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[netCDF #ASX-279014]: Building netcdf-fortran-4.2 on 64-bit CentOS 5.6
- Subject: [netCDF #ASX-279014]: Building netcdf-fortran-4.2 on 64-bit CentOS 5.6
- Date: Fri, 18 May 2012 10:02:26 -0600
Jennifer,
You could try setting LD_LIBRARY_PATH with /opt/netcdf/4.2/intel/11.1.064/lib/
*before* /opt/netcdf/4.2/gnu/4.1.2/lib (or eliminate the latter from
LD_LIBRARY_PATH). Then run configure, though I don't know why that should be
necessary, given that you've set LDFLAGS -L/opt/netcdf/4.2/gnu/4.1.2/lib.
--Russ
> > 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
>
>
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