[Wrf-users] error compiling (icc & ifort) WRFV3.3 with NetCDF V4.12

[Andrew Penny]

We are having problems getting the latest version of WRF compiled with the latest version of NetCDF.

Here are the compilation options we are using for NetCDF 4.1.2:

--------------------------------------------------- 
export CC=mpicc
export CXX=mpicxx

export FC=mpif90
export F77=mpif77
export F90=mpif90

export CPP='icpc -E'
export CXXCPP='icpc -E'

export CFLAGS='-O3 -xSSSE3 -ip -no-prec-div -m64 -fPIC'
export CXXFLAGS='-O3 -xSSSE3 -ip -no-prec-div -m64 -fPIC'
export CPPFLAGS='-DpgiFortran -I/opt/hdf5/intel/include -I/opt/hdf4/intel/include -I/opt/udunits/intel/include -I/usr/include -I/opt/szip/intel/include -I/usr/mpi/intel/mvapich2-1.6/include'

export FFLAGS='-DpgiFortran -O3 -xSSSE3 -ip -no-prec-div -m64 -fPIC -assume nounderscore'
export FCFLAGS='-DpgiFortran -O3 -xSSSE3 -ip -no-prec-div -m64 -fPIC -assume nounderscore'
export FCFLAGS_f90='-DpgiFortran -O3 -xSSSE3 -ip -no-prec-div -m64 -fPIC -assume nounderscore'
export F90FLAGS='-DpgiFortran -O3 -xSSSE3 -ip -no-prec-div -m64 -fPIC -assume nounderscore'
export LDFLAGS='-DpgiFortran -O3 -xSSSE3 -ip -no-prec-div -m64 -fPIC'

export LIBS="-L/opt/hdf5/intel/lib -lhdf5_fortran -lhdf5_hl -lhdf5 -L/opt/hdf4/intel/lib -ldf -L/opt/udunits/intel/lib -ludunits2 -L/usr/lib64 -lz -lm -L/opt/szip/intel/lib -lsz"

./configure --disable-shared --enable-large-file-tests --enable-fortran --enable-f90 --enable-f77 --disable-netcdf-4 --enable-netcdf4 --enable-parallel --enable-cxx-4 --enable-cxx --enable-hdf4 --enable-utilities --with-libcf --with-zlib=/usr --with-szlib=/opt/szip/intel --with-hdf4=/opt/hdf4/intel --with-hdf5=/opt/hdf5/intel --with-curl-config=/usr/bin --prefix=/path/to/netcdf
---------------------------------------------------

The mpif77/mpicc/mpif90 binaries are compiled using the Intel C++/FORTRAN compilers.


Here is the "LIB_EXTERNAL" variable setting in the 'configure.wrf' file for compiling WRF version 3.3:

---------------------------------------------------
 LIB_EXTERNAL    = \
                      -L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf -L/path/to/netcdf/lib -lnetcdff -lnetcdf   -L$(WRF_SRC_ROOT_DIR)/external/io_grib2 -lio_grib2 -L/opt/jasper/intel/lib -ljasper -L/opt/hdf4/intel/lib -ldf -lmfhdf -L/opt/hdf5/intel/lib -lhdf5_fortran -lhdf5_hl -lhdf5 -L/opt/g2clib/intel/lib -lgrib2c -L/usr/lib64 -lcurl
---------------------------------------------------

Here are the error messages that show up during the './compile em_real' process:

---------------------------------------------------
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_text_':
fort-attio.c:(.text+0x7a): undefined reference to `nc_put_att_text'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_text_':
fort-attio.c:(.text+0x18d): undefined reference to `nc_get_att_text'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_int1_':
fort-attio.c:(.text+0x2af): undefined reference to `nc_put_att_schar'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_int1_':
fort-attio.c:(.text+0x3bd): undefined reference to `nc_get_att_schar'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_int2_':
fort-attio.c:(.text+0x4df): undefined reference to `nc_put_att_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_int2_':
fort-attio.c:(.text+0x5ed): undefined reference to `nc_get_att_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_int_':
fort-attio.c:(.text+0x70f): undefined reference to `nc_put_att_int'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_int_':
fort-attio.c:(.text+0x81d): undefined reference to `nc_get_att_int'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_real_':
fort-attio.c:(.text+0x93f): undefined reference to `nc_put_att_float'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_real_':
fort-attio.c:(.text+0xa4d): undefined reference to `nc_get_att_float'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_double_':
fort-attio.c:(.text+0xb6f): undefined reference to `nc_put_att_double'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_double_':
fort-attio.c:(.text+0xc7d): undefined reference to `nc_get_att_double'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_create_':
fort-control.c:(.text+0x64): undefined reference to `nc_create'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf__create_':
fort-control.c:(.text+0x1a0): undefined reference to `nc__create'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_open_':
fort-control.c:(.text+0x2b4): undefined reference to `nc_open'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf__open_':
fort-control.c:(.text+0x3d8): undefined reference to `nc__open'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_set_fill_':
fort-control.c:(.text+0x491): undefined reference to `nc_set_fill'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_redef_':
fort-control.c:(.text+0x4a4): undefined reference to `nc_redef'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_enddef_':
fort-control.c:(.text+0x4b4): undefined reference to `nc_enddef'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf__enddef_':
fort-control.c:(.text+0x4d0): undefined reference to `nc__enddef'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_sync_':
fort-control.c:(.text+0x4e4): undefined reference to `nc_sync'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_close_':
fort-control.c:(.text+0x4f4): undefined reference to `nc_close'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_delete_':
fort-control.c:(.text+0x55a): undefined reference to `nc_delete'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf__create_mp_':
fort-control.c:(.text+0x68a): undefined reference to `nc__create_mp'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf__open_mp_':
fort-control.c:(.text+0x7d0): undefined reference to `nc__open_mp'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_delete_mp_':
fort-control.c:(.text+0x8e3): undefined reference to `nc_delete_mp'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_set_base_pe_':
fort-control.c:(.text+0x986): undefined reference to `nc_set_base_pe'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_inq_base_pe_':
fort-control.c:(.text+0x99f): undefined reference to `nc_inq_base_pe'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_abort_':
fort-control.c:(.text+0x9b4): undefined reference to `nc_abort'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-control.o): In function `nf_set_default_format_':
fort-control.c:(.text+0x9cf): undefined reference to `nc_set_default_format'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-dim.o): In function `nf_def_dim_':
fort-dim.c:(.text+0x78): undefined reference to `nc_def_dim'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-dim.o): In function `nf_inq_dimid_':
fort-dim.c:(.text+0x19b): undefined reference to `nc_inq_dimid'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-dim.o): In function `nf_inq_dim_':
fort-dim.c:(.text+0x2e5): undefined reference to `nc_inq_dim'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-dim.o): In function `nf_inq_dimname_':
fort-dim.c:(.text+0x4bb): undefined reference to `nc_inq_dimname'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-dim.o): In function `nf_inq_dimlen_':
fort-dim.c:(.text+0x614): undefined reference to `nc_inq_dimlen'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-dim.o): In function `nf_rename_dim_':
fort-dim.c:(.text+0x695): undefined reference to `nc_rename_dim'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_inq_att_':
fort-genatt.c:(.text+0x87): undefined reference to `nc_inq_att'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_inq_attid_':
fort-genatt.c:(.text+0x19e): undefined reference to `nc_inq_attid'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_inq_atttype_':
fort-genatt.c:(.text+0x2ae): undefined reference to `nc_inq_atttype'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_inq_attlen_':
fort-genatt.c:(.text+0x3be): undefined reference to `nc_inq_attlen'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_inq_attname_':
fort-genatt.c:(.text+0x4f7): undefined reference to `nc_inq_attname'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_copy_att_':
fort-genatt.c:(.text+0x6c8): undefined reference to `nc_copy_att'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_rename_att_':
fort-genatt.c:(.text+0x842): undefined reference to `nc_rename_att'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genatt.o): In function `nf_del_att_':
fort-genatt.c:(.text+0x9d5): undefined reference to `nc_del_att'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-geninq.o): In function `nf_inq_':
fort-geninq.c:(.text+0x34): undefined reference to `nc_inq'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-geninq.o): In function `nf_inq_ndims_':
fort-geninq.c:(.text+0x8f): undefined reference to `nc_inq_ndims'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-geninq.o): In function `nf_inq_nvars_':
fort-geninq.c:(.text+0xaf): undefined reference to `nc_inq_nvars'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-geninq.o): In function `nf_inq_natts_':
fort-geninq.c:(.text+0xcf): undefined reference to `nc_inq_natts'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-geninq.o): In function `nf_inq_unlimdim_':
fort-geninq.c:(.text+0xf7): undefined reference to `nc_inq_unlimdim'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-geninq.o): In function `nf_inq_format_':
fort-geninq.c:(.text+0x12f): undefined reference to `nc_inq_format'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_def_var_':
fort-genvar.c:(.text+0xa0): undefined reference to `nc_def_var'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_inq_var_':
fort-genvar.c:(.text+0x217): undefined reference to `nc_inq_var'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_inq_varid_':
fort-genvar.c:(.text+0x424): undefined reference to `nc_inq_varid'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_inq_varname_':
fort-genvar.c:(.text+0x55b): undefined reference to `nc_inq_varname'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_inq_vartype_':
fort-genvar.c:(.text+0x6b4): undefined reference to `nc_inq_vartype'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_inq_varndims_':
fort-genvar.c:(.text+0x6e4): undefined reference to `nc_inq_varndims'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_inq_vardimid_':
fort-genvar.c:(.text+0x724): undefined reference to `nc_inq_vardimid'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_inq_varnatts_':
fort-genvar.c:(.text+0x764): undefined reference to `nc_inq_varnatts'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_rename_var_':
fort-genvar.c:(.text+0x7e5): undefined reference to `nc_rename_var'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-genvar.o): In function `nf_copy_var_':
fort-genvar.c:(.text+0x88a): undefined reference to `nc_copy_var'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `c2f_dimids':
fort-lib.c:(.text+0x10): undefined reference to `nc_inq_varndims'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `c2f_chunksizes':
fort-lib.c:(.text+0x130): undefined reference to `nc_inq_varndims'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `f2c_chunksizes':
fort-lib.c:(.text+0x1d0): undefined reference to `nc_inq_varndims'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `f2c_coords':
fort-lib.c:(.text+0x270): undefined reference to `nc_inq_varndims'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `f2c_counts':
fort-lib.c:(.text+0x320): undefined reference to `nc_inq_varndims'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o):fort-lib.c:(.text+0x3d0): more undefined references to `nc_inq_varndims' follow
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `nc_inq_varids_f':
fort-lib.c:(.text+0x47c): undefined reference to `nc_inq_varids'
fort-lib.c:(.text+0x4b0): undefined reference to `nc_inq_varids'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `nc_inq_dimids_f':
fort-lib.c:(.text+0x5f6): undefined reference to `nc_inq_dimids'
fort-lib.c:(.text+0x631): undefined reference to `nc_inq_dimids'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `nc_insert_array_compound_f':
fort-lib.c:(.text+0x81f): undefined reference to `nc_insert_array_compound'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-lib.o): In function `nc_inq_compound_field_f':
fort-lib.c:(.text+0x8ac): undefined reference to `nc_inq_compound_field'
fort-lib.c:(.text+0x8e0): undefined reference to `nc_inq_compound_field'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-misc.o): In function `nf_inq_libvers_':
fort-misc.c:(.text+0xa): undefined reference to `nc_inq_libvers'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-misc.o): In function `nf_strerror_':
fort-misc.c:(.text+0x16e): undefined reference to `nc_strerror'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_put_var_text_':
fort-vario.c:(.text+0x8): undefined reference to `nc_put_var_text'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_get_var_text_':
fort-vario.c:(.text+0x18): undefined reference to `nc_get_var_text'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_put_var_int1_':
fort-vario.c:(.text+0x28): undefined reference to `nc_put_var_schar'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_get_var_int1_':
fort-vario.c:(.text+0x38): undefined reference to `nc_get_var_schar'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_put_var_int2_':
fort-vario.c:(.text+0x48): undefined reference to `nc_put_var_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_get_var_int2_':
fort-vario.c:(.text+0x58): undefined reference to `nc_get_var_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_put_var_int_':
fort-vario.c:(.text+0x68): undefined reference to `nc_put_var_int'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_get_var_int_':
fort-vario.c:(.text+0x78): undefined reference to `nc_get_var_int'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_put_var_real_':
fort-vario.c:(.text+0x88): undefined reference to `nc_put_var_float'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_get_var_real_':
fort-vario.c:(.text+0x98): undefined reference to `nc_get_var_float'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_put_var_double_':
fort-vario.c:(.text+0xa8): undefined reference to `nc_put_var_double'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_get_var_double_':
fort-vario.c:(.text+0xb8): undefined reference to `nc_get_var_double'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_put_var_':
fort-vario.c:(.text+0xc8): undefined reference to `nc_put_var'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-vario.o): In function `nf_get_var_':
fort-vario.c:(.text+0xd8): undefined reference to `nc_get_var'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_text_':
fort-varaio.c:(.text+0x5c): undefined reference to `nc_put_vara_text'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_text_':
fort-varaio.c:(.text+0xcc): undefined reference to `nc_get_vara_text'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_int1_':
fort-varaio.c:(.text+0x13c): undefined reference to `nc_put_vara_schar'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_int1_':
fort-varaio.c:(.text+0x1ac): undefined reference to `nc_get_vara_schar'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_int2_':
fort-varaio.c:(.text+0x21c): undefined reference to `nc_put_vara_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_int2_':
fort-varaio.c:(.text+0x28c): undefined reference to `nc_get_vara_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_int2_':
fort-varaio.c:(.text+0x21c): undefined reference to `nc_put_vara_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_int2_':
fort-varaio.c:(.text+0x28c): undefined reference to `nc_get_vara_short'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_int_':
fort-varaio.c:(.text+0x2fc): undefined reference to `nc_put_vara_int'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_int_':
fort-varaio.c:(.text+0x36c): undefined reference to `nc_get_vara_int'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_real_':
fort-varaio.c:(.text+0x3dc): undefined reference to `nc_put_vara_float'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_real_':
fort-varaio.c:(.text+0x44c): undefined reference to `nc_get_vara_float'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_double_':
fort-varaio.c:(.text+0x4bc): undefined reference to `nc_put_vara_double'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_double_':
fort-varaio.c:(.text+0x52c): undefined reference to `nc_get_vara_double'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_':
fort-varaio.c:(.text+0x59c): undefined reference to `nc_put_vara'
/work/sbarve/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_':
fort-varaio.c:(.text+0x60c): undefined reference to `nc_get_vara'
make[2]: [diffwrf] Error 1 (ignored)

---------------------------------------------------


What are we doing wrong here?

Thanks

Andrew Penny
Research Associate - Meteorology Department
Naval Postgraduate School
Monterey, CA 93943
Phone: (831) 656-3101




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