Installation Issues...

[ge...@stanford.edu]

Hello, 

I've been using the GOTM GUI on my windows machine for some time now, but I'd like to get the regular version working on my Mac, and I'm having some issues with the compiling. I've followed all of the directions on github (https://github.com/gotm-model/code), and am able to get through the configuration step without any issues. However, once I execute $GOTM_BASE/scripts/linux/gotm_build.sh,  I get the following warning:

 f951: Warning: Nonexistent include directory '/Users/gegan/GOTM/code/src/nf-config not yet implemented for cmake builds' [-Wmissing-include-dirs]

and the error:

/Users/gegan/GOTM/code/src/output/netcdf_output.F90:6:7:

    use netcdf

       1

Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No such file or directory

compilation terminated.

make[3]: *** [CMakeFiles/output_manager.dir/output/netcdf_output.F90.o] Error 1

make[2]: *** [CMakeFiles/output_manager.dir/output/netcdf_output.F90.o.provides] Error 2

make[1]: *** [CMakeFiles/output_manager.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs....

[ 93%] Built target meanflow

make: *** [all] Error 2

I have looked through this user group for information on this type of error. I have made sure that I set NETCDF_VERSION = NETCDF4, and I also see that it's suggested that I type in: nf-config --all. This results in:

nf-config not yet implemented for cmake builds

So it seems like the issue may be with my installation of NetCDF...I have tried installing it with both: 

brew install netcdf --with-fortran    and  conda install -c conda-forge netcdf-fortran

But I get the same errors either way. No one else in my group uses GOTM at the moment so I'm at a loss as far as troubleshooting goes. Any further suggestions?

Thanks,

Galen Egan

[Karsten Bolding]

Hello

The problem is not a GOTM issue but a problem with the NetCDF installation - and it must be sorted out first.

On my Mac I get:

ModelGroup-MBP:gotm bold$ type nf-config

nf-config is /opt/local/bin/nf-config

I use port to install additional software. 

Best regards,

Karsten

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Karsten Bolding

kar...@bolding-bruggeman.com

+4564422058

[ge...@stanford.edu]

Thank you Karsten, it was indeed a NetCDF issue. If anyone else is having similar issues, I fixed it by starting from scratch (deleted all GOTM/FABM files, uninstalled ports and netcdf and gfortran), and then installed the newest version of macports. Then I did:

1. sudo port install gcc6

2. sudo port install netcdf-fortran

Then after following the instructions on github it compiled without any errors. 

Thanks!

-Galen

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[Fenjuan Hu]

Hi all

 
I report the same error with homebrew installed netcdf version. It is indeed a netcdf issue,but there's very little information on internet about this issue. I am not an advanced Mac user, and I DO NOT want to mess up with homebrew/macports, and want to just stick to homebrew. And I bileve this is not macports/homebrew issue.
For example, if I just type nf-config in terminal, I got same message:

nf-config not yet implemented for cmake builds

Then I ran nc-config -all, I got:
his netCDF 4.6.0 has been built with the following features:

  --cc        -> /usr/local/Homebrew/Library/Homebrew/shims/super/clang
  --cflags    -> -I/usr/local/Cellar/netcdf/4.6.0/include
  --libs      -> -L/usr/local/Cellar/netcdf/4.6.0/lib -lnetcdf -lhdf5_hl -lhdf5 -lsz -lz -ldl -lm -lcurl

  --has-c++   -> no
  --cxx       ->

  --has-c++4  -> no
  --cxx4      ->

  --has-fortran-> yes
  --fc        -> nf-config not yet implemented for cmake builds
  --fflags    -> nf-config not yet implemented for cmake builds
  --flibs     -> nf-config not yet implemented for cmake builds
  --has-f90   -> nf-config not yet implemented for cmake builds
  --has-f03   -> nf-config not yet implemented for cmake builds

  --has-dap   -> yes
  --has-dap2  -> yes
  --has-dap4  -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-logging-> no
  --has-pnetcdf-> no
  --has-szlib -> no
  --has-cdf5 -> no
  --has-parallel-> no

  --prefix    -> /usr/local/Cellar/netcdf/4.6.0
  --includedir-> /usr/local/Cellar/netcdf/4.6.0/include
  --libdir    -> /usr/local/Cellar/netcdf/4.6.0/lib
  --version   -> netCDF 4.6.0



Notice that the same message appeared with many fortran related settings, such as --has-f90,--has-f03...

Any mac user can help with this?

Best regards
Fen

[Fenjuan Hu]

   
Updated on topic of mac installation problem: nf-config not yet implemented for cmake builds
This is indeed netcdf problem, not gotm problem. But might be useful for other mac-user 'GOTMer' having the same problem. Following Galen's last post, the newest version of netcdf in macports needs to install netcdf-cxx and netcdf-fortran seperately, after installed netcdf.
Therefore, after installing macports,then ran:
1. sudo port install netcdf (after this it will give you information for the next two steps)
2. sudo port install netcdf-gxx
3. sudo port install netcdf-fortran
 
Then it works for me.

PS: I removed all homebrew related installation and homebrew itself, and cleaned all the residuals. Since I could not find way around homebrew way of solving this problem.

Hope more advanced mac user could give a better explaination.


Best regards
Fen