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Source code for the General Ocean Turbulence Model
https://gotm.net
GNU General Public License v2.0
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Compiling gotm lake branch under macOS #4

Open robertladwig opened 4 years ago

robertladwig commented 4 years ago

I'm currently trying to compile GOTM lake v5.3-673 under macOS (Catalina v10.15.3) after having no problems in compiling it under Ubuntu (18.04). I added the line -DGOTM_USE_STIM=on \ to gotm_configure.sh to include ice dynamics.

Now, running gotm_configure.sh works without problems and creates a gfortran directory, but gotm_build.sh reaches 100% and then fails in building the executable:

[100%] Linking Fortran executable gotm
Undefined symbols for architecture x86_64:
  "___netcdf_MOD_nf90_close", referenced from:
      ___netcdf_output_MOD_finalize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_create", referenced from:
      ___netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_def_dim", referenced from:
      _get_dim_id.4982 in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_def_var_manydims", referenced from:
      ___netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_enddef", referenced from:
      ___netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_get_att_text", referenced from:
      ___input_netcdf_MOD_check_restart_time in libinput_manager.a(input_netcdf.F90.o)
  "___netcdf_MOD_nf90_get_var_1d_eightbytereal", referenced from:
      ___input_netcdf_MOD_read_restart_data in libinput_manager.a(input_netcdf.F90.o)
  "___netcdf_MOD_nf90_get_var_eightbytereal", referenced from:
      ___input_netcdf_MOD_read_restart_data in libinput_manager.a(input_netcdf.F90.o)
  "___netcdf_MOD_nf90_inq_libvers", referenced from:
      _print_version_ in libgotm.a(print_version.F90.o)
  "___netcdf_MOD_nf90_inq_varid", referenced from:
      ___input_netcdf_MOD_read_restart_data in libinput_manager.a(input_netcdf.F90.o)
      ___input_netcdf_MOD_check_restart_time in libinput_manager.a(input_netcdf.F90.o)
  "___netcdf_MOD_nf90_open", referenced from:
      ___input_netcdf_MOD_read_restart_data in libinput_manager.a(input_netcdf.F90.o)
      ___input_netcdf_MOD_check_restart_time in libinput_manager.a(input_netcdf.F90.o)
  "___netcdf_MOD_nf90_put_att_one_eightbytereal", referenced from:
      ___netcdf_output_MOD_put_att_typed_real in liboutput_manager.a(netcdf_output.F90.o)
      ___netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_put_att_one_fourbyteint", referenced from:
      ___netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_put_att_one_fourbytereal", referenced from:
      ___netcdf_output_MOD_put_att_typed_real in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_put_att_text", referenced from:
      ___netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_put_var_1d_eightbytereal", referenced from:
      ___netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_put_var_2d_eightbytereal", referenced from:
      ___netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_put_var_3d_eightbytereal", referenced from:
      ___netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_put_var_eightbytereal", referenced from:
      ___netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_strerror", referenced from:
      ___input_netcdf_MOD_handle_err in libinput_manager.a(input_netcdf.F90.o)
      ___netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o)
      ___netcdf_output_MOD_finalize in liboutput_manager.a(netcdf_output.F90.o)
      _get_dim_id.4982 in liboutput_manager.a(netcdf_output.F90.o)
      ___netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o)
  "___netcdf_MOD_nf90_sync", referenced from:
      ___netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [gotm] Error 1
make[1]: *** [CMakeFiles/gotm_exe.dir/all] Error 2
make: *** [all] Error 2

Any recommendations/ideas why it's failing during the last step? Both my systems (macOS and Ubuntu) are 64bit.

edit: It seems all errors are somehow related to netcdf. When running check_netcdf.sh, I get

robertladwig$ ./check_netcdf.sh 

Checking if CMake can find NetCDF compile and link information ...

-- Found NetCDF: -L/usr/local/Cellar/netcdf/4.7.3_1/lib  
CMake Error at extern/flexout/cmake/Modules/FindNetCDF.cmake:86 (add_library):
  add_library command is not scriptable

The above MUST include - Found NetCDF - to successfully continue

Thanks Robert

bolding commented 4 years ago

Hi Robert

You must subscribe to gotm-users@googlegroups.com in order to hope to get response.

Best regards, Karsten

Den fre. 28. feb. 2020 kl. 20.22 skrev Robert Ladwig < notifications@github.com>:

I'm currently trying to compile GOTM lake v5.3-673 under macOS (Catalina v10.15.3) after having no problems in compiling it under Ubuntu (18.04). I added the line -DGOTM_USE_STIM=on \ to gotm_configure.sh to include ice dynamics.

Now, running gotm_configure.sh works without problems and creates a gfortran directory, but gotm_build.sh reaches 100% and then fails in building the executable:

[100%] Linking Fortran executable gotm Undefined symbols for architecture x86_64: "_netcdf_MOD_nf90_close", referenced from: _netcdf_output_MOD_finalize in liboutput_manager.a(netcdfoutput.F90.o) "netcdf_MOD_nf90_create", referenced from: _netcdf_output_MOD_initialize in liboutput_manager.a(netcdfoutput.F90.o) "netcdf_MOD_nf90_def_dim", referenced from: _get_dim_id.4982 in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90_def_varmanydims", referenced from: netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90enddef", referenced from: netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90_get_atttext", referenced from: input_netcdf_MOD_check_restart_time in libinput_manager.a(input_netcdf.F90.o) "___netcdf_MOD_nf90_get_var_1deightbytereal", referenced from: input_netcdf_MOD_read_restart_data in libinput_manager.a(input_netcdf.F90.o) "_netcdf_MOD_nf90_get_var_eightbytereal", referenced from: _input_netcdf_MOD_read_restart_data in libinput_manager.a(inputnetcdf.F90.o) "netcdf_MOD_nf90_inq_libvers", referenced from: _printversion in libgotm.a(printversion.F90.o) "netcdf_MOD_nf90_inq_varid", referenced from: _input_netcdf_MOD_read_restart_data in libinput_manager.a(input_netcdf.F90.o) _input_netcdf_MOD_check_restart_time in libinput_manager.a(inputnetcdf.F90.o) "netcdf_MOD_nf90_open", referenced from: _input_netcdf_MOD_read_restart_data in libinput_manager.a(inputnetcdf.F90.o) input_netcdf_MOD_check_restart_time in libinput_manager.a(input_netcdf.F90.o) "___netcdf_MOD_nf90_put_att_oneeightbytereal", referenced from: netcdf_output_MOD_put_att_typed_real in liboutput_manager.a(netcdf_output.F90.o) _netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o) "___netcdf_MOD_nf90_put_att_onefourbyteint", referenced from: netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90_put_att_onefourbytereal", referenced from: netcdf_output_MOD_put_att_typed_real in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90_put_att_text", referenced from: _netcdf_output_MOD_initialize in liboutput_manager.a(netcdfoutput.F90.o) "netcdf_MOD_nf90_put_var_1deightbytereal", referenced from: netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90_put_var_2deightbytereal", referenced from: netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90_put_var_3deightbytereal", referenced from: netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90_put_var_eightbytereal", referenced from: _netcdf_output_MOD_save in liboutput_manager.a(netcdfoutput.F90.o) "netcdf_MOD_nf90_strerror", referenced from: ___input_netcdf_MOD_handle_err in libinput_manager.a(inputnetcdf.F90.o) netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o) _netcdf_output_MOD_finalize in liboutput_manager.a(netcdf_output.F90.o) _get_dim_id.4982 in liboutput_manager.a(netcdfoutput.F90.o) netcdf_output_MOD_initialize in liboutput_manager.a(netcdf_output.F90.o) "_netcdf_MOD_nf90sync", referenced from: netcdf_output_MOD_save in liboutput_manager.a(netcdf_output.F90.o) ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make[2]: [gotm] Error 1 make[1]: [CMakeFiles/gotm_exe.dir/all] Error 2 make: *** [all] Error 2

Any recommendations/ideas why it's failing during the last step? Both my systems (macOS and Ubuntu) are 64bit.

Thanks Robert

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-- Karsten Bolding karsten@bolding-bruggeman.com +4564422058

lexiemerk commented 9 months ago

Hi! Was this ever resolved? I have run into the same issue.

bolding commented 9 months ago

Hello

I'm not sure if it was resolved - but I do remember that the NetCDF link information was not included properly on Mac. Whether this has been solved or not - I don't know. It is also outside what can be fixed in GOTM. I've have an old Mac for testing purposes - and I don't have the problem.

Karsten

robertladwig commented 9 months ago

I did solve my issues back then by specifying the cmake command: cmake ~/GOTM/code -DCMAKE_EXE_LINKER_FLAGS="-lnetcdff -lnetcdf"

Here's the link to the google groups thread: https://groups.google.com/g/gotm-users/c/I5ApEpqt6YA/m/STUl4DGoBgAJ

bolding commented 9 months ago

Hi

The two errors are related but not quite the same. Anyway the solution for the first problem can be used to solve the other.

Try: nc-config --libs -L/usr/local/Cellar/netcdf/4.9.2_1/lib -lnetcdf

The first is the folder where the netcdf C library is.

cmake -B ./build -S . -DGOTM_USE_FABM=off -DCMAKE_EXE_LINKER_FLAGS="-L/usr/local/Cellar/netcdf/4.9.2_1/lib

will create the build environment in the build folder.

For me compilation passes the issue with -lnetcdf. Unfortunately, another error comes up.

Undefined symbols for architecture x86_64: "_reporterror", referenced from: ___settings_MOD_type_input_create in libconfig.a(settings.F90.o) ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status

I'm not sure what to do with this one.

Karsten

bolding commented 9 months ago

thanks to Robert for digging up the solution