The reason is that the default now in the netcdf configure script is to compile
fortran into a separate library. There has been some discussion in the
nettcdf-group mail-lsit as to why this was desirable. The netcdff library is
the one that contains fortran. The comment to check nc-config when things
aren't working correctly is a good one.
-Roy
On Apr 3, 2011, at 3:35 PM, John Helly wrote:
> Hi.
>
> I'm posting this to both groups (ROMS, netcdf) since it really appears to be
> an integration issue that both development teams should be aware of. It
> didn't have to do with bytesex, just a missing library as the netcdf folks
> suggested.
>
> The solution to the problem is that, for reasons I don't understand, I had to
> add the -lnetcdff library as an argument. So, I created a local version of
> the Darwin-gfortran.mk file (and Linux-gfortran.mk for the other) and
> modified the line 52 as follows:
>
> before:
> LIBS := -L$(NETCDF_LIBDIR) -lnetcdf
>
> after:
> LIBS := -L$(NETCDF_LIBDIR) -lnetcdf -lnetcdff
>
> Then changed the $COMPILERS variable to point to the local copy. Now both
> builds (OSX, Centos) complete and run.
>
> 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
>
> On Apr 3, 2011, at 12:51 PM, John Helly wrote:
>
> Hi.
>
> I'm trying to build ROMS 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-4.1.2 --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 conflict (maybe
> with netcdf). Any insight what/how to fix this would be appreciated.
>
> < excerpt begins here>
> ...
> 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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> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
**********************
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097
e-mail: Roy.Mendelssohn@xxxxxxxx (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
