GENIE BiogemTutorial

Andy Ridgwell (andy@seao2.org)

Exercise 1. Climate-only

Expected learning outcome stuff:

1. Set up and running genie_eb_go_gs_ac_bg
2. Configure data saving (time-slice and time-series operation)
3. Explore basic biogem data output (about the physical climate system)

Instructions

1. First, download the configuration set biogem_exp_1.tar.gz from:
   1. www.seao2.org/genie_workshop/
   2. to $HOME/genie_input
   3. and unpack ($ tar zxf biogem_exp_1.tar.gz)
2. Using a text editor, explore the contents of the tracer selection files: gem_config_atm.par, gem_config_atm.par, gem_config_atm.par
   1. Note that the only tracers selected are temperature and salinity (humidity in the case of the atmospheric tracers).
   2. Also note that in biogem_config.par, no biological option is selected (or rather, the ‘null’ option NONE is selected, with the corresponding biological configuration file biogem_bio_NONE_config.par containing no parameter information.
3. Run the model for 1 year (refer to the rungenie.README file for the description of the options passed to the rungenie configuration script), i.e.:
   1. $ ./rungenie genie_eb_go_gs_ac_bg_itfclsd_08l n 0 1 biogem_exp_1
4. Now browse the results directory: genie_output/genie_eb_go_gs_ac_bg_itfclsd_08l.biogem_exp_1/biogem
   1. The cupboard is (almost) bare. A re-start file has been saved for biogem (biogem), but if you attempt to open either of the the netCDF output files you will get an error message. No data has been saved, for two reasons:
      1. No year has been set for a results time-slice in the file biogem_save_timeslice.dat (in $HOME/genie_input/biogem_exp_1). Actually, you were warned to this fact in the run-time output as biogem was initialized:
         1. WARNING -> Originating location in code [module,subroutine]: biogem_data,sub_init_data_save -> ERROR MESSAGE: No time-slice dates listed in file biogem_save_timeslice.dat fall within the model start and end years -> ERROR ACTION: CONTINUING
      2. No data categories for time-slice saving have been selected in biogem_config.par.
5. Re-run the model, but with a time-slice mid-point of 0.5 years set in biogem_save_timeslice.dat (any earlier or later that this will not work because the integration interval is set as 1.0 years by default in biogem_config.par (near the bottom of the I/O - TIME-SERIES section) and the run is only 1 year long …), and select (as t) ocean 'physical' properties as a time-slice data save in biogem_config.par. Explore the contents of fields_biogem_3d.nc. Note that much of the physical grid information is as dull as ditchwater (and also note that ocn_sal and ocn_temp fields are erroneously created, but with no data saved to them – a bug to be fixed :o) ). Also note that nothing is being saved yet in the 2-D netCDF file: fields_biogem_2d.nc.
6. The important ‘physics’ is saved by selecting miscellaneous properties as a time-slice data save. De-select ocean 'physical' properties and select miscellaneous properties instead and re-run.
7. A second type of data that can be saved is ‘time-series’ data: i.e., time series of global of surface averaged properties. The time-series configuration file: biogem_save_sig.dat is already populated for you. This file contains the mid-point years at which a time-series data point are to be saved. Again the data is time-integrated, with the integration interval specified in biogem_config.par (near the bottom of the I/O - TIME-SERIES section). Try selecting miscellaneous properties time-series data saving and re-run the model. The results directory now contains time-series files in ASCII (plain text) format. There is a header describing the information and units of each column.
8. Do any other playing with the options you like.