Run SPBM & BROM_biogeochemisty with gfrotran on Windows Subsystem for Linux

1. Install Windows Subsystem for Linux (Microsoft tutorial)

In this example we use Debian. Open bash (command line), create username and password.

The bash will look like: root@some_adress:~#, ending :~# means you are in your working directory.

You should install everything to that folder.

2. Install libraries:

sudo apt-get install gfortran Gfortran

sudo apt-get install libnetcdf-dev libnetcdff-dev Netcdf Libraries for Fortran

sudo apt-get install gitGit to download source code

sudo apt-get install vim Text editor VIM

sudo apt-get -y install cmake Cmake

sudo apt-get install mc Midnight commander (optionally)

3. Clone codes for the model:

SPBM

git clone https://github.com/BottomRedoxModel/SPBM.git
cd SPBM
git checkout [branch for you case scenario]

BROM_BIOGEOCHEMISTRY

git clone https://github.com/BottomRedoxModel/brom_niva_module.git
cd brom_niva_module/
git checkout [branch for you case scenario]

FABM

git clone https://github.com/BottomRedoxModel/fabm.git
cd fabm
git checkout tags/spbm_v0.2 -b spbm_v0.2

Configuration files (for you case,example one is for Arctic)

git clone https://github.com/BottomRedoxModel/data_spbm_laptev.git #for Arctic Case

4. Manage environment variables:

Add FABMDIR, BROMDIR, and NetCDF_ROOT environment variables. Check that you have .bashrc file

ls -a # Prints all files including hidden

Open ~/.bashrc with vim

vim .bashrc

add to ~/.bashrc current lines (anywhere in the file):

export FABMDIR='~/fabm'
export BROMDIR='~/brom_niva_module'

run it

source ~/.bashrc

5. Build solution

Go to SPBM folder cd SPBM, Run bash script build_release.sh to make build

$ bash build_release.sh

it will make a build directory, copy there all necessary data files, and launch cmake to make a build.

6. Compile the code.

Go to SPBM/build and write:

make

7. Run the compiled code.

Now you have executable file SPBM in the ~SPBM/build, run it:

./SPBM

**8. Get and Plot results

The model output consists of 9 files:

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