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Revision 1.4 - (hide annotations) (download)
Fri Mar 17 17:01:38 2023 UTC (2 years, 4 months ago) by dimitri
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adding link to ECCO Drive to replace ftp site

1 dimitri 1.1 MITgcm, 36km resolution, Arctic Ocean regional simulation ‘How to’ guide
2    
3     Dr Jonny Williams, School of Geographical Sciences, Bristol University, UK
4     jonny.williams@bristol.ac.uk
5    
6     1. cd to your MITgcm central directory and check out the code and (some of the) required
7     input files
8     a. cvs co -d cs_36km_tutorial MITgcm_contrib/arctic/cs_36km/
9    
10     2. cd to this new directory and make a ‘build’ directory
11    
12     3. Personally I recommend outputting NetCDF files. You will need to do the following if you
13     want to do this
14     a. add a line with “mnc” on it to cs_36km_tutorial/code/packages.conf
15     b. add a line with “useMNC=.TRUE.,” to cs_36km_tutorial/input/data.pkg
16     c. add a “data.mnc” file which you can copy from the input directory of any of the
17     verification experiments that use NetCDF output
18    
19     4. Compile in the usual way (system dependent)
20    
21 dimitri 1.4 NOTE: the ftp sites listed below are no longer available but the files have
22     been moved to: https://ecco.jpl.nasa.gov/drive/files/ECCO2/Arctic/arctic_36km
23    
24 dimitri 1.1 5. The following files are all required in the run directory
25     a. the executable you get when compiling “mitgcmuv”
26 dimitri 1.3 b. ftp://ecco2.jpl.nasa.gov/data2/data/runoff/runoff-360x180x12.bin
27     c. ftp://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/*1979*
28 dimitri 1.1 i. note that the following files may need their “.txt” suffixes removed
29     1. jra25_v10m_1979
30     2. jra25_u10m_1979
31     3. jra25_spfh2m_1979
32     4. jra25_temp2m_1979
33     d. Also, the run requires the following files which are not included in the
34 dimitri 1.3 ftp://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/ directory (I have simply created
35 dimitri 1.1 cymbolic links to the 1979 equivalents).
36     i. jra25_dlw_1978
37     ii. jra25_dsw_1978
38     iii. jra25_rain_1978
39 dimitri 1.3 e. ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/*
40 dimitri 1.1
41     6. There are some duplicate file names in
42 dimitri 1.3 ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/ and cs_36km_tutorial/input and it is
43 dimitri 1.1 crucial that those in the latter are used. I have done this by copying them to my run
44     directory (platform dependent) second to automatically overwrite the other ones.
45    
46     7. The model also requires several files which need to be renamed and so I have created
47     symbolic links to them.
48     a. ln -s OBWv_arctic_210x192.bin OBWv_arctic_210x192_19792014m.bin
49     b. ln -s OBWu_arctic_210x192.bin OBWu_arctic_210x192_19792014m.bin
50     c. ln -s OBWt_arctic_210x192.stable OBWt_arctic_210x192_19792014m.stable
51     d. ln -s OBWt_arctic_210x192.bin OBWt_arctic_210x192_19792014m.bin
52     e. ln -s OBWs_arctic_210x192.stable OBWs_arctic_210x192_19792014m.stable
53     f. ln -s OBWs_arctic_210x192.bin OBWs_arctic_210x192_19792014m.bin
54     g. ln -s OBNv_arctic_210x192.bin OBNv_arctic_210x192_19792014m.bin
55     h. ln -s OBNu_arctic_210x192.bin OBNu_arctic_210x192_19792014m.bin
56     i. ln -s OBNt_arctic_210x192.stable OBNt_arctic_210x192_19792014m.stable
57     j. ln -s OBNt_arctic_210x192.bin OBNt_arctic_210x192_19792014m.bin
58     k. ln -s OBNs_arctic_210x192.stable OBNs_arctic_210x192_19792014m.stable
59     l. ln -s OBNs_arctic_210x192.bin OBNs_arctic_210x192_19792014m.bin
60     m. ln -s OBEv_arctic_210x192.bin OBEv_arctic_210x192_19792014m.bin
61     n. ln -s OBEu_arctic_210x192.bin OBEu_arctic_210x192_19792014m.bin
62     o. ln -s OBEt_arctic_210x192.stable OBEt_arctic_210x192_19792014m.stable
63     p. ln -s OBEt_arctic_210x192.bin OBEt_arctic_210x192_19792014m.bin
64     q. ln -s OBEs_arctic_210x192.stable OBEs_arctic_210x192_19792014m.stable
65     r. ln -s OBEs_arctic_210x192.bin OBEs_arctic_210x192_19792014m.bin
66    
67     8. I suggest changing the following in the “data” file just to get you going
68     a. endtime=86400.,
69     i. i.e. 1 day in seconds
70     b. dumpFreq = 2400.,
71     i. i.e. outputting data on every timestep, i.e. every 40 minutes in
72     seconds
73    
74     9. Submit the job (platform dependent)
75    
76     10. Note that the NetCDF output from this simulation will consist of one file for each processor
77     (80 by default here, nPx × nPy in the cs_36km_tutorial/code/SIZE.h file).
78    
79     Acknowledgments
80     Getting this simulation to run would not have been possible without Fanny Monteiro in the author’s
81     home institution, members of the MITgcm-support online community and in particular, Dimitris
82     Menemenlis, Renske Gelderloos and Patrick Heimbach.
83 dimitri 1.2
84     =======================
85    
86     Directory contents for
87 dimitri 1.3 ftp://ecco2.jpl.nasa.gov/data1/arctic/run_template2/
88 dimitri 1.2
89     Matlab script "mk_run_template2.m" was used to generate many of the model
90     input files described below.
91    
92     Grid information files needed when OLD_GRID_IO option is defined in
93     CPP_OPTIONS.h. See GRID.h for a digram of various distances.
94     LONC.bin longitude east of cell center
95     LATC.bin latitude north of cell center
96     LONG.bin longitude east of southwest corner of cell
97     LATG.bin latitude north of southwest corner of cell
98     DYF.bin meridional distance in m between V-points
99     DXF.bin zonal distance in m between U-points
100     DYU.bin meridional distance in m between U-points
101     DXV.bin zonal distance in m between V-points
102     DYC.bin meridional distance in m between tracer points
103     DXC.bin zonal distance in m between tracer points
104     DYG.bin meridional distance in m between cell corners
105     DXG.bin zonal distance in m between cell corners
106     RAZ.bin vertical face area in m^2 for vorticity points
107     RAW.bin vertical face area in m^2 for u cells
108     RAS.bin vertical face area in m^2 for v cells
109     RA.bin vertical face area in m^2 for tracer cells
110    
111     Model bathymetry, initial, and surface boundary condition files.
112     ETOPO2_210x192_arctic model bathymetry (m)
113     WGHC_S_210x192x50_arctic initial salinity (g/kg)
114     WGHC_T_210x192x50_arctic initial potential temperature (deg C)
115     AREA_210x192_arctic.cube81 initial ice concentration (fractional >=0, <=1)
116     HEFF_210x192_arctic.cube81 initial effective sea ice thickness (m)
117     HSALT_210x192_arctic.cube81 initial effective sea ice salinity (g/m^2)
118     HSNOW_210x192_arctic.cube81 initial effective snow thickness (m)
119    
120     Open boundary condition files.
121     OBNs_arctic_210x192.stable North open boundary conditions, salinity (g/kg)
122     OBNt_arctic_210x192.stable North open boundary conditions, temperature (deg C)
123     OBNu_arctic_210x192.bin North open boundary conditions, U-velocity (m/s)
124     OBNv_arctic_210x192.bin North open boundary conditions, V-velocity (m/s)
125     OBEs_arctic_210x192.stable South open boundary conditions, salinity (g/kg)
126     OBEt_arctic_210x192.stable South open boundary conditions, temperature (deg C)
127     OBEu_arctic_210x192.bin South open boundary conditions, U-velocity (m/s)
128     OBEv_arctic_210x192.bin South open boundary conditions, V-velocity (m/s)
129     OBWs_arctic_210x192.stable West open boundary conditions, salinity (g/kg)
130     OBWt_arctic_210x192.stable West open boundary conditions, temperature (deg C)
131     OBWu_arctic_210x192.bin West open boundary conditions, U-velocity (m/s)
132     OBWv_arctic_210x192.bin West open boundary conditions, V-velocity (m/s)
133    
134     Runtime parameter files.
135     eedata
136     data
137     data.pkg
138     data.cal
139     data.exf
140     data.gmredi
141     data.seaice
142     data.obcs
143     data.kpp
144     data.salt_plume
145     data.diagnostics

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