errors when running upwelling case

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Author
yong.liang
Posts: 6
Joined: Wed Apr 08, 2015 3:16 pm
Location: University of California Berkeley

errors when running upwelling case

#1 Unread post by yong.liang »

Hi All,

When I ran upwelling case following the instructions here https://www.myroms.org/wiki/index.php/ROMS_UNSW2008, I got the following error messages. I set FORT=gfortran in the build.bash file. Could anyone tell me what is wrong here? Thanks.

"
lling/Build/libNLM_sed.a /home/liang/Projects/upwelling/Build/libANA.a /home/liang/Projects/upwelling/Build/libUTIL.a /home/liang/Projects/upwelling/Build/libMODS.a -L/usr/local/lib -lnetcdf
/home/liang/Projects/upwelling/Build/libUTIL.a(close_io.o): In function `close_out_':
/home/liang/Projects/upwelling/Build/close_io.f90:195: undefined reference to `__netcdf_MOD_nf90_strerror'
/home/liang/Projects/upwelling/Build/close_io.f90:197: undefined reference to `__netcdf_MOD_nf90_strerror'
/home/liang/Projects/upwelling/Build/libUTIL.a(lbc.o): In function `lbc_getatt_':
/home/liang/Projects/upwelling/Build/lbc.f90:84: undefined reference to `__netcdf_MOD_nf90_get_att_text'
/home/liang/Projects/upwelling/Build/libUTIL.a(lbc.o): In function `lbc_putatt_':
/home/liang/Projects/upwelling/Build/lbc.f90:452: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/libUTIL.a(nf_fwrite2d.o): In function `__nf_fwrite2d_mod_MOD_nf_fwrite2d':
/home/liang/Projects/upwelling/Build/nf_fwrite2d.f90:143: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libUTIL.a(nf_fwrite3d.o): In function `__nf_fwrite3d_mod_MOD_nf_fwrite3d':
/home/liang/Projects/upwelling/Build/nf_fwrite3d.f90:155: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libUTIL.a(def_dim.o): In function `def_dim_':
/home/liang/Projects/upwelling/Build/def_dim.f90:56: undefined reference to `__netcdf_MOD_nf90_def_dim'
/home/liang/Projects/upwelling/Build/libUTIL.a(def_info.o): In function `def_info_':
/home/liang/Projects/upwelling/Build/def_info.f90:157: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_info.f90:169: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_info.f90:183: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_info.f90:232: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_info.f90:244: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/libUTIL.a(def_info.o):/home/liang/Projects/upwelling/Build/def_info.f90:253: more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
/home/liang/Projects/upwelling/Build/libUTIL.a(def_var.o): In function `__def_var_mod_MOD_def_var':
/home/liang/Projects/upwelling/Build/def_var.f90:113: undefined reference to `__netcdf_MOD_nf90_def_var_scalar'
/home/liang/Projects/upwelling/Build/def_var.f90:116: undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
/home/liang/Projects/upwelling/Build/def_var.f90:133: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:150: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:168: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:186: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:204: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/home/liang/Projects/upwelling/Build/def_var.f90:207: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:210: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:230: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/home/liang/Projects/upwelling/Build/def_var.f90:233: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:236: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:258: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:263: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:289: undefined reference to `__netcdf_MOD_nf90_put_att_fourbyteint'
/home/liang/Projects/upwelling/Build/def_var.f90:292: undefined reference to `__netcdf_MOD_nf90_put_att_fourbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:295: undefined reference to `__netcdf_MOD_nf90_put_att_eightbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:301: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:325: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:342: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:359: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:376: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/libUTIL.a(def_var.o):/home/liang/Projects/upwelling/Build/def_var.f90:393: more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
/home/liang/Projects/upwelling/Build/libUTIL.a(def_var.o): In function `__def_var_mod_MOD_def_var':
/home/liang/Projects/upwelling/Build/def_var.f90:428: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/home/liang/Projects/upwelling/Build/def_var.f90:431: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:434: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:454: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/home/liang/Projects/upwelling/Build/def_var.f90:457: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:460: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:480: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbyteint'
/home/liang/Projects/upwelling/Build/def_var.f90:483: undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:486: undefined reference to `__netcdf_MOD_nf90_put_att_one_eightbytereal'
/home/liang/Projects/upwelling/Build/def_var.f90:505: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:522: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:597: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:615: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/def_var.f90:632: undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/liang/Projects/upwelling/Build/libUTIL.a(nf_fread2d.o): In function `__nf_fread2d_mod_MOD_nf_fread2d':
/home/liang/Projects/upwelling/Build/nf_fread2d.f90:213: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libUTIL.a(nf_fread3d.o): In function `__nf_fread3d_mod_MOD_nf_fread3d':
/home/liang/Projects/upwelling/Build/nf_fread3d.f90:200: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libUTIL.a(nf_fread4d.o): In function `__nf_fread4d_mod_MOD_nf_fread4d':
/home/liang/Projects/upwelling/Build/nf_fread4d.f90:203: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_sync':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4502: undefined reference to `__netcdf_MOD_nf90_sync'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_redef':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4448: undefined reference to `__netcdf_MOD_nf90_redef'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_open':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4392: undefined reference to `__netcdf_MOD_nf90_open'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4394: undefined reference to `__netcdf_MOD_nf90_open'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4396: undefined reference to `__netcdf_MOD_nf90_open'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_enddef':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4335: undefined reference to `__netcdf_MOD_nf90_enddef'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_create':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4283: undefined reference to `__netcdf_MOD_nf90_create'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_close':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4217: undefined reference to `__netcdf_MOD_nf90_get_att_text'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4225: undefined reference to `__netcdf_MOD_nf90_close'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_svar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4126: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4144: undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_svar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4019: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:4035: undefined reference to `__netcdf_MOD_nf90_put_var_text'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_lvar_2d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3901: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3928: undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_lvar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3782: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3807: undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_lvar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3660: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3684: undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3687: undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_ivar_2d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3551: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3565: undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_ivar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3447: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3461: undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_ivar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3338: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3353: undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3356: undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_4d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3233: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3247: undefined reference to `__netcdf_MOD_nf90_put_var_4d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_3d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3129: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3143: undefined reference to `__netcdf_MOD_nf90_put_var_3d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_2d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3025: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:3039: undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2921: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2935: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_put_fvar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2812: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2827: undefined reference to `__netcdf_MOD_nf90_put_var_eightbytereal'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2830: undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_svar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2710: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2713: undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2715: undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_svar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2608: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2611: undefined reference to `__netcdf_MOD_nf90_get_var_text'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2613: undefined reference to `__netcdf_MOD_nf90_get_var_text'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_ivar_2d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2507: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2510: undefined reference to `__netcdf_MOD_nf90_get_var_2d_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2512: undefined reference to `__netcdf_MOD_nf90_get_var_2d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_ivar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2404: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2407: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2409: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_ivar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2301: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2304: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2307: undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_lvar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2162: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2165: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2169: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2171: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2184: undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2186: undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_lvar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2022: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2025: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2029: undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2032: undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2043: undefined reference to `__netcdf_MOD_nf90_get_var_text'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:2045: undefined reference to `__netcdf_MOD_nf90_get_var_text'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_4d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1857: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1860: undefined reference to `__netcdf_MOD_nf90_get_var_4d_eightbytereal'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1862: undefined reference to `__netcdf_MOD_nf90_get_var_4d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_3d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1678: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1681: undefined reference to `__netcdf_MOD_nf90_get_var_3d_eightbytereal'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1683: undefined reference to `__netcdf_MOD_nf90_get_var_3d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_2d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1504: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1507: undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1509: undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_1d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1330: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1333: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1335: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fvar_0d':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1197: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1200: undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1203: undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_fatt':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1067: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1070: undefined reference to `__netcdf_MOD_nf90_inq_attname'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:1075: undefined reference to `__netcdf_MOD_nf90_get_att_one_eightbytereal'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_inq_varid':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:982: undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_inq_var':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:706: undefined reference to `__netcdf_MOD_nf90_inquire'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:718: undefined reference to `__netcdf_MOD_nf90_inquire_variable'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:722: undefined reference to `__netcdf_MOD_nf90_inq_attname'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:810: undefined reference to `__netcdf_MOD_nf90_inquire_dimension'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:821: undefined reference to `__netcdf_MOD_nf90_inq_attname'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:826: undefined reference to `__netcdf_MOD_nf90_inquire_attribute'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:832: undefined reference to `__netcdf_MOD_nf90_get_att_one_fourbyteint'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:848: undefined reference to `__netcdf_MOD_nf90_get_att_one_eightbytereal'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:862: undefined reference to `__netcdf_MOD_nf90_get_att_text'
/home/liang/Projects/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_dim':
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:212: undefined reference to `__netcdf_MOD_nf90_inquire'
/home/liang/Projects/upwelling/Build/mod_netcdf.f90:222: undefined reference to `__netcdf_MOD_nf90_inquire_dimension'
"
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jcwarner
Posts: 1200
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: errors when running upwelling case

#2 Unread post by jcwarner »

undefined reference to `__netcdf_MOD_
....
looks like the build can not find your netcdf libraries.
you can set the path to these libs by setting environment variables using something like:

setenv NETCDF_INCDIR /usr/local/apps/netcdf-4.2/include
setenv NETCDF_LIBDIR /usr/local/apps/netcdf-4.2/lib

or similar to point to the places of your netcdf files.

you need to make sure that version of netcdf has been compiled with the same compiler that you are using now.
-j
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User avatar
kate
Posts: 4091
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: errors when running upwelling case

#3 Unread post by kate »

Also, you need to link with -lnetcdff, the library created by netcdf-fortran. Did you set USE_NETCDF4?
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yong.liang
Posts: 6
Joined: Wed Apr 08, 2015 3:16 pm
Location: University of California Berkeley

Re: errors when running upwelling case

#4 Unread post by yong.liang »

Hi Jcwarner,

I installed NetCDF in the default directory /usr/local and updated NETCDF_INCDIR and NETCDF_LIBDIR everywhere in the build.bash. I will check if it was compiled with the same compiler as I am using. Thanks.
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yong.liang
Posts: 6
Joined: Wed Apr 08, 2015 3:16 pm
Location: University of California Berkeley

Re: errors when running upwelling case

#5 Unread post by yong.liang »

Hi Kate,

I did not set USE_NETCDF4. But could you tell me how to link with -lnetcdff? Thanks.
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User avatar
kate
Posts: 4091
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: errors when running upwelling case

#6 Unread post by kate »

If you compiled a recent netcdf, you also need to download and compile netcdf-fortran. Then you can turn on USE_NETCDF4, set NC_CONFIG, and it will attempt to link in -lnetcdff for you.
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