This has information about the MITgcm not specific to running on Odyssey or Svante, but which can help you to understand what is going on!

Explanation of directories:

global_oce_cs32 = ocean circulation code

darwin = plankton model (we do not need to run ourselves; we use archived output from previous run)

llc90 = lat-lon-cap (grid setup on surface of earth); 90 is related to the tile size dimensions

How to customize your simulation:

Duration of simulation:

For this you just need to modify the elements listed below within the "data" file: ~username/MITgcm/verification/global_hg_llc90/run/data

• nTimestep: number of timesteps (in hours) you would like your run to be. "nTimestep=8," is great for debugging. "nTimestep=175332," is for 20 years (longest possible simulation).
• taveFreq (length of averaging time for tracer output) and dumpfreq (frequency of output) in seconds (and MUST be 'floating point' - must have a decimal point): set both to 3600. for debugging (once per hour); modify to longer for year-long or multi-year simulations (e.g., 31557600.0 for once per year). 

Turning on and off species/tracers:

Edit the file HG_OPTIONS.h within the "code" directory ~username/MITgcm/verification/global_hg_llc90/code/ to turn on and off things like methylmercury. 

• "define" will turn on options. "undefine" or "undef" will turn them off. **More information will be added here on how to do this and still get your code to compile.**
• If you get a namelist error when you run your code, make sure there is consistency between the files HG_OPTIONS.h and GCHEM_OPTIONS.h (both within code directory) and data, data.ptracers, data.hg, and data.diagnostics (all within run directory). It's possible one of the files is, for example, requiring something like MeHg but it's been undefined in your HG_OPTIONS.h file. 

General help for MITgcm

Join the MITgcm-support mailing list: http://mitgcm.org/mailman/listinfo/mitgcm-support . You can search through the archives for similar problems and email the list when you get compilation or run errors you can't figure out. And don't forget the manual.