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[netcdfgroup] ROMS/netcdf-4 integration problem...more insight?

  • To: John Helly <hellyj@xxxxxxxx>
  • Subject: [netcdfgroup] ROMS/netcdf-4 integration problem...more insight?
  • From: John Helly <hellyj@xxxxxxxx>
  • Date: Sun, 3 Apr 2011 12:38:35 -0700
Hi. Here's the text of the message I just sent to the ROMS forum.  I think I 
might not have built netcdf in 64-bit mode.  Can anyone comment on this?

I'm trying to build ROMS (an ocean model) for the first time on OSX 10.6.7 and 
appear to be having problems with netcdf-4. I rebuilt netcdf-4.1.3 using 
hdf-1.8.6 (with\
 zlib-1.2.5) and everything appeared to go well with that using this configure 
command:

./configure --prefix=/usr/local/netcdf-4.1.3 --enable-netcdf-4 --enable-f90  
--with-hdf5=/usr/local/hdf5-1.8.6

This is then symbolically linked to /usr/local/netcdf as reflected below.

However, when I try to build ROMS against that this is the relevant excerpt of 
what happens.  Can anyone suggest whant this might be due to?  I have a sense 
from the highlighted text that there is a 32/64-bit problem maybe with netcdf.

...
ar -r /Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_arrays.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_average.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_bbl.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_biology.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_boundary.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_clima.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_coupler.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_coupling.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_diags.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_eclight.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_eoscoef.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_floats.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_forces.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_fourdvar.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_grid.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_iounits.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_kinds.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_mixing.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_ncparam.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_nesting.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_netcdf.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_obs.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_ocean.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_parallel.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_param.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_scalars.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_sedbed.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_sediment.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_sources.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_stepping.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_storage.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_strings.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/mod_tides.o
ar: creating archive /Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_bbl.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_biology.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_boundary.o) has 
no symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_clima.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_coupler.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_eclight.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_eoscoef.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_floats.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_fourdvar.o) has 
no symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_kinds.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_nesting.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_obs.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_sedbed.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_sediment.o) has 
no symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_sources.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_storage.o) has no 
symbols
/usr/bin/ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_tides.o) has no 
symbols
ranlib /Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_bbl.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_biology.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_boundary.o) has 
no symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_clima.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_coupler.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_eclight.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_eoscoef.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_floats.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_fourdvar.o) has 
no symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_kinds.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_nesting.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_obs.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_sedbed.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_sediment.o) has 
no symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_sources.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_storage.o) has no 
symbols
ranlib: file: 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a(mod_tides.o) has no 
symbols
/usr/bin/cpp -P -traditional -DDARWIN -DI386 -DGFORTRAN 
-D'ROOT_DIR="/Users/hellyj/src/ROMS/trunk"' -DUPWELLING 
-D'HEADER="upwelling.h"' 
-D'ROMS_HEADER="/Users/hellyj/src/ROMS/Projects/Upwelling/upwelling.h"' 
-DNestedGrids=1 -D'ANALYTICAL_DIR="/Users/hellyj/src/ROMS/Projects/Upwelling"' 
-D'MY_ANALYTICAL="on"' -D'SVN_REV="544M"' -IROMS/Include 
-I/Users/hellyj/src/ROMS/Projects/Upwelling -IROMS/Nonlinear 
-IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility 
-IROMS/Drivers -IROMS/Functionals -I/Users/hellyj/src/ROMS/Projects/Upwelling 
-IMaster -ICompilers -D'HEADER_DIR="/Users/hellyj/src/ROMS/Projects/Upwelling"' 
 Master/esmf_roms.F > 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/esmf_roms.f90
ROMS/Bin/cpp_clean /Users/hellyj/src/ROMS/Projects/Upwelling/Build/esmf_roms.f90
cd /Users/hellyj/src/ROMS/Projects/Upwelling/Build; /usr/local/bin/gfortran -c 
-frepack-arrays -O3 -ffast-math esmf_roms.f90
/usr/bin/cpp -P -traditional -DDARWIN -DI386 -DGFORTRAN 
-D'ROOT_DIR="/Users/hellyj/src/ROMS/trunk"' -DUPWELLING 
-D'HEADER="upwelling.h"' 
-D'ROMS_HEADER="/Users/hellyj/src/ROMS/Projects/Upwelling/upwelling.h"' 
-DNestedGrids=1 -D'ANALYTICAL_DIR="/Users/hellyj/src/ROMS/Projects/Upwelling"' 
-D'MY_ANALYTICAL="on"' -D'SVN_REV="544M"' -IROMS/Include 
-I/Users/hellyj/src/ROMS/Projects/Upwelling -IROMS/Nonlinear 
-IROMS/Nonlinear/Biology -IROMS/Nonlinear/Sediment -IROMS/Utility 
-IROMS/Drivers -IROMS/Functionals -I/Users/hellyj/src/ROMS/Projects/Upwelling 
-IMaster -ICompilers -D'HEADER_DIR="/Users/hellyj/src/ROMS/Projects/Upwelling"' 
 Master/master.F > /Users/hellyj/src/ROMS/Projects/Upwelling/Build/master.f90
ROMS/Bin/cpp_clean /Users/hellyj/src/ROMS/Projects/Upwelling/Build/master.f90
cd /Users/hellyj/src/ROMS/Projects/Upwelling/Build; /usr/local/bin/gfortran -c 
-frepack-arrays -O3 -ffast-math master.f90
/usr/local/bin/gfortran -frepack-arrays -O3 -ffast-math  
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/esmf_roms.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/master.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/ocean_control.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/ocean_coupler.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/propagator.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/roms_export.o 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/roms_import.o -o 
/Users/hellyj/src/ROMS/Projects/Upwelling/oceanS  
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libNLM.a 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libNLM_bio.a 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libNLM_sed.a 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libANA.a 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libUTIL.a 
/Users/hellyj/src/ROMS/Projects/Upwelling/Build/libMODS.a 
-L/usr/local/netcdf/lib -lnetcdf -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -lz 
-lcurl
Undefined symbols for architecture x86_64:
  "___netcdf_MOD_nf90_strerror", referenced from:
      _close_io_ in libUTIL.a(close_io.o)
  "___netcdf_MOD_nf90_def_dim", referenced from:
      _def_dim_ in libUTIL.a(def_dim.o)
  "___netcdf_MOD_nf90_put_att_text", referenced from:
      _def_info_ in libUTIL.a(def_info.o)
      ___def_var_mod_MOD_def_var in libUTIL.a(def_var.o)
  "___netcdf_MOD_nf90_def_var_manydims", referenced from:
      ___def_var_mod_MOD_def_var in libUTIL.a(def_var.o)
  "___netcdf_MOD_nf90_put_att_one_eightbytereal", referenced from:
      ___def_var_mod_MOD_def_var in libUTIL.a(def_var.o)
  "___netcdf_MOD_nf90_put_att_eightbytereal", referenced from:
      ___def_var_mod_MOD_def_var in libUTIL.a(def_var.o)
  "___netcdf_MOD_nf90_put_att_one_fourbytereal", referenced from:
      ___def_var_mod_MOD_def_var in libUTIL.a(def_var.o)


Thanks.

Cheers.
--------------
John Helly, University of California, San Diego / San Diego Supercomputer 
Center / Scripps Institution of Oceanography / 760 840 8660 mobile / 
stonesteps7 (Skype) / stonesteps7 (iChat) / http://www.sdsc.edu/~hellyj
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