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Fri Oct 25 23:53:10 2013 UTC (11 years, 8 months ago) by dimitri
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adding Jonny Williams' instructions

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     5. The following files are all required in the run directory
22     a. the executable you get when compiling “mitgcmuv”
23     b. http://ecco2.jpl.nasa.gov/data2/data/runoff/runoff-360x180x12.bin
24     c. http://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/*1979*
25     i. note that the following files may need their “.txt” suffixes removed
26     1. jra25_v10m_1979
27     2. jra25_u10m_1979
28     3. jra25_spfh2m_1979
29     4. jra25_temp2m_1979
30     d. Also, the run requires the following files which are not included in the
31     http://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/ directory (I have simply created
32     cymbolic links to the 1979 equivalents).
33     i. jra25_dlw_1978
34     ii. jra25_dsw_1978
35     iii. jra25_rain_1978
36     e. http://ecco2.jpl.nasa.gov/data1/arctic/run_template2/*
37    
38     6. There are some duplicate file names in
39     http://ecco2.jpl.nasa.gov/data1/arctic/run_template2/ and cs_36km_tutorial/input and it is
40     crucial that those in the latter are used. I have done this by copying them to my run
41     directory (platform dependent) second to automatically overwrite the other ones.
42    
43     7. The model also requires several files which need to be renamed and so I have created
44     symbolic links to them.
45     a. ln -s OBWv_arctic_210x192.bin OBWv_arctic_210x192_19792014m.bin
46     b. ln -s OBWu_arctic_210x192.bin OBWu_arctic_210x192_19792014m.bin
47     c. ln -s OBWt_arctic_210x192.stable OBWt_arctic_210x192_19792014m.stable
48     d. ln -s OBWt_arctic_210x192.bin OBWt_arctic_210x192_19792014m.bin
49     e. ln -s OBWs_arctic_210x192.stable OBWs_arctic_210x192_19792014m.stable
50     f. ln -s OBWs_arctic_210x192.bin OBWs_arctic_210x192_19792014m.bin
51     g. ln -s OBNv_arctic_210x192.bin OBNv_arctic_210x192_19792014m.bin
52     h. ln -s OBNu_arctic_210x192.bin OBNu_arctic_210x192_19792014m.bin
53     i. ln -s OBNt_arctic_210x192.stable OBNt_arctic_210x192_19792014m.stable
54     j. ln -s OBNt_arctic_210x192.bin OBNt_arctic_210x192_19792014m.bin
55     k. ln -s OBNs_arctic_210x192.stable OBNs_arctic_210x192_19792014m.stable
56     l. ln -s OBNs_arctic_210x192.bin OBNs_arctic_210x192_19792014m.bin
57     m. ln -s OBEv_arctic_210x192.bin OBEv_arctic_210x192_19792014m.bin
58     n. ln -s OBEu_arctic_210x192.bin OBEu_arctic_210x192_19792014m.bin
59     o. ln -s OBEt_arctic_210x192.stable OBEt_arctic_210x192_19792014m.stable
60     p. ln -s OBEt_arctic_210x192.bin OBEt_arctic_210x192_19792014m.bin
61     q. ln -s OBEs_arctic_210x192.stable OBEs_arctic_210x192_19792014m.stable
62     r. ln -s OBEs_arctic_210x192.bin OBEs_arctic_210x192_19792014m.bin
63    
64     8. I suggest changing the following in the “data” file just to get you going
65     a. endtime=86400.,
66     i. i.e. 1 day in seconds
67     b. dumpFreq = 2400.,
68     i. i.e. outputting data on every timestep, i.e. every 40 minutes in
69     seconds
70    
71     9. Submit the job (platform dependent)
72    
73     10. Note that the NetCDF output from this simulation will consist of one file for each processor
74     (80 by default here, nPx × nPy in the cs_36km_tutorial/code/SIZE.h file).
75    
76     Acknowledgments
77     Getting this simulation to run would not have been possible without Fanny Monteiro in the author’s
78     home institution, members of the MITgcm-support online community and in particular, Dimitris
79     Menemenlis, Renske Gelderloos and Patrick Heimbach.

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