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 IPBM. For the VisualStudio solution under Windows pre-compiled NetCDF libraries are provided.
Then:
- Download all required programs into the one folder:
download IPBM
$ git clone https://github.com/limash/IPBM.git
download FABM and switch to dev-sham branch
$ git clone https://github.com/limash/FABM.git --branch dev-sham
download biogeochemistry model and switch to dev-sham branch
$ git clone https://github.com/limash/brom_niva_module.git --branch dev-sham
and download ecosystem model
$ git clone https://github.com/limash/ERSEM.git
- Add FABMDIR and NetCDF_ROOT environment variables
For example you can add to ~/.bashrc current lines:
export FABMDIR='/path/to/FABM'
export NetCDF_ROOT='/path/to/NetCDF/bin'
Don't forget reload .bashrc $ source ~/.bashrc
- Make a build
Enter IPBM folder and execute $ bash build_release.sh
- Compile the code
From build folder execute $ make
- Run IPBM
From build folder execute $ ./IPBM
- Download all required programs
Right-click in Windows Explorer within the directory where you want to place the IPBM directory, and choose "Git Bash Here", or use PowerShell program. In the terminal that appears to download IPBM type:
$ git clone https://github.com/limash/IPBM.git
then download FABM and switch to dev-sham branch
$ git clone https://github.com/limash/FABM.git --branch dev-sham
download biogeochemistry model and switch to dev-sham branch
$ git clone https://github.com/limash/brom_niva_module.git --branch dev-sham
and download ecosystem model
$ git clone https://github.com/limash/ERSEM.git
if using other software, use these URLs.
- Add IPBMDIR environment variable (only if you are going to use pre-compiled NetCDF libraries)
- In Search, search for and then select: System (Control Panel)
- Click the Advanced system settings link
- Click Environment Variables. In the section System Variables click New
- In the New System Variable specify the name IPBMDIR and the value path:\to\IPBM
- Make a build
- Start "CMake"
- Browse the Where is the source code to the path:\to\IPBM\src
- Browse the Where to build the binaries - e.g. path:\to\IPBM\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 IPBM 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. Specify FABM_ERSEM_BASE as well. Then click the Configure button again. Select Advanced option and specify -DFABM_NIVA_BASE to
path/to/brom_niva_modulealso. - 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\IPBM\build\IPBM.sln, right click on IPBM in Solution Explorer and select Set as StartUp Project) or typing make if using a build system based on makefiles.
- Run IPBM
Now you have IPBM.exe file in your path:\to\IPBM\build\Debug(Release) directory. It needs fabm.yaml and KaraSea.nc files as input data. You can find it in ..\IPBM\data folder. In case of running IPBM under Visual Studio remember to specify the working directory (..\IPBM\data).
For the IPBM output files visualisation you can use: https://github.com/lisapro/ice_brom_pic