Problem with MEGAN compiling

[s.e.ne...@gmail.com]

Hello everyone,

 

I have faced a problem in compiling MEGAN model. I have loaded required libraries (NETcdf and PGI compiler). However,

> make_util megan_bio_emiss

command still doesn't work. The error is:

command not found.

I have tried other ways such as 
> make -f make_util
and also other ways but I cannot compile MEGAN yet. I was wondering if anyone had similar problem and could help me to find how can I compile MEGAN.
Thanks in advance for your help.


Best,

Soroush

[Stacy Walters]

Soroush,

Please try the command:

./make_util megan_bio_emiss

Stacy

[Soroush E. Neyestani]

Thank you for the reply Stacy. But it doesn't help. Now the permission denied error appears. I have also tried it on my personal computer as root, but I received the same error. So I think the problem might be from the code and not from the user access.

I would appreciate it if you can give other suggestions for this problem.

Thanks,

Soroush

[Stacy Walters]

Soroush,

The error you are getting is a system level error.  Basically the op system can not find

the command

make_util

Can you verify that this script file, make_util, is in the directory you are trying to run from.

I assure you this is not an error with the code.

Stacy

[Soroush E. Neyestani]

Yes, make_util script file is in the run directory.

Anyway thanks for the comment. I am looking for the solution and I'll share it if find anything.

Soroush

[Guido Conto Echeverria]

Hello
Soroush

If you use ubuntu try to get permissions to the file make_util, with the command

>sudo chmod 777 make_util

Then you run it, it should work.

My problem is that running does not generate the executable megan_bio_emiss. I have configured netcdf correctly, but I do not know why the program looks for another location that I have not written in the make_util and I get the following error:

=============================================================================
Using gfortran fortran compiler
=============================================================================
=============================================================================
netcdf top level directory = /home/guido/Build_WRF/LIBRARIES/netcdf
=============================================================================
gfortran -g -ffree-line-length-none -c -I/home/guido/Build_WRF/LIBRARIES/netcdf/include misc_definitions_module.f90
gfortran -g -ffree-line-length-none -c -I/home/guido/Build_WRF/LIBRARIES/netcdf/include constants_module.f90
gfortran -g -ffree-line-length-none -c -I/home/guido/Build_WRF/LIBRARIES/netcdf/include bio_types.f90
gfortran -g -ffree-line-length-none -c -I/home/guido/Build_WRF/LIBRARIES/netcdf/include area_mapper.f90
gfortran -g -ffree-line-length-none -c -I/home/guido/Build_WRF/LIBRARIES/netcdf/include bio_emiss.f90
gfortran -o megan_bio_emiss misc_definitions_module.o constants_module.o bio_types.o area_mapper.o bio_emiss.o -L/home/guido/Build_WRF/LIBRARIES/netcdf/lib -lnetcdf -lnetcdff
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_text_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-attio.c:14: undefined reference to `nc_put_att_text'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_text_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-attio.c:21: undefined reference to `nc_get_att_text'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_put_att_int1_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-attio.c:29: undefined reference to `nc_put_att_schar'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-attio.o): In function `nf_get_att_int1_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-attio.c:47: undefined reference to `nc_get_att_schar'
\
\
\
\

/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_int_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-varaio.c:115: undefined reference to `nc_get_vara_int'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_real_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-varaio.c:130: undefined reference to `nc_put_vara_float'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_real_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-varaio.c:142: undefined reference to `nc_get_vara_float'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_double_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-varaio.c:150: undefined reference to `nc_put_vara_double'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_double_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-varaio.c:157: undefined reference to `nc_get_vara_double'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_put_vara_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-varaio.c:160: undefined reference to `nc_put_vara'
/home/guido/Build_WRF/LIBRARIES/netcdf/lib/libnetcdff.a(fort-varaio.o): In function `nf_get_vara_':
/home/guido/Build_WRF/LIBRARIES/netcdf-4.1.3/fortran/fort-varaio.c:163: undefined reference to `nc_get_vara'
collect2: error: ld returned 1 exit status
Makefile:45: recipe for target 'megan_bio_emiss' failed
make: *** [megan_bio_emiss] Error 1
Failed to build megan_bio_emiss

Someone happened to this by compiling megan bio_emiss, could they help me?
Thank you.

regards,

Guido

[s.e.ne...@gmail.com]

Hi Guido,

Thank you for the comment. for me (on CentOS 6.5) the command for getting permission was a little different:
chmod +x ./make_util
and after that:
./make_util megan_bio_emiss

I had exactly the same error you mentioned on my personal computer (with gfortran compiler). However, when I tried it on another system with PGI compiler, I faced no error. I'm not sure if my compiler (gfortran) is not loaded correctly or the code has problems with gfortran (I have to add that I had no similar problem with compiler for other programs).
Do you have any other system with different compiler?
Sorry that I cannot be more helpful.

Best,
Soroush 

[Guido Conto Echeverria]

Hello Soroush

Very well that you have solved it.

I unfortunately only have fortran compiler, I'll keep trying and reading to see how I can solve it.
Also in the manuals are very persistent in the use of the same compiler for the whole model, so I only have one.

If you know something about MEGAN or MOZART (I have the same problem in both) let me know.

Thank you very much

Best,
Guido