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[netCDF #YWH-955421]: Error during "make check," NetCDF 4.2 Fortran libs, Janus supercomputer



Hi Dan,

> Per request by NCAR, I've been attempting to build NetCDF 4.2 on the Janus 
> supercomputer (RHEL 5.6, kernel 2.6.18-238.12.1).  I had no problems building 
> the NetCDF 4.2 C libraries, but I can't get the Fortran libraries to install. 
>  Here are the options I've used to build netcdf-fortran-4.2:
> 
> CC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpicc
> FC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpif90
> F90=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpif90
> F77=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpif90
> CXX=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpic++
> MPICXX=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpic++
> MPICC=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpicc
> MPIF77=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpif77
> MPIF90=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin/mpif90
> CPPFLAGS="-DgFortran 
> -I/curc/tools/x_86_64/rh5/netcdf/4.2/hdf5/1.8.8/openmpi/1.4.5/intel/12.1.4/include"
> LDFLAGS=-L/curc/tools/x_86_64/rh5/netcdf/4.2/hdf5/1.8.8/openmpi/1.4.5/intel/12.1.4/lib
> LD_LIBRARY_PATH=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/lib:/curc/tools/nonfree/redhat_5_x86_64/intel-12.1.4/composer_xe_2011_sp1.10.319/debugger/lib/intel64:/curc/tools/nonfree/redhat_5_x86_64/intel-12.1.4/composer_xe_2011_sp1.10.319/mkl/lib/intel64:/curc/tools/nonfree/redhat_5_x86_64/intel-12.1.4/composer_xe_2011_sp1.10.319/compiler/lib/intel64:/curc/tools/free/redhat_5_x86_64/sun_jdk-1.6.0_23-x86_64/lib:/curc/tools/free/redhat_5_x86_64/torque-2.5.8/lib
> FFLAGS=-I/curc/tools/x_86_64/rh5/netcdf/4.2/hdf5/1.8.8/openmpi/1.4.5/intel/12.1.4/include
> 
> ./configure 
> --prefix=/curc/tools/x_86_64/rh5/netcdf/4.2/intel/netcdf-4.2_intel-12.1.4_hdf5-1.8.8_openmpi-1.4.5_fortran
>  -disable-shared
> 
> I can configure and make the Fortran libraries successfully, but the 
> following error is thrown during "make check:"
> 
> [snip]
> 
> /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:115: undefined reference 
> to `nc_get_vars_int'
> ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function `nf_put_vars_real_':
> /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:130: undefined reference 
> to `nc_put_vars_float'
> ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function `nf_get_vars_real_':
> /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:142: undefined reference 
> to `nc_get_vars_float'
> ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function 
> `nf_put_vars_double_':
> /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:150: undefined reference 
> to `nc_put_vars_double'
> ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function 
> `nf_get_vars_double_':
> /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:157: undefined reference 
> to `nc_get_vars_double'
> ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function `nf_put_vars_':
> /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:160: undefined reference 
> to `nc_put_vars'
> ../fortran/.libs/libnetcdff.a(fort-varsio.o): In function `nf_get_vars_':
> /tmp/netcdf/netcdf-fortran-4.2/fortran/fort-varsio.c:163: undefined reference 
> to `nc_get_vars'
> make[2]: *** [nf_test] Error 1
> make[2]: Leaving directory `/tmp/netcdf/netcdf-fortran-4.2/nf_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/tmp/netcdf/netcdf-fortran-4.2/nf_test'
> make: *** [check-recursive] Error 1
> 
> What is causing this issue?

I suspect it may be that the fortran/cfortran.h header file, used to handle
differences in how C functions are called from Fortran for different compilers, 
is failing to provide the right macros for the mpif90 compiler you are using.

One thing you could try is setting your PATH to include the directory in which
the compilers are found, and just setting the environment variables that 
configure
is using to the names of the executables, e.g.

  PATH=/curc/tools/free/redhat_5_x86_64/openmpi-1.4.5_intel-12.1.4/bin:$PATH
  FC=mpif90
  F90=mpif90
  F77=mpif90
 ...

to see if that gets the right definitions of the cfortran.h macros.

Alternatively, you could try the new beta release of the separate Fortran 
package,
that makes use of the Fortran-2003 C-interoperability features, assuming your
mpif90 compiler supports this.  That completely avoids the old cfortran.h 
macros.

Just get this version of the netCDF-Fortran package:

  ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4-beta1.tar.gz

also available as the beta release from the downloads page:

  http://www.unidata.ucar.edu/downloads/netcdf/netcdf-fortran/index.jsp

In building it, just tell it where to find the installed netCDF-3 libraries,
with CPPFLAGS and LDFLAGS, as you did for the netcdf-fortran-4.2 package.

Please let us know if that works.

--Russ


Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: YWH-955421
Department: Support netCDF
Priority: Normal
Status: Closed


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