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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 > > > _______________________________________________ > netcdfgroup mailing list > 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"
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