/.
Is there a netCDF-4.2 C library installed there, or did it get deleted when you 
started over?

If it's there, I'm not sure what's going on ...

--Russ

> ../fortran/.libs/libnetcdff.so: undefined reference to `ncattdel'
> ../fortran/.libs/libnetcdff.so: undefined reference to `nc_get_att_float'
> <lots of undefined references snipped>
> ../fortran/.libs/libnetcdff.so: undefined reference to `nc_inq_var'
> ../fortran/.libs/libnetcdff.so: undefined reference to `nc_get_var_int'
> ../fortran/.libs/libnetcdff.so: undefined reference to `nc__create_mp'
> make[2]: *** [nf_test] Error 1
> make[2]: Leaving directory `/opt/netcdf/4.2/intel/11.1.064/src/nf_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/opt/netcdf/4.2/intel/11.1.064/src/nf_test'
> make: *** [check-recursive] Error 1
> 
> I can't even get to the point where I'm testing for v2 and v4 APIs!


> On May 16, 2012, at 11:37 AM, Unidata netCDF Support wrote:
> 
> > Hi Jennifer,
> >
> >> I have successfully built the C version of netcdf-4.2 with lots of
> >> important features enabled, here is the output from nc-config:
> >>
> >> # /opt/netcdf/4.2/gnu/4.1.2/bin/nc-config --all
> >>
> >> This netCDF 4.2 has been built with the following features:
> >> --cc        -> /usr/bin/gcc
> >> --cflags    ->  -I/opt/netcdf/4.2/gnu/4.1.2/include 
> >> -I/opt/hdf5/1.8.8/intel/11.1.064/include 
> >> -I/opt/hdf/4.2.6/intel/11.1.064/include -I/opt/szip/2.1/include
> >> --libs      -> -L/opt/netcdf/4.2/gnu/4.1.2/lib -lnetcdf
> >> --cxx       -> @CXX@
> >> --has-c++   -> @HAS_CXX@
> >> --fc        -> @FC@
> >> --fflags    -> @FFLAGS@ @MOD_FLAG@/opt/netcdf/4.2/gnu/4.1.2/include
> >> --flibs     -> -L/opt/netcdf/4.2/gnu/4.1.2/lib @NC_FLIBS@
> >> --has-f77   -> @HAS_F77@
> >> --has-f90   -> @HAS_F90@
> >> --has-dap   -> yes
> >> --has-nc2   -> yes
> >> --has-nc4   -> yes
> >> --has-hdf5  -> yes
> >> --has-hdf4  -> yes
> >> --has-pnetcdf-> no
> >> --has-szlib ->
> >> --prefix    -> /opt/netcdf/4.2/gnu/4.1.2
> >> --includedir-> /opt/netcdf/4.2/gnu/4.1.2/include
> >> --version   -> netCDF 4.2
> >>
> >> We use a module system to set paths and the right environment, here is
> >> the output from the 'env | grep netcdf' command:
> >>
> >> PATH=/opt/netcdf/4.2/gnu/4.1.2/bin:/opt/hdf/4.2.6/intel/11.1.064/bin:/opt/hdf5/1.8.8/intel/11.1.064/bin:/opt/intel/compiler/11.1.064/bin/intel64:/homes/jma/bin:/homes/jma/ncl-6.0.0/bin:/homes/colagds/bin:/usr/local/grads/2.0:/usr/local/grads:/usr/kerberos/bin:/usr/java/default/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:.
> >> PWD=/opt/netcdf/4.2/intel/11.1.064
> >> LD_LIBRARY_PATH=/opt/netcdf/4.2/gnu/4.1.2/lib:/opt/szip/2.1/gnu/4.1.2/lib:/opt/hdf/4.2.6/intel/11.1.064/lib:/opt/hdf5/1.8.8/intel/11.1.064/lib:/opt/intel/compiler/11.1.064/ipp/em64t/sharedlib:/opt/intel/compiler/11.1.064/mkl/lib/em64t:/opt/intel/compiler/11.1.064/tbb/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/compiler/11.1.064/lib/intel64:/opt/udunits/2.1.23/lib
> >> MANPATH=/opt/netcdf/4.2/gnu/4.1.2/share/man:/opt/intel/compiler/11.1.064/mkl/man:/opt/intel/compiler/11.1.064/man:/usr/java/default/man:
> >> LOADEDMODULES=intel/11.1.064:hdf5/1.8.8/intel/11.1.064:hdf/4.2.6/intel/11.1.064:szip/2.1/gnu/4.1.2:netcdf/4.2/gnu/4.1.2
> >> INCLUDE=/opt/netcdf/4.2/gnu/4.1.2/include:/opt/szip/2.1/gnu/4.1.2/include:/opt/hdf/4.2.6/intel/11.1.064/include:/opt/hdf5/1.8.8/intel/11.1.064/include:/opt/intel/compiler/11.1.064/ipp/em64t/include:/opt/intel/compiler/11.1.064/mkl/include
> >> INFOPATH=/opt/netcdf/4.2/gnu/4.1.2/share/info
> >> LIBRARY_PATH=/opt/netcdf/4.2/gnu/4.1.2/lib:/opt/szip/2.1/gnu/4.1.2/lib:/opt/hdf/4.2.6/intel/11.1.064/lib:/opt/hdf5/1.8.8/intel/11.1.064/lib:/opt/intel/compiler/11.1.064/ipp/em64t/lib:/opt/intel/compiler/11.1.064/mkl/lib/em64t:/opt/intel/compiler/11.1.064/tbb/intel64/cc4.1.0_libc2.4_kernel2.6.16.21/lib
> >> NETCDF=/opt/netcdf/4.2/gnu/4.1.2
> >> NETCDF_HOME=/opt/netcdf/4.2/gnu/4.1.2
> >> _LMFILES_=/opt/Modules/modulefiles/intel/11.1.064:/opt/Modules/modulefiles/hdf5/1.8.8/intel/11.1.064:/opt/Modules/modulefiles/hdf/4.2.6/intel/11.1.064:/opt/Modules/modulefiles/szip/2.1/gnu/4.1.2:/opt/Modules/modulefiles/netcdf/4.2/gnu/4.1.2
> >>
> >>
> >> Now I am trying to build the fortran version of 4.2. We have the intel
> >> fortran compiler, ifort, version 11.1.064. Before I begin I set three
> >> environment vars, then run ./configure with only the --prefix option:
> >>
> >> setenv FC ifort
> >> setenv CPPFLAGS -I/opt/netcdf/4.2/gnu/4.1.2/include
> >> setenv LDFLAGS -I/opt/netcdf/4.2/gnu/4.1.2/lib
> >> ./configure --prefix=/opt/netcdf/4.2/intel/11.1.064
> >>
> >> Configure and make all work fine, but nf-config says I don't have nc4
> >> support:
> >>
> >> is6[jma]:/opt/netcdf/4.2/intel/11.1.064/src # ../bin/nf-config --all
> >> This netCDF-Fortran 4.2 has been built with the following features:
> >> --cc        -> /usr/bin/gcc
> >> --cflags    ->  -I/opt/netcdf/4.2/intel/11.1.064/include 
> >> -I/opt/netcdf/4.2/gnu/4.1.2/include
> >> --libs      -> -L/opt/netcdf/4.2/intel/11.1.064/lib 
> >> -I/opt/netcdf/4.2/gnu/4.1.2/lib -lnetcdf
> >> --fc        -> ifort
> >> --fflags    -> -g -I/opt/netcdf/4.2/intel/11.1.064/include
> >> --flibs     -> -L/opt/netcdf/4.2/intel/11.1.064/lib -lnetcdff 
> >> -I/opt/netcdf/4.2/gnu/4.1.2/lib -lnetcdf
> >> --has-f90   -> yes
> >> --has-nc2   -> no
> >> --has-nc4   -> no
> >> --prefix    -> /opt/netcdf/4.2/intel/11.1.064
> >> --includedir-> /opt/netcdf/4.2/intel/11.1.064/include
> >> --version   -> netCDF-Fortran 4.2
> >>
> >> It doesn't say whether the fortran library is dap-enabled, but I need
> >> that too. The --enable-netcdf-4 option does not appear to be valid with
> >> the fortran version of the configure script. I am primarily a C
> >> programmer, not all that experienced in building fortran code. Can you
> >> see what I am doing wrong here? Let me know if you need any more
> >> information...
> >
> > These are symptoms of bugs in nc-config and nf-config, not calling each 
> > other
> > to determine what features are supported.  We need to get out a bug-fix 
> > release
> > for netcdf-fortran soon, because I think these bugs are fixed in the 
> > current snapshot.
> > Unfortunately, there's no bundled snapshot release of netcdf-fortran yet, 
> > only
> > an svn source tree. The issue for tracking is here:
> >
> >  https://www.unidata.ucar.edu/jira/browse/NCF-165
> >
> > I believe running "make check" for the Fortran release should verify that 
> > you actually
> > have support for version 2 interfaces and for the netCDF-4 APIs.  Let me 
> > know if your
> > "make check" for Fortran does not include these lines:
> >
> >  *** Testing netCDF v2 api for F77.
> >  *** SUCCESS!
> > PASS: tst_f77_v2
> >
> > *** Testing definition of netCDF-4 vars from Fortran 77.
> > *** SUCCESS!
> > PASS: ftst_vars
> >
> > *** Testing netCDF-4 vars from F77 with new types.
> > *** SUCCESS!
> > PASS: ftst_vars2
> >
> > *** Testing enum and opaque types.
> > *** SUCCESS!
> > PASS: ftst_vars3
> >
> > *** Testing VLEN types.
> > *** SUCCESS!
> > PASS: ftst_vars4
> >
> > *** Testing compound types.
> > *** SUCCESS!
> > PASS: ftst_vars5
> >
> > If you see all those, then that verifies "nf-config --all" is wrong
> > about the supported features.  Also, DAP access is supported in the
> > Fortran APIs as a consequence of support in the separate C library,
> > but I see it's not explicitly tested for when "make check" is run.
> >
> > The current versions of nc-config.in for the C release and nf-config.in
> > for the Fortran release are available here:
> >
> >  http://svn.unidata.ucar.edu/repos/netcdf/trunk/nc-config.in
> >  http://svn.unidata.ucar.edu/repos/netcdf-fortran/trunk/nf-config.in
> >
> > Unfortunately to fix nc-config and nf-config requires starting over by
> > copying the two files above into the top source directory of the respective
> > releases, rerunning configure, make check, make install for the C release,
> > then rerunning configure, make check, make install for the Fortran release.
> >
> > Please let us know if that doesn't fix the problems with nf-config returning
> > the wrong information, and thanks for reporting the bugs!
> >
> > --Russ
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: ASX-279014
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> 
> --
> Jennifer M. Adams
> IGES/COLA
> 4041 Powder Mill Road, Suite 302
> Calverton, MD 20705
> address@hidden
> 
> 
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: ASX-279014
Department: Support netCDF
Priority: Normal
Status: Closed