error with inlet_test example

[nma]

Dear friends,

I was trying inlet test case where ROMS is coupled to SWAN. The input files I got from Inlet Test case homepage: https://www.myroms.org/wiki/index.php/INLET_TEST_CASE
I use Redhat linux, gfortran compiler. Here is the tail of the build errors:


ROMS/Bin/cpp_clean /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/master.f90
cd /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build; /m/raid2/nma/libs/test/mpich2-1.4/MPICH2/bin/mpif90 -c -frepack-arrays -g -fbounds-check -I/m/raid2/nma/libs/test/MCT/buildMCT/include master.f90
/m/raid2/nma/libs/test/mpich2-1.4/MPICH2/bin/mpif90 -frepack-arrays -g -fbounds-check -I/m/raid2/nma/libs/test/MCT/buildMCT/include /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/esmf_roms.o /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/master.o /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/ocean_control.o /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/ocean_coupler.o /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/propagator.o /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/roms_export.o /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/roms_import.o -o /m/raid3/nma/ocean_model/roms/Projects/inlet_test/oceanG /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libNLM.a /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libNLM_bio.a /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libNLM_sed.a /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libANA.a /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a /m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libSWAN.a -L/llocal1/SL64/netcdf-4.1.3-gfortran44/lib -lnetcdf -L/m/raid2/nma/libs/test/MCT/buildMCT/lib -lmct -lmpeu
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(close_io.o): In function `close_out':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/close_io.f90:133: undefined reference to `__netcdf_MOD_nf90_strerror'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/close_io.f90:135: undefined reference to `__netcdf_MOD_nf90_strerror'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(distribute.o): In function `__distribute_mod_MOD_mp_ncwrite2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(distribute.o): In function `__distribute_mod_MOD_mp_ncwrite1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(distribute.o): In function `__distribute_mod_MOD_mp_ncread2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(distribute.o): In function `__distribute_mod_MOD_mp_ncread1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(nf_fwrite2d.o): In function `__nf_fwrite2d_mod_MOD_nf_fwrite2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/nf_fwrite2d.f90:157: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(nf_fwrite3d.o): In function `__nf_fwrite3d_mod_MOD_nf_fwrite3d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/nf_fwrite3d.f90:168: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(def_info.o): In function `def_info':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_info.f90:161: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_info.f90:173: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_info.f90:187: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_info.f90:236: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_info.f90:248: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(def_info.o):/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_info.f90:257: more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(def_var.o): In function `__def_var_mod_MOD_def_var':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:116: undefined reference to `__netcdf_MOD_nf90_def_var_scalar'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:119: undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:136: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:153: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:171: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:189: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:207: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:210: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:213: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:233: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:236: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:239: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:261: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:266: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:292: undefined reference to `__netcdf_MOD_nf90_put_att_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:295: undefined reference to `__netcdf_MOD_nf90_put_att_fourbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:298: undefined reference to `__netcdf_MOD_nf90_put_att_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:304: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:328: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:345: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:362: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:379: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(def_var.o):/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:396: more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(def_var.o): In function `__def_var_mod_MOD_def_var':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:431: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:434: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:437: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:457: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:460: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:463: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:483: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:486: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:489: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:508: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:525: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:600: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:618: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:635: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:662: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_var.f90:665: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(nf_fread2d.o): In function `__nf_fread2d_mod_MOD_nf_fread2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/nf_fread2d.f90:229: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(nf_fread3d.o): In function `__nf_fread3d_mod_MOD_nf_fread3d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/nf_fread3d.f90:217: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(nf_fread4d.o): In function `__nf_fread4d_mod_MOD_nf_fread4d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/nf_fread4d.f90:219: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libUTIL.a(def_dim.o): In function `def_dim':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/def_dim.f90:59: undefined reference to `__netcdf_MOD_nf90_def_dim'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_sync':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4967: undefined reference to `__netcdf_MOD_nf90_sync'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_redef':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4905: undefined reference to `__netcdf_MOD_nf90_redef'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_open':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4839: undefined reference to `__netcdf_MOD_nf90_open'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4841: undefined reference to `__netcdf_MOD_nf90_open'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4843: undefined reference to `__netcdf_MOD_nf90_open'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_enddef':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4774: undefined reference to `__netcdf_MOD_nf90_enddef'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_create':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4712: undefined reference to `__netcdf_MOD_nf90_create'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_close':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4634: undefined reference to `__netcdf_MOD_nf90_get_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4642: undefined reference to `__netcdf_MOD_nf90_close'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_svar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4532: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4550: undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_svar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4414: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4430: undefined reference to `__netcdf_MOD_nf90_put_var_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_lvar_2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4285: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4312: undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_lvar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4155: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4180: undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_lvar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4022: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4046: undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:4049: undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_ivar_2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_ivar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_ivar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_4d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_4d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_3d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_3d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_svar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_svar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_ivar_2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_2d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_2d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_ivar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_ivar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_lvar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_lvar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_4d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_4d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_4d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_3d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_3d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_3d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_2d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_1d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_0d':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fatt':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_attname'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_get_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_inq_varid':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90 undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_inq_var':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:729: undefined reference to `__netcdf_MOD_nf90_inquire'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:745: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:749: undefined reference to `__netcdf_MOD_nf90_inq_attname'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:855: undefined reference to `__netcdf_MOD_nf90_inquire_dimension'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:866: undefined reference to `__netcdf_MOD_nf90_inq_attname'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:871: undefined reference to `__netcdf_MOD_nf90_inquire_attribute'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:877: undefined reference to `__netcdf_MOD_nf90_get_att_one_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:893: undefined reference to `__netcdf_MOD_nf90_get_att_one_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:907: undefined reference to `__netcdf_MOD_nf90_get_att_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_dim':
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:212: undefined reference to `__netcdf_MOD_nf90_inquire'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:226: undefined reference to `__netcdf_MOD_nf90_inquire_dimension'
collect2: ld returned 1 exit status
make: *** [/m/raid3/nma/ocean_model/roms/Projects/inlet_test/oceanG] Error 1

Thanks for your help and suggestions.
with regards, nilima

[kate]

This falls under the category of Errors at link time. Please let us know if we're missing something there.

[d.kobashi]

Dear all

I also had similar errors while compiling inlet_test case (revision 566), but mines are associated with MCT, which I compiled using the same compiler as the one I used for ROMS compile (intel fortran 11.1).

I checked the website which Kate indicated (Errors at link time), but my errors do not seem to be related to "underscores".
For example, for the following errors, I checked the library links and there were no underscore issues (the number of underscores on the error did match that in the library). I checked several lines containing "undefined reference" error and they were the same as their "nm" outputs.

===========================errors(extracted)================================
/home/s2766679/modelling/MCT/mct/libmct.a(m_MCTWorld.o): In function `m_mctworld_mp_initr__.':
m_MCTWorld.F90:(.text+0x719): undefined reference to `m_die_mp_mpdie2__'
m_MCTWorld.F90:(.text+0x74a): undefined reference to `m_die_mp_mpdie2__'
m_MCTWorld.F90:(.text+0x77b): undefined reference to `m_die_mp_mpdie2__'
m_MCTWorld.F90:(.text+0x847): undefined reference to `m_die_mp_die2__'
m_MCTWorld.F90:(.text+0x940): undefined reference to `m_die_mp_die2__'
m_MCTWorld.F90:(.text+0xba4): undefined reference to `m_die_mp_mpdie2__'
m_MCTWorld.F90:(.text+0xdc1): undefined reference to `m_die_mp_mpdie2__'
m_MCTWorld.F90:(.text+0xde7): undefined reference to `m_die_mp_die2__'


===========library check======================
s2766679@s2766679-desktop:~/modelling/ROMS/src/Compilers$ nm /home/s2766679/modelling/MCT/mct/libmct.a | grep m_mctworld_mp_initr
000006c0 T m_mctworld_mp_initr__
000006cc T m_mctworld_mp_initr__.


I also checked intel fortran flag options related to the underscores and found the following options. Those did not work.

-assume nounderscore
-assume 2underscores
-assume no2underscores.


Any suggestions would be appreciated. I compiled coupled ROMS-SWAN on Ubuntu 10.04 with Intel Fortran 11.1 and MPICH2. I don't use netcdf4 option.

Thanks in advance.

Sincerely,

DJ

[m.hadfield]

Nma, your undefined references are from the Fortran-90 interface and I suspect you are missing a "-lnetcdff" on your link command. NetCDF-4 has a script called nc-config that should provide the right linker options.

Now that g77 is long gone, these problems are never (well hardly ever) related to the "*underscore" compiler options.

Dkobashi (and everyone else reporting linker errors), when reporting problems, *always* include the command that caused them to be generated.

Edit: Kate, oops sorry didn't notice the netcdff thing is covered by the link you gave.

[nma]

Thanks Kate and Mark for your suggestions. I could solve this build error using -lnetcdff flag suggested by you. After building it, when I try to run the executive it gives me following error:

[nma@k6 inlet_test]$ mpirun -np 4 oceanM coupling_inlet_test.in
[proxy:0:0@k6] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file oceanM (No such file or directory)
[proxy:0:0@k6] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file oceanM (No such file or directory)
[proxy:0:0@k6] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file oceanM (No such file or directory)
[proxy:0:0@k6] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file oceanM (No such file or directory)

This looks like an error related to MPI. I am using MPICH2 library. While checking 'which mpirun' and 'which mpif90' both gave me the same path:
[nma@k6 inlet_test]$ which mpif90
/m/raid2/nma/libs/test/mpich2-1.4/MPICH2/bin/mpif90
[nma@k6 inlet_test]$ which mpirun
/m/raid2/nma/libs/test/mpich2-1.4/MPICH2/bin/mpirun

kindly advice if I am making basic mistakes in using MPI...
thanks and regards, nilima

[kate]

Actually, the error is on oceanM. Is that file in your current directory? If so, how about trying ./oceanM there? This could be necessary if . is not in your path.

[nma]

Thanks Kate, there was an error with the path. I have all the input and make files in my /roms/Projects/inlet_test directory. While running the executable, I see the following error:

[nma@k6 inlet_test]$ mpirun -np 4 ./oceanM coupling_inlet_test.in
Coupled Input File name = coupling_inlet_test.in







Model Coupling Parallel Threads:

Ocean Model MPI nodes: 000 - 001
Waves Model MPI nodes: 002 - 003


Ocean Export: bath:SSH:Ubar:Vbar:ZO
Waves Export: Wdir:Wamp:Wlen:Wptop:Wpbot:Wubot



Model Input Parameters: ROMS/TOMS version 3.5
Sunday - August 21, 2011 - 8:08:05 PM
-----------------------------------------------------------------------------

SWAN is preparing computation ...


Inlet Test Case

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran44
Compiler command : /m/raid2/nma/libs/test/mpich2-1.4/MPICH2/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -I/m/raid2/nma/libs/test/MCT/buildMCT/include -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-for

Input Script : ocean_inlet_test.in

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 566M

Local Root : /m/raid3/nma/ocean_model/roms
Header Dir : /m/raid3/nma/ocean_model/roms/Projects/inlet_test
Header file : inlet_test.h
Analytical Dir: /m/raid3/nma/ocean_model/roms/Projects/inlet_test

Resolution, Grid 01: 0075x0070x008, Parallel Nodes: 2, Tiling: 001x001

ROMS/TOMS: Wrong choice of domain 01 partition or number of parallel threads.
NtileI * NtileJ must be equal to the number of parallel nodes.
Change -np value to mpirun or
change domain partition in input script.

Elapsed CPU time (seconds):


ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Partition error ......... exit_flag: 6


ERROR: Illegal domain partition.
MCT::m_MCTWorld::clean_: deallocate(MCTW,...) error, stat =2
MCT::m_MCTWorld::clean_: deallocate(MCTW,...) error, stat =2

=====================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=====================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)


Looks like I am not correct with number of processors and its partitions. Please suggest..
thanks and regards, nilima

[m.hadfield]

The model coupling code has allocated 2 processors (numbers 0 and 1) to ROMS and 2 processors (numbers 2 and 3) to SWAN. However your ROMS input file evidently has NtileI and NtileJ both equal to 1. Set one of them to 2.

[nma]

Thanks Mark, it solved that error. I am pasting the screen output for the mpirun, where the results are not formed in /roms/Projects/inlet_test directory, as expected:

[nma@k6 inlet_test]$ mpirun -np 4 ./oceanM coupling_inlet_test.in
Coupled Input File name = coupling_inlet_test.in





Model Coupling Parallel Threads:

Ocean Model MPI nodes: 000 - 001
Waves Model MPI nodes: 002 - 003


Ocean Export: bath:SSH:Ubar:Vbar:ZO
Waves Export: Wdir:Wamp:Wlen:Wptop:Wpbot:Wubot





Model Input Parameters: ROMS/TOMS version 3.5
Monday - August 22, 2011 - 11:20:35 AM
-----------------------------------------------------------------------------

SWAN is preparing computation ...


Inlet Test Case

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran44
Compiler command : /m/raid2/nma/libs/test/mpich2-1.4/MPICH2/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -I/m/raid2/nma/libs/test/MCT/buildMCT/include -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-for

Input Script : ocean_inlet_test.in

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 566M

Local Root : /m/raid3/nma/ocean_model/roms
Header Dir : /m/raid3/nma/ocean_model/roms/Projects/inlet_test
Header file : inlet_test.h
Analytical Dir: /m/raid3/nma/ocean_model/roms/Projects/inlet_test

Resolution, Grid 01: 0075x0070x008, Parallel Nodes: 2, Tiling: 001x002


Physical Parameters, Grid: 01
=============================

34560 ntimes Number of timesteps for 3-D equations.
5.000 dt Timestep size (s) for 3-D equations.
20 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.
1 ERstr Starting ensemble/perturbation run number.
1 ERend Ending ensemble/perturbation run number.
0 nrrec Number of restart records to read from disk.
T LcycleRST Switch to recycle time-records in restart file.
720 nRST Number of timesteps between the writing of data
into restart fields.
1 ninfo Number of timesteps between print of information
to standard output.
T ldefout Switch to create a new output NetCDF file(s).
720 nHIS Number of timesteps between the writing fields
into history file.
1.0000E-03 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
5.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
5.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
5.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
5.0000E-06 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
5.0000E-06 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
3.000 gls_p GLS stability exponent.
1.500 gls_m GLS turbulent kinetic energy exponent.
-1.000 gls_n GLS turbulent length scale exponent.
7.6000E-06 gls_Kmin GLS minimum value of turbulent kinetic energy.
1.0000E-12 gls_Pmin GLS minimum value of dissipation.
5.4770E-01 gls_cmu0 GLS stability coefficient.
1.4400E+00 gls_c1 GLS shear production coefficient.
1.9200E+00 gls_c2 GLS dissipation coefficient.
-4.0000E-01 gls_c3m GLS stable buoyancy production coefficient.
1.0000E+00 gls_c3p GLS unstable buoyancy production coefficient.
1.0000E+00 gls_sigk GLS constant Schmidt number for TKE.
1.3000E+00 gls_sigp GLS constant Schmidt number for PSI.
1400.000 charnok_alpha Charnok factor for Zos calculation.
0.500 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.250 sz_alpha Factor for Wave dissipation surface tke flux .
100.000 crgban_cw Factor for Craig/Banner surface tke flux.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
2.5000E-02 rdrg2 Quadratic bottom drag coefficient.
1.5000E-02 Zob Bottom roughness (m).
5.0000E-01 Zos Surface roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
1.0000E+00 theta_s S-coordinate surface control parameter.
1.0000E+00 theta_b S-coordinate bottom control parameter.
0.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
10.000 T0 Background potential temperature (C) constant.
30.000 S0 Background salinity (PSU) constant.
1027.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.7000E-04 Tcoef Thermal expansion coefficient (1/Celsius).
7.6000E-04 Scoef Saline contraction coefficient (1/PSU).
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
T Hout(idBath) Write out time-dependent bathymetry.
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idUbrs) Write out bottom U-current stress.
T Hout(idVbrs) Write out bottom V-current stress.
T Hout(idUbws) Write out wind-induced, bottom U-wave stress.
T Hout(idVbws) Write out wind-induced, bottom V-wave stress.
T Hout(idUbcs) Write out max wind + current, bottom U-wave stress.
T Hout(idVbcs) Write out max wind + current, bottom V-wave stress.
T Hout(idW2xx) Write out 2D radiation stress, Sxx.
T Hout(idW2xy) Write out 2D radiation stress, Sxy.
T Hout(idW2yy) Write out 2D radiation stress, Syy.
T Hout(idWamp) Write out wave height.
T Hout(idWlen) Write out wavelength.
T Hout(idWdir) Write out wave direction.
T Hout(idBott) Write out bottom property 01: grain_diameter
T Hout(idBott) Write out bottom property 02: grain_density
T Hout(idBott) Write out bottom property 03: settling_vel
T Hout(idBott) Write out bottom property 04: erosion_stress
T Hout(idBott) Write out bottom property 05: ripple_length
T Hout(idBott) Write out bottom property 06: ripple_height
T Hout(idBott) Write out bottom property 07: bed_wave_amp
T Hout(idBott) Write out bottom property 08: Zo_def
T Hout(idBott) Write out bottom property 09: Zo_app

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Physical parameters File: ocean_inlet_test.in
Input Grid File: inlet_test_grid.nc

Tile partition information for Grid 01: 0075x0070x0008 tiling: 001x002

tile Istr Iend Jstr Jend Npts

0 1 75 1 35 21000
1 1 75 36 70 21000

Tile minimum and maximum fractional grid coordinates:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 75.50 0.50 35.50 RHO-points
1 0.50 75.50 35.50 70.50 RHO-points

0 1.00 75.00 0.50 35.50 U-points
1 1.00 75.00 35.50 70.50 U-points

0 0.50 75.50 1.00 35.50 V-points
1 0.50 75.50 35.50 70.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 255
HaloSizeJ(1) = 144
TileSide(1) = 79
TileSize(1) = 3318



Sediment Parameters, Grid: 01
=============================


Size Sd50 Csed Srho Wsed Erate poros
Class (mm) (kg/m3) (kg/m3) (mm/s) (kg/m2/s) (nondim)

1 1.0000E-01 0.0000E+00 2.6500E+03 1.0000E+01 5.0000E-03 0.0000E+00

tau_ce tau_cd nl_tnu2 nl_tnu4 Akt_bak Tnudg
(N/m2) (N/m2) (m2/s) (m4/s) (m2/s) (day)

1 1.0000E-01 1.0000E-02 0.0000E+00 0.0000E+00 5.0000E-06 0.0000E+00

morph_fac
(nondim)

1 1.0000E+01

New bed layer formed when deposition exceeds 0.10000E-01 (m).
Two first layers are combined when 2nd layer smaller than 0.10670E+00 (m).
Rate coefficient for bed load transport = 0.15000E+00

T Hout(idTvar) Write out sediment01: mud_01
T Hout(idfrac) Write out bed fraction, sediment 01: mudfrac_01
T Hout(idfrac) Write out mass, sediment 01: mudmass_01
T Hout(idSbed) Write out BED property 01: bed_thickness
T Hout(idSbed) Write out BED property 02: bed_age
T Hout(idSbed) Write out BED property 03: bed_porosity

Activated C-preprocessing Options:

INLET_TEST Inlet Test Case
ANA_BPFLUX Analytical bottom passive tracers fluxes.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_INITIAL Analytical initial conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_SEDIMENT Analytical sediment initial conditions.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SPFLUX Analytical surface passive tracer fluxes.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSGRADIENT Eastern edge, free-surface, gradient condition.
EAST_M2GRADIENT Eastern edge, 2D momentum, gradient condition.
EAST_M3GRADIENT Eastern edge, 3D momentum, gradient condition.
FSOBC_REDUCED Using free-surface data in reduced physics condtions
GLS_MIXING Generic Length-Scale turbulence closure.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MCT_LIB Using Model Coupling Toolkit library.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NEARSHORE_MELLOR08 Nearshore Radiation Stress Terms (Mellor 2008).
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
NORTH_FSGRADIENT Northern edge, free-surface, gradient condition.
NORTH_M2REDUCED Northern edge, 2D momentum, reduced-physics condition.
NORTH_M3GRADIENT Northern edge, 3D momentum, gradient condition.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
!RST_SINGLE Double precision fields in restart NetCDF file.
SEDIMENT Cohesive and noncohesive sediments.
SED_MORPH Allow bottom model elevation to evolve.
SUSPLOAD Activate suspended sediment transport.
SOLVE3D Solving 3D Primitive Equations.
SOUTHERN_WALL Wall boundary at Southern edge.
SPLINES Conservative parabolic spline reconstruction.
SSW_BBL Styles and Glenn Bottom Boundary Layer - modified.
SSW_CALC_ZNOT Internal computation of bottom roughness.
SWAN_COUPLING Two-way SWAN/ROMS coupling.
THREE_GHOST Using three Ghost Points in halo regions.
TS_MPDATA Recursive flux corrected MPDATA 3D advection of tracers.
UV_ADV Advection of momentum.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
WAVES_OCEAN Two-way wave-ocean models coupling.
WEST_FSGRADIENT Western edge, free-surface, gradient condition.
WEST_M2GRADIENT Western edge, 2D momentum, gradient condition.
WEST_M3GRADIENT Western edge, 3D momentum, gradient condition.

Process Information:

Node # 0 (pid= 21177) is active.
Node # 1 (pid= 21178) is active.


The last line shows both the processes are active, however after that there is no output (history or restart files) made. Following is the list of files I could see after the mpirun:

-rwxr-xr-x 1 nma palmod 13437 Aug 21 19:19 build.bash
-rwxr-xr-x 1 nma palmod 4581992 Aug 21 19:21 oceanM
drwxr-xr-x 2 nma palmod 28672 Aug 21 19:21 Build
-rw-r--r-- 1 nma palmod 1061 Aug 21 19:28 swaninit
-rw-r--r-- 1 nma palmod 92558 Aug 21 22:14 ocean_inlet_test.in
-rw-r--r-- 1 nma palmod 14316 Aug 21 22:34 out.txt
drwxr-xr-x 4 nma palmod 4096 Aug 22 15:04 .
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 PRINT-002
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 PRINT-001
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 Errfile-002
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 Errfile-001

These output files are empty and does not give me any hint of what's going wrong...
This is what I have in my ocean_inlet_test.in



! Input/Output parameters.

NRREC == 0
LcycleRST == T
NRST == 720
NSTA == 1
NFLT == 1
NINFO == 1

! Output history, average, diagnostic files parameters.

LDEFOUT == T
NHIS == 720
NDEFHIS == 0
NTSAVG == 1
NAVG == 3600
NDEFAVG == 0
NTSDIA == 1
NDIA == 3600
NDEFDIA == 0

............................................................
....................................................
........................................

! Output NetCDF file names, [1:Ngrids].

GSTNAME == ocean_gst.nc
RSTNAME == ocean_rst.nc
HISNAME == ocean_his.nc
TLMNAME == ocean_tlm.nc
TLFNAME == ocean_tlf.nc
ADJNAME == ocean_adj.nc
AVGNAME == ocean_avg.nc
DIANAME == ocean_dia.nc
STANAME == ocean_sta.nc
FLTNAME == ocean_flt.nc

Any idea of why it is not forming the restart and history output files..

thanks and regards, nilima

[jcwarner]

if there is an Errorxx-xxx file, then SWAN is having a problem. Try running with just 1 proc for swan. the error is most likely a path issue or a filename issue.
-j

[nma]

Thanks John, did you mean using the same executable (oceanM) and one processor...if so, it gave following:


[nma@k6 inlet_test]$ mpirun -np 1 ./oceanM coupling_inlet_test.in
Coupled Input File name = coupling_inlet_test.in

MOD_COUPLER - Number assigned processors: 003
not equal to spawned MPI nodes: 001

Later I changed NtileI and NtileJ to 1 (same value), still it gave the above comment.

For information, these are various input files I am having in my Project folder:

-rw-r--r-- 1 nma palmod 9505960 Oct 25 2008 inlet_init.nc
-rw-r-xr-- 1 nma palmod 88776 Jan 5 2009 inlet_test_bathy.bot
-rw-r--r-- 1 nma palmod 8951 Jan 5 2009 coupling.dat
-rw-r--r-- 1 nma palmod 155381 Jan 13 2009 inlet_test_grid_coord.grd
-rw-r--r-- 1 nma palmod 28965 Jul 5 16:02 sediment_inlet_test.in
-rw-r--r-- 1 nma palmod 150328 Jul 5 16:02 varinfo.dat
-rw-r--r-- 1 nma palmod 1976 Jul 5 16:02 inlet_test.h
-rw-r--r-- 1 nma palmod 13641 Jul 5 16:02 ana_m2obc.h
-rw-r--r-- 1 nma palmod 15498 Jul 5 16:02 ana_sediment.h
-rw-r--r-- 1 nma palmod 6443 Jul 5 16:02 ana_fsobc.h
-rw-r--r-- 1 nma palmod 2680 Jul 5 16:02 swan_inlet_test.in
-rw-r--r-- 1 nma palmod 1236384 Jul 5 16:03 inlet_test_grid.nc
-rw-r--r-- 1 nma palmod 14218 Aug 18 19:15 coupling_inlet_test.in
-rw-r--r-- 1 nma palmod 6209 Aug 21 18:49 Linux-gfortran44.mk
-rw-r--r-- 1 nma palmod 19454 Aug 21 19:15 makefile
-rwxr-xr-x 1 nma palmod 13437 Aug 21 19:19 build.bash
-rwxr-xr-x 1 nma palmod 4581992 Aug 21 19:21 oceanM
drwxr-xr-x 2 nma palmod 28672 Aug 21 19:21 Build
-rw-r--r-- 1 nma palmod 1061 Aug 21 19:28 swaninit
-rw-r--r-- 1 nma palmod 14316 Aug 21 22:34 out.txt
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 PRINT-002
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 PRINT-001
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 Errfile-002
-rw-r--r-- 1 nma palmod 0 Aug 22 15:24 Errfile-001
-rw-r--r-- 1 nma palmod 92558 Aug 22 19:12 ocean_inlet_test.in
drwxr-xr-x 4 nma palmod 4096 Aug 22 19:12 .

I am trying to keep all input files under /roms/Project/inlet_test directory.

thanks and regards, nilima

[jcwarner]

1) in the coupling. in file, you need to set the number of processors for roms, and the number for swan.
2) in the ocean.in file, the tiling for roms should be = to the number of procs set for roms. so if roms is tiled 1x2, then it needs 2 procs.
3) the tiling for swan is automatic, so u do not need to set the swan tiling anywhere.
4) the total number of procs, roms + swan, is needed on the command line
mpirun -np X (= #roms + #swan) ./oceanM Projects/.......

[nma]

Thanks John, you rightly said about incorrect path of input file, which gave the above errors.

Thanks Kate, Mark and John to help me making this test work
warm regards, nilima

[CharlesJames]

I've been working with the inlet_test case with ROMS 3.6 (rev 572), MCT 2.6.0,
I'm compiling with mpif90 for MPICH version 1.2.1p1 with ifort 10.1

I've run into a couple of things:

First, I've encountered what may be a bug that causes the program to fail at the last hurdle - the mpi_barrier call in master.f90 causes a segmentation fault after the swan and roms models have finished executing. It appears, at least in my case, that mpi_barrier needs to be called with the error status flag in order for the program to progress past the barrier.

In mct_coupler.h line 162 the current version has
CALL mpi_barrier (MPI_COMM_WORLD)

the program builds and runs to completion if this is changed to
CALL mpi_barrier (MPI_COMM_WORLD,MyError)

The other issue is that now, after it finishes running, I don't seem to be able to read in the .mat files that are created - are these supposed to be matlab compatible?

cheers,
Charles

[arango]

Yes, great catch I have noticed that warning before but I was not able to find the cause. The simulation runs to conclusion but it cannot finalize MPI. At one point I though that it was from the MCT library. Indeed, the Fortran call to mpi_barrier (MPI_COMM_WORLD, MyError) has two arguments. However, the C-language call just has one argument. Probably, the confusion comes from that.