Coupled simulation of ice, water column, and sediment biogeochemistry.
- recent gfortran compiler (part of GCC)
- Intel Fortran Compiler version 12.1 or higher
At first you must have compliant compiler, Git, CMake, and NetCDF Fortran library compiled with the same Fortran compiler as used for compiling SPBM. For the VisualStudio solution under Windows pre-compiled NetCDF libraries are provided. In case of you do not use any biogeochemical model you do not need to specify a corresponding environment variable.
Then:
- Download all required programs:
download SPBM, configuration files and data for SPBM;
git clone https://github.com/BottomRedoxModel/SPBM.git
git clone https://github.com/BottomRedoxModel/SPBM_data.git
download FABM from the following repository, that version has SPBM registered as the host program already;
git clone https://github.com/BottomRedoxModel/fabm.git
cd fabm
git checkout spbm
cd ..
download biogeochemistry model BROM;
git clone https://github.com/BottomRedoxModel/brom_niva_module
cd brom_niva_module
git checkout dev-sham
cd ..
- Add FABMDIR, BROMDIR, NetCDF_ROOT, NetCDF_modules environment variables.
For example you can add to ~/.bashrc current lines:
export FABMDIR='/path/to/fabm'
export BROMDIR='/path/to/brom_niva_module'
export NetCDF_ROOT='/path/to/NetCDF/bin'
export NetCDF_modules='/path/to/NetCDF/modules'
NetCDF_ROOT should point to the nf-config location.
NetCDF_modules should point to netcdf module *.mod files location.
For some OS these variables point to the similar location.
Sometimes, in case of installing NetCDF libraries into the standard directory it is not
necessary to specify their location.
Reload .bashrc $ source ~/.bashrc
- Make a build.
Enter SPBM folder and execute $./prepare_build.sh north, it will make a build
directory with all necessary data files.
- Compile the code.
From build folder execute $ make
- Run SPBM:
$ ./SPBM.
SPBM program needs to be launched:
- The data file with forcing (for example
wadden_sea_out.nc); - Two configuration files: SPBM configuration file itself - spbm.yaml and the second FABM configuration file specified in spbm.yaml (for example fabm_brom.yaml).
- Download all required programs:
Right-click in Windows Explorer within the directory where you want to place the SPBM directory, and choose "Git Bash Here", or use PowerShell program. Then input the commands from the previous section.
- Add SPBMDIR environment variable (only if you are going to use pre-compiled NetCDF libraries).
- In Search, search for and then select: Environment variables or something similar
- In the user variables specify the name SPBMDIR and the value path:\to\SPBM
- Make a build.
- Start "CMake"
- Browse the Where is the source code to the path:\to\SPBM\src
- Browse the Where to build the binaries - e.g. path:\to\SPBM\build
- Click the Configure button. Select a build system generator, if you use Intel Visual Fortran with Visual Studio integration and want to use NetCDF libraries that come with SPBM please select a 32-bit generator.
- Now all configuration variables for the build system are listed and you can change them according to your preferences. You need set FABM_BASE variable to the directory where you have downloaded FABM. Then click the Configure button again. Select Advanced option and specify -DFABM_NIVA_BASE to path/to/brom_niva_module also.
- Click the Configure button until no new (red-coloured) configuration variables appear, then press Generate button.
- Compile the code.
After generating the build system, you should build the software. You can do either by opening Visual Studio and choosing Build All (after opening path:\to\SPBM\build\SPBM.sln, right click on SPBM in Solution Explorer and select Set as StartUp Project) or typing make if using a build system based on makefiles.
- Run SPBM.
For the SPBM output files visualisation you can use the python script or any other software recognizing NetCDF files.