MITgcm, 36km resolution, Arctic Ocean regional simulation ‘How to’ guide Dr Jonny Williams, School of Geographical Sciences, Bristol University, UK jonny.williams@bristol.ac.uk 1. cd to your MITgcm central directory and check out the code and (some of the) required input files a. cvs co -d cs_36km_tutorial MITgcm_contrib/arctic/cs_36km/ 2. cd to this new directory and make a ‘build’ directory 3. Personally I recommend outputting NetCDF files. You will need to do the following if you want to do this a. add a line with “mnc” on it to cs_36km_tutorial/code/packages.conf b. add a line with “useMNC=.TRUE.,” to cs_36km_tutorial/input/data.pkg c. add a “data.mnc” file which you can copy from the input directory of any of the verification experiments that use NetCDF output 4. Compile in the usual way (system dependent) NOTE: the ftp sites listed below are no longer available but the files have been moved to: https://ecco.jpl.nasa.gov/drive/files/ECCO2/Arctic/arctic_36km 5. The following files are all required in the run directory a. the executable you get when compiling “mitgcmuv” b. ftp://ecco2.jpl.nasa.gov/data2/data/runoff/runoff-360x180x12.bin c. ftp://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/*1979* i. note that the following files may need their “.txt” suffixes removed 1. jra25_v10m_1979 2. jra25_u10m_1979 3. jra25_spfh2m_1979 4. jra25_temp2m_1979 d. Also, the run requires the following files which are not included in the ftp://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/ directory (I have simply created cymbolic links to the 1979 equivalents). i. jra25_dlw_1978 ii. jra25_dsw_1978 iii. jra25_rain_1978 e. ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/* 6. There are some duplicate file names in ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/ and cs_36km_tutorial/input and it is crucial that those in the latter are used. I have done this by copying them to my run directory (platform dependent) second to automatically overwrite the other ones. 7. The model also requires several files which need to be renamed and so I have created symbolic links to them. a. ln -s OBWv_arctic_210x192.bin OBWv_arctic_210x192_19792014m.bin b. ln -s OBWu_arctic_210x192.bin OBWu_arctic_210x192_19792014m.bin c. ln -s OBWt_arctic_210x192.stable OBWt_arctic_210x192_19792014m.stable d. ln -s OBWt_arctic_210x192.bin OBWt_arctic_210x192_19792014m.bin e. ln -s OBWs_arctic_210x192.stable OBWs_arctic_210x192_19792014m.stable f. ln -s OBWs_arctic_210x192.bin OBWs_arctic_210x192_19792014m.bin g. ln -s OBNv_arctic_210x192.bin OBNv_arctic_210x192_19792014m.bin h. ln -s OBNu_arctic_210x192.bin OBNu_arctic_210x192_19792014m.bin i. ln -s OBNt_arctic_210x192.stable OBNt_arctic_210x192_19792014m.stable j. ln -s OBNt_arctic_210x192.bin OBNt_arctic_210x192_19792014m.bin k. ln -s OBNs_arctic_210x192.stable OBNs_arctic_210x192_19792014m.stable l. ln -s OBNs_arctic_210x192.bin OBNs_arctic_210x192_19792014m.bin m. ln -s OBEv_arctic_210x192.bin OBEv_arctic_210x192_19792014m.bin n. ln -s OBEu_arctic_210x192.bin OBEu_arctic_210x192_19792014m.bin o. ln -s OBEt_arctic_210x192.stable OBEt_arctic_210x192_19792014m.stable p. ln -s OBEt_arctic_210x192.bin OBEt_arctic_210x192_19792014m.bin q. ln -s OBEs_arctic_210x192.stable OBEs_arctic_210x192_19792014m.stable r. ln -s OBEs_arctic_210x192.bin OBEs_arctic_210x192_19792014m.bin 8. I suggest changing the following in the “data” file just to get you going a. endtime=86400., i. i.e. 1 day in seconds b. dumpFreq = 2400., i. i.e. outputting data on every timestep, i.e. every 40 minutes in seconds 9. Submit the job (platform dependent) 10. Note that the NetCDF output from this simulation will consist of one file for each processor (80 by default here, nPx × nPy in the cs_36km_tutorial/code/SIZE.h file). Acknowledgments Getting this simulation to run would not have been possible without Fanny Monteiro in the author’s home institution, members of the MITgcm-support online community and in particular, Dimitris Menemenlis, Renske Gelderloos and Patrick Heimbach. ======================= Directory contents for ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/ Matlab script "mk_run_template2.m" was used to generate many of the model input files described below. Grid information files needed when OLD_GRID_IO option is defined in CPP_OPTIONS.h. See GRID.h for a digram of various distances. LONC.bin longitude east of cell center LATC.bin latitude north of cell center LONG.bin longitude east of southwest corner of cell LATG.bin latitude north of southwest corner of cell DYF.bin meridional distance in m between V-points DXF.bin zonal distance in m between U-points DYU.bin meridional distance in m between U-points DXV.bin zonal distance in m between V-points DYC.bin meridional distance in m between tracer points DXC.bin zonal distance in m between tracer points DYG.bin meridional distance in m between cell corners DXG.bin zonal distance in m between cell corners RAZ.bin vertical face area in m^2 for vorticity points RAW.bin vertical face area in m^2 for u cells RAS.bin vertical face area in m^2 for v cells RA.bin vertical face area in m^2 for tracer cells Model bathymetry, initial, and surface boundary condition files. ETOPO2_210x192_arctic model bathymetry (m) WGHC_S_210x192x50_arctic initial salinity (g/kg) WGHC_T_210x192x50_arctic initial potential temperature (deg C) AREA_210x192_arctic.cube81 initial ice concentration (fractional >=0, <=1) HEFF_210x192_arctic.cube81 initial effective sea ice thickness (m) HSALT_210x192_arctic.cube81 initial effective sea ice salinity (g/m^2) HSNOW_210x192_arctic.cube81 initial effective snow thickness (m) Open boundary condition files. OBNs_arctic_210x192.stable North open boundary conditions, salinity (g/kg) OBNt_arctic_210x192.stable North open boundary conditions, temperature (deg C) OBNu_arctic_210x192.bin North open boundary conditions, U-velocity (m/s) OBNv_arctic_210x192.bin North open boundary conditions, V-velocity (m/s) OBEs_arctic_210x192.stable South open boundary conditions, salinity (g/kg) OBEt_arctic_210x192.stable South open boundary conditions, temperature (deg C) OBEu_arctic_210x192.bin South open boundary conditions, U-velocity (m/s) OBEv_arctic_210x192.bin South open boundary conditions, V-velocity (m/s) OBWs_arctic_210x192.stable West open boundary conditions, salinity (g/kg) OBWt_arctic_210x192.stable West open boundary conditions, temperature (deg C) OBWu_arctic_210x192.bin West open boundary conditions, U-velocity (m/s) OBWv_arctic_210x192.bin West open boundary conditions, V-velocity (m/s) Runtime parameter files. eedata data data.pkg data.cal data.exf data.gmredi data.seaice data.obcs data.kpp data.salt_plume data.diagnostics