error with inlet_test example

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Author
nma
Posts: 21
Joined: Thu Jan 28, 2010 3:06 pm
Location: University of Bremen

error with inlet_test example

#1 Post by nma » Wed Aug 17, 2011 5:44 pm

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.f90:2658: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90:2660: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90:2699: 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.f90:2448: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90:2450: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90:2486: 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.f90:2262: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90:2274: 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.f90:2060: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/distribute.f90:2070: 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.f90:3902: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3916: 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.f90:3787: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3801: 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.f90:3667: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3682: undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3685: 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.f90:3551: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3565: 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.f90:3436: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3450: 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.f90:3321: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3335: 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.f90:3206: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3220: 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.f90:3086: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3101: undefined reference to `__netcdf_MOD_nf90_put_var_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:3104: 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.f90:2970: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2973: undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2975: 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.f90:2854: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2857: undefined reference to `__netcdf_MOD_nf90_get_var_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2859: 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.f90:2739: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2742: undefined reference to `__netcdf_MOD_nf90_get_var_2d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2744: 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.f90:2622: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2625: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2627: 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.f90:2505: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2508: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2511: 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.f90:2352: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2355: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2359: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2361: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2374: undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2376: 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.f90:2198: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2201: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2205: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2208: undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2219: undefined reference to `__netcdf_MOD_nf90_get_var_text'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2221: 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.f90:2019: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2022: undefined reference to `__netcdf_MOD_nf90_get_var_4d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:2024: 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.f90:1826: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1829: undefined reference to `__netcdf_MOD_nf90_get_var_3d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1831: 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.f90:1638: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1641: undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1643: 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.f90:1450: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1453: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1455: 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.f90:1303: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1306: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1309: 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.f90:1144: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1147: undefined reference to `__netcdf_MOD_nf90_inq_attname'
/m/raid3/nma/ocean_model/roms/Projects/inlet_test/Build/mod_netcdf.f90:1152: 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.f90:1049: 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
Attachments
inlet_test_error.txt
complete build report
(336.96 KiB) Downloaded 173 times

User avatar
kate
Posts: 3770
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: error with inlet_test example

#2 Post by kate » Wed Aug 17, 2011 8:43 pm

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

d.kobashi
Posts: 55
Joined: Tue Sep 28, 2010 11:59 pm
Location: Texas A&M University

Re: error with inlet_test example

#3 Post by d.kobashi » Thu Aug 18, 2011 4:25 am

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

User avatar
m.hadfield
Posts: 520
Joined: Tue Jul 01, 2003 4:12 am
Location: NIWA

Re: error with inlet_test example

#4 Post by m.hadfield » Fri Aug 19, 2011 1:59 am

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
Posts: 21
Joined: Thu Jan 28, 2010 3:06 pm
Location: University of Bremen

Re: error with inlet_test example

#5 Post by nma » Fri Aug 19, 2011 2:39 pm

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

User avatar
kate
Posts: 3770
Joined: Wed Jul 02, 2003 5:29 pm
Location: IMS/UAF, USA

Re: error with inlet_test example

#6 Post by kate » Fri Aug 19, 2011 4:18 pm

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
Posts: 21
Joined: Thu Jan 28, 2010 3:06 pm
Location: University of Bremen

Re: error with inlet_test example

#7 Post by nma » Sun Aug 21, 2011 6:12 pm

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

User avatar
m.hadfield
Posts: 520
Joined: Tue Jul 01, 2003 4:12 am
Location: NIWA

Re: error with inlet_test example

#8 Post by m.hadfield » Sun Aug 21, 2011 7:41 pm

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
Posts: 21
Joined: Thu Jan 28, 2010 3:06 pm
Location: University of Bremen

Re: error with inlet_test example

#9 Post by nma » Mon Aug 22, 2011 2:15 pm

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
Posts: 834
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: error with inlet_test example

#10 Post by jcwarner » Mon Aug 22, 2011 2:34 pm

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
Posts: 21
Joined: Thu Jan 28, 2010 3:06 pm
Location: University of Bremen

Re: error with inlet_test example

#11 Post by nma » Mon Aug 22, 2011 5:24 pm

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
Posts: 834
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: error with inlet_test example

#12 Post by jcwarner » Mon Aug 22, 2011 5:52 pm

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
Posts: 21
Joined: Thu Jan 28, 2010 3:06 pm
Location: University of Bremen

Re: error with inlet_test example

#13 Post by nma » Mon Aug 22, 2011 6:37 pm

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

User avatar
CharlesJames
Posts: 32
Joined: Thu May 24, 2007 12:12 pm
Location: South Australian Research and Development Institute

Re: error with inlet_test example

#14 Post by CharlesJames » Mon Oct 31, 2011 5:14 am

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

User avatar
arango
Site Admin
Posts: 1107
Joined: Wed Feb 26, 2003 4:41 pm
Location: IMCS, Rutgers University
Contact:

Re: error with inlet_test example

#15 Post by arango » Mon Oct 31, 2011 4:03 pm

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.

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