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20040131: Installation Problem of netCDF package

>From: address@hidden
>Organization: Buffalo
>Keywords: 200401311709.i0VH9NAl013525 netCDF f77 g77

Vikas,

>My name is Vikas Patel and I am currently doing research in which I am 
>required to use the netCDF package. But I am having some trouble with 
>it. I have a fortran program [sbbx2nc.f - attached], which converts 
>binary data file into netCDF file using g77 compiler. Now, the program 
>is compiled fine [command to compile: g77 -c -I/usr/include 
>sbbx2nc.f], but when I run the program [command to run: g77 -w -o 
>sbbx2nc sbbx2nc.o /usr/lib/libnetcdf.a], I get errors [e.g. 
>Undefined                       first referenced
> symbol                             in file
>nf_create__                         sbbx2nc.o]

In looking through the log files you attached, I see that you built
the netCDF library using the Sun compilers, but are trying to use the
g77 compiler to compile and link your module, sbbx2nc.f.  I suspect
that the entry points in libnetcdf.a have a single trailing underscore
while the code compiled with g77 expects to see two (i.e., nf_create__
versus nf_create_).

Note that the output in test.log shows that the Fortran test routine
builds and runs fine using the Sun Fortran compiler: it finds and uses
nf_create with no problems:

   ...
  
  Making `test' in directory /home/unmdue/vkpatel/netcdf-3.5.1-beta13/src/libsrc
  
   ...
  
  c89 -c -O   -DNDEBUG fortlib.c
  f77 -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 ../libsrc/libnetcdf.a  -lm 
  ./nf_test -c
  ./nf_test
  *** Testing nf_strerror ... 
  *** Testing nf_open ... 
  *** Testing nf_close ... 
  *** Testing nf_inq ... 
  *** Testing nf_inq_dimid ... 
  *** Testing nf_inq_dim ... 
  *** Testing nf_inq_dimlen ... 
  *** Testing nf_inq_dimname ... 
  *** Testing nf_inq_varid ... 
  *** Testing nf_inq_var ... 
  *** Testing nf_inq_natts ... 
  *** Testing nf_inq_ndims ... 
  *** Testing nf_inq_nvars ... 
  *** Testing nf_inq_unlimdim ... 
  *** Testing nf_inq_vardimid ... 
  *** Testing nf_inq_varname ... 
  *** Testing nf_inq_varnatts ... 
  *** Testing nf_inq_varndims ... 
  *** Testing nf_inq_vartype ... 
  *** Testing nf_get_var1_text ... 
  *** Testing nf_get_var1_int1 ... 
  *** Testing nf_get_var1_int2 ... 
  *** Testing nf_get_var1_int ... 
  *** Testing nf_get_var1_real ... 
  *** Testing nf_get_var1_double ... 
  *** Testing nf_get_var_text ... 
  *** Testing nf_get_var_int1 ... 
  *** Testing nf_get_var_int2 ... 
  *** Testing nf_get_var_int ... 
  *** Testing nf_get_var_real ... 
  *** Testing nf_get_var_double ... 
  *** Testing nf_get_vara_text ... 
  *** Testing nf_get_vara_int1 ... 
  *** Testing nf_get_vara_int2 ... 
  *** Testing nf_get_vara_int ... 
  *** Testing nf_get_vara_real ... 
  *** Testing nf_get_vara_double ... 
  *** Testing nf_get_vars_text ... 
  *** Testing nf_get_vars_int1 ... 
  *** Testing nf_get_vars_int2 ... 
  *** Testing nf_get_vars_int ... 
  *** Testing nf_get_vars_real ... 
  *** Testing nf_get_vars_double ... 
  *** Testing nf_get_varm_text ... 
  *** Testing nf_get_varm_int1 ... 
  *** Testing nf_get_varm_int2 ... 
  *** Testing nf_get_varm_int ... 
  *** Testing nf_get_varm_real ... 
  *** Testing nf_get_varm_double ... 
  *** Testing nf_get_att_text ... 
  *** Testing nf_get_att_int1 ... 
  *** Testing nf_get_att_int2 ... 
  *** Testing nf_get_att_int ... 
  *** Testing nf_get_att_real ... 
  *** Testing nf_get_att_double ... 
  *** Testing nf_inq_att ... 
  *** Testing nf_inq_attname ... 
  *** Testing nf_inq_attid ... 
  *** Testing nf_inq_attlen ... 
  *** Testing nf_inq_atttype ... 
  *** Testing nf_create ... 
  *** Testing nf_redef ... 
  *** Testing nf_enddef ... 
  *** Testing nf_sync ... 
  *** Testing nf_abort ... 
  *** Testing nf_def_dim ... 
  *** Testing nf_rename_dim ... 
  *** Testing nf_def_var ... 
  *** Testing nf_put_var1_text ... 
  *** Testing nf_put_var1_int1 ... 
  *** Testing nf_put_var1_int2 ... 
  *** Testing nf_put_var1_int ... 
  *** Testing nf_put_var1_real ... 
  *** Testing nf_put_var1_double ... 
  *** Testing nf_put_var_text ... 
  *** Testing nf_put_var_int1 ... 
  *** Testing nf_put_var_int2 ... 
  *** Testing nf_put_var_int ... 
  *** Testing nf_put_var_real ... 
  *** Testing nf_put_var_double ... 
  *** Testing nf_put_vara_text ... 
  *** Testing nf_put_vara_int1 ... 
  *** Testing nf_put_vara_int2 ... 
  *** Testing nf_put_vara_int ... 
  *** Testing nf_put_vara_real ... 
  *** Testing nf_put_vara_double ... 
  *** Testing nf_put_vars_text ... 
  *** Testing nf_put_vars_int1 ... 
  *** Testing nf_put_vars_int2 ... 
  *** Testing nf_put_vars_int ... 
  *** Testing nf_put_vars_real ... 
  *** Testing nf_put_vars_double ... 
  *** Testing nf_put_varm_text ... 
  *** Testing nf_put_varm_int1 ... 
  *** Testing nf_put_varm_int2 ... 
  *** Testing nf_put_varm_int ... 
  *** Testing nf_put_varm_real ... 
  *** Testing nf_put_varm_double ... 
  *** Testing nf_rename_var ... 
  *** Testing nf_put_att_text ... 
  *** Testing nf_put_att_int1 ... 
  *** Testing nf_put_att_int2 ... 
  *** Testing nf_put_att_int ... 
  *** Testing nf_put_att_real ... 
  *** Testing nf_put_att_double ... 
  *** Testing nf_copy_att ... 
  *** Testing nf_rename_att ... 
  *** Testing nf_del_att ... 
  *** Testing nf_set_fill ... 
   Total number of failures:   0
  *** Success ***
  
  Returning to directory /home/unmdue/vkpatel/netcdf-3.5.1-beta13/src
  
  
  Making `test' in directory 
/home/unmdue/vkpatel/netcdf-3.5.1-beta13/src/fortran
  
  ar cru ../libsrc/libnetcdf.a fort-attio.o      fort-control.o  fort-dim.o     
 fort-genatt.o   fort-geninq.o   fort-genvar.o   fort-lib.o      fort-misc.o    
 fort-v2compat.o         fort-vario.o    fort-var1io.o   fort-varaio.o   
fort-varmio.o   fort-varsio.o
  ranlib ../libsrc/libnetcdf.a
  f77 -o ftest   ftest.o ../libsrc/libnetcdf.a  
  ./ftest
  *** Testing nccre ...
  *** Testing ncddef ...
  *** Testing ncvdef ...
  *** Testing ncapt, ncaptc ...
  *** Testing ncclos ...
  *** Testing ncvpt1 ...
  *** Testing ncvgt1 ...
  *** Testing ncvpt ...
  *** Testing ncopn, ncinq, ncdinq, ncvinq, ncanam, ncainq ...
  *** Testing ncvgt, ncvgtc ...
  *** Testing ncagt, ncagtc ...
  *** Testing ncredf, ncdren, ncvren, ncaren, ncendf ...
  *** Testing ncacpy ...
  *** Testing ncadel ...
  *** Testing fill values ...
  
  Returning to directory /home/unmdue/vkpatel/netcdf-3.5.1-beta13/src


There are two simple solutions to the situation you are in now:

1) compile your module using the Sun f77 compiler

2) rebuild libnetcdf.a using g77 as the Fortran compiler.  Note that
   this will require that you specify the -Df2cFortran flag in
   the Unix environment variable CPPFLAGS _before_ you create
   the new netCDF library:

   make distclean
   <define CPPFLAGS correctly>
   ./configure
   make
   
Option 1) is probably the first thing to try since you already have
a libnetcdf.a built using the Sun f77 compiler.

>I do not know if there is a problem in the program or in the 
>installation of the netCDF package.

The problem lies in your mixing use of Sun Fortran and g77.

>The program works fine on Mac OS 
>X, but it is not available to me. So, it may be the case where the 
>netCDF pacakge is not compatible with my system.

The netCDF runs with no problems on Sun systems.

>Following is the list 
>of information, which you require to find out if there is any 
>installation problem.
>
>A. SunOS yeager.cse.Buffalo.EDU 5.9 Generic_112233-08 sun4u sparc 
>SUNW, Ultra-4
>
>B. 3.5.1-beta13
>
>C. macros.make - attached
>
>D. C compiler: /opt/SUNWspro/bin/c89
>   Fortran compilers: /opt/SUNWspro/bin/f77
>                      /opt/SUNWspro/bin/f90
>                      /oldutil/bin/g77
>   C++ compiler: /opt/SUNWspro/bin/CC
>
>E. configure.log - attached
>F. config.log - attached
>G. make.log - attached
>H. test.log - attached
>
>Please let me know if I have installation problem or any other problem 
>regarding the netCDF package and the solution for it.
>
>Thank you for your help.
>
>Sincerely,
>Vikas Patel.
>---MOQ10755689631b9c65ba382ceaef8f364e0a2d57b6a6
>Content-Type: text/plain; name="macros.make"
>Content-Transfer-Encoding: 8bit
>Content-Disposition: attachment; filename="macros.make"
>
># $Id: macros.make.in,v 1.33 2001/07/11 16:30:33 steve Exp $
>
># The purpose of this file is to contain common make(1) macros.
># It should be processed by every execution of that utility.
>
>
># POSIX shell.  Shouldn't be necessary -- but is under IRIX 5.3.
>SHELL          = /bin/sh
>
>
># Installation Directories:
>SRCDIR         = /home/unmdue/vkpatel/netcdf-3.5.1-beta13/src
>prefix         = ..
>exec_prefix    = $(prefix)
>INCDIR         = $(exec_prefix)/include
>LIBDIR         = $(exec_prefix)/lib
>BINDIR         = $(exec_prefix)/bin
>MANDIR         = $(prefix)/man
>
>
># Preprocessing:
>M4             = m4
>M4FLAGS                = -B10000
>CPP            = c89 -E
>CPPFLAGS       = $(INCLUDES) $(DEFINES) -DNDEBUG
>FPP            = 
>FPPFLAGS       = 
>CXXCPPFLAGS    = $(CPPFLAGS)
>
>
># Compilation:
>CC             = c89
>CXX            = CC
>FC             = f77
>F90            = f90
>CFLAGS         = -O
>CXXFLAGS       = 
>FFLAGS         = 
>F90FLAGS       = 
>CC_MAKEDEPEND  = cc -xM
>COMPILE.c      = $(CC) -c $(CFLAGS) $(CPPFLAGS)
>COMPILE.cxx    = $(CXX) -c $(CXXFLAGS) $(CXXCPPFLAGS)
>COMPILE.f      = $(FC) -c $(FFLAGS)
>COMPILE.F90    = $(F90) -c $(F90FLAGS)
># The following command isn't available on some systems; therefore, the
># `.F.o' rule is relatively complicated.
>COMPILE.F      = $(COMPILE.f) $(FPPFLAGS)
>
>
># Linking:
>MATHLIB                = -lm
>FLIBS          = 
>F90LIBS                = 
>LIBS           = 
>F90LDFLAGS     = $(LDFLAGS)
>LINK.c         = $(CC) -o $@ $(CFLAGS) $(LDFLAGS)
>LINK.cxx       = $(CXX) -o $@ $(CXXFLAGS) $(LDFLAGS)
>LINK.F         = $(FC) -o $@ $(FFLAGS) $(FLDFLAGS)
>LINK.f         = $(FC) -o $@ $(FFLAGS) $(FLDFLAGS)
>LINK.F90       = $(F90) -o $@ $(F90FLAGS) $(F90LDFLAGS)
>
>
># Manual pages:
>WHATIS         = windex
># The following macro should be empty on systems that don't
># allow users to create their own manual-page indexes.
>MAKEWHATIS_CMD = catman -w -M $(MANDIR)
>
>
># Misc. Utilities:
>AR             = ar
>ARFLAGS                = cru
>RANLIB         = ranlib
>TARFLAGS       = -chf
>
>
># Dummy macros: used only as placeholders to silence GNU make.  They are
># redefined, as necessary, in subdirectory makefiles.
>HEADER         = dummy_header
>HEADER1                = dummy_header1
>HEADER2                = dummy_header2
>HEADER3                = dummy_header3
>LIBRARY                = dummy_library.a
>MANUAL         = dummy_manual
>PROGRAM                = dummy_program
>
>
># Distribution macros:
>FTPDIR         = /home/ftp/pub/$(PACKAGE)
>FTPBINDIR      = /home/ftp/pub/binary/dummy_system
>VERSION                = dummy_version

Please let us know if the options I suggested above do not get you
going.

Tom Yoksas
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