bio models give a build error: missing separator

[troy_rob]

Hi all,
I am new to the game.
I have successfully compiled and run the default UPWELLING case and am now trying to get one of the biological models running to no avail.
When I try compiling any of the biological models (ecosim, bio_fennel, bio_toy) I get an error: make_macros.mk:1: *** missing separator. Stop.

When I check this file I find:
SUBROUTINE biology (ng, tile)
!
!svn
...

I cannot see what the problem is with line 1.
I been trying to compile using the build.bash script in a separate Projects directory which worked for the default UPWELLING case.

Can anyone help me out?


Troy

[kate]

The problem is not in biology.F, but in make_macros.mk. Mine looks like:

Code: Select all

pingo5 1002% more Build/make_macros.mk
  USE_ADJOINT :=
  USE_TANGENT :=
  USE_REPRESENTER :=
  USE_SEAICE := on
  USE_WRF :=
  USE_SWAN :=
  USE_REFDIF :=
  USE_ARPACK :=
  USE_MCT :=
  USE_ESMF :=

How about yours?

[troy_rob]

Thanks for the reply Kate,

Yes, I had seen previous postings about extraneous text in the make_macros.mk. My post included the first couple of lines from the file. There are two subroutines that keep getting written to the file: biology and biology_tile. 2234 lines of code in total. At the bottom of the file are the same lines as yours. I can remove the file but it is rewritten with these subroutines upon build. Any ideas why?
Cheers
Troy

[kate]

Hmmm. What are you calling your case? The name that's like UPWELLING? If you were to call it ECOSIM, that would be bad. It would go looking for the ecosim.h file to contain the cpp directives and instead find the ecosim.h file containing the biological model. From the top level ROMS directory, doing a listing of */*/*.h will show you the names which are off limits as cpp case names. PRSGRD32, SSW_BBL, and T3DMIX4_GEO would all be problematic.

You deserve an award for finding a new way to get into trouble.

[troy_rob]

Hmm ,
So what then do the instructions:
"set BPARNAM correctly and activate the corresponding CPP option" mean?

Set the BPARNAM value to ECOSIM in the ocean.in file
And then I thought set ROMS_APPLICATION=ECOSIM in the build.bash script?
No?

Troy

[kate]

What exactly are you reading? What should be done is to change UPWELLING to say TROY_TEST, then copy upwelling.h to troy_test.h. Now in troy_test.h, change the cppdefs, so you would #define ECOSIM in that file. We are using the C preprocessor to do conditional compilation.

[robertson]

Troy,

So what then do the instructions:
"set BPARNAM correctly and activate the corresponding CPP option" mean?

BPARNAM is the location and name of your biology input parameters file. An example for EcoSim is can be found at ROMS/External/ecosim.in. I would suggest copying this file to your project directory and setting BPARNAM to ecosim.in. Then as Kate said, #define ECOSIM in your troy_test.h file.

Dave

[troy_rob]

Thanks,
I had got bio_fennel to compile and run by setting MY_CPP_FLAGS="-DBIO_FENNEL" and modifying the ocean.in to use the example bio_Fennel.in file.
I am starting to get a handle on what's happening.
I will have a go as you suggest with ECOSIM.

I would recommend that some sort of high-level description or flow diagram of the ROMS process might help to give new users some sort of overview on what's happening. I have dug threw the wiki but am still left in the dark about many aspects of how it all works (time to start reading code). Possibly that is just because I am not from either an ocean physics or modelling background.

Thanks for your help
Troy

[kate]

It's because the wiki is an unfunded extra in which only those who already know too much have write access.