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revision 1.1 by dimitri, Wed Sep 17 21:45:51 2003 UTC revision 1.26 by dimitri, Thu Nov 4 13:22:09 2004 UTC
# Line 3  Ocean Inversion Project Line 3  Ocean Inversion Project
3    
4  Instructions for using pkg/ptracers to compute tracer  Instructions for using pkg/ptracers to compute tracer
5  Green's functions for Gruber's ocean inversion project  Green's functions for Gruber's ocean inversion project
6  (http://quercus.igpp.ucla.edu/OceanInversion/).  (see quercus.igpp.ucla.edu/OceanInversion/ for details).
7    
8  =====================================  Preprocessed OceanInversion input files are available
9    under directories region_mask, takahashi, and
10  To run a pkg/ptracers test case using salt initial and boundary conditions:  atm_co2 in this package.  All netcdf input files
11    have been converted to binary format in order to avoid
12    having to link netcdf library with MITgcm code.  See
13    respective README files in each directory for details.
14   cd MITgcm/bin  
15   cp ../verification/global_with_exf/code/* .  
16   cp ../code/.genmakerc .  ===============================================
17   cp ../code/* .  First check that pkg/ptracers works OK by using
18   cp ../code/ptracers_forcing.F.test ptracers_forcing.F  salinity initial and boundary conditions
19   cp ../code/ptracers_init.F.test ptracers_init.F  ===============================================
20   cp ../code/ptracers_read_mask.F.test ptracers_read_mask.F  
21   ../tools/genmake  1 ===> get MITgcm code from cvs repository
22    
23     cvs co -r checkpoint51n_branch MITgcm_code
24     cvs co -r checkpoint51n_branch MITgcm/verification/testreport
25     cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf
26    
27    2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
28    
29     cd MITgcm
30     cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project
31    
32    3 ===> compile and link
33    
34     mkdir bin exe
35     cd bin
36     \cp ../verification/global_with_exf/code/* .
37     \cp ../ocean_inversion_project/code/* .
38     \rm ptracers_*.F PTRACERS_OPTIONS.h
39     ../tools/genmake2
40       (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
41       (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
42   make depend   make depend
43   make   make -j 16
  cd ../exe  
  cp ../verification/global_with_exf/input/* .  
  cp ../input/* .  
  cp ../input/data.ptracers.test data.ptracers  
  mitgcmuv > output .txt  
   
 ===> check that PTRACER output is identical to salinity output  
44    
45   diff PTRACER30.0000000020.001.001.data PTRACER01.0000000020.001.001.data  4 ===> execute
  diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data  
46    
47  ===> examine interpolation output for 30-region mask   cd ../exe
48     \cp ../verification/global_with_exf/input/eedata .
49     \cp ../verification/global_with_exf/input/data.* .
50     \cp ../verification/global_with_exf/input/POLY3.COEFFS .
51     \ln -sf ../verification/global_with_exf/input/*.bin .
52     \cp ../ocean_inversion_project/input/* .
53     \cp data.test data
54     \cp data.ptracers.test data.ptracers
55     ./mitgcmuv >! output.txt
56    
57   matlab  5 ===> check that PTRACER output and salinity output are identical.
  mask=zeros(94,44,30);  
  load fort.10  
  for i=1:length(fort)  
   mask(fort(i,2)+2,fort(i,3)+2,fort(i,1))=fort(i,4);  
  end  
  for i=1:30  
   mypcolor(mask(3:92,3:42,i)');  
   colorbar,title(i),pause  
  end  
  mypcolor(sum(mask,3)'); colorbar  
58    
59  =====================================   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
60     diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data
61     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
62     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
63    
64    
65  Global ocean experiment with ptracers  ==========================================================
66  =====================================  MPI instructions for carrying out a 3000-year quasi-stationary
67    integration using the global_ocean.90x40x15 configuration.
68    ==========================================================
69    
70     cd MITgcm/exe
71     rm *
72     cd ../bin
73     rm *
74     cp ../verification/global_with_exf/code/* .
75     cp ../ocean_inversion_project/code/* .
76     rm PTRACERS_OPTIONS.h
77     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
78     cp SIZE.h_mpi SIZE.h
79     ../tools/genmake2
80       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
81     make depend
82     make
83     cd ../exe
84     cp ../verification/global_with_exf/input/eedata .
85     cp ../verification/global_with_exf/input/data.* .
86     cp ../verification/global_with_exf/input/POLY3.COEFFS .
87     ln -sf ../verification/global_with_exf/input/*.bin .
88     cp ../ocean_inversion_project/input/* .
89     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
90     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
91     cp data.stationary.1 data
92     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
93       (on orion: qsub job.orion)
94    
95    
96    ==========================================================
97    MPI instructions for carrying out time-dependent, 1765-2005,
98    anthropogenic carbon perturbation tracer experiments using
99    the global_ocean.90x40x15 configuration.
100    ==========================================================
101    
102     cd MITgcm/exe
103     rm *
104     cd ../bin
105     rm *
106     cp ../verification/global_with_exf/code/* .
107     cp ../ocean_inversion_project/code/* .
108     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
109     cp SIZE.h_mpi SIZE.h
110     ../tools/genmake2
111       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
112     make depend
113     make
114     cd ../exe
115     cp ../verification/global_with_exf/input/eedata .
116     cp ../verification/global_with_exf/input/data.* .
117     cp ../verification/global_with_exf/input/POLY3.COEFFS .
118     ln -sf ../verification/global_with_exf/input/*.bin .
119     cp ../ocean_inversion_project/input/* .
120     cp data.1765-2005 data
121     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
122     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
123     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
124     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
125       (on orion: qsub job.orion.td)
126    
127    
128    ==========================================================
129    Instructions for carrying out time-dependent, 1765-2005,
130    anthropogenic carbon perturbation tracer experiments using
131    global_ocean.90x40x15 configuration and netcdf output.
132    This assumes that the appropriate libnetcdf.a exists
133    and that it be specified in the genmake2 option file.
134    ==========================================================
135    
136     cd MITgcm/exe
137     rm *
138     cd ../bin
139     rm *
140     cp ../verification/global_with_exf/code/* .
141     cp ../ocean_inversion_project/code/* .
142     cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
143     cp ../ocean_inversion_project/write_netCDF/*  .
144     \rm mk_output.F
145    
146  ===> set up and integrate 30-tracer computation  ### need customized option file; example below is for nireas
147     ../tools/genmake2 -of linux_ia32_g77_netcdf
148    
  cd MITgcm/bin  
  cp ../verification/global_with_exf/code/* .  
  cp ../code/.genmakerc .  
  cp ../code/* .  
  ../tools/genmake  
149   make depend   make depend
150   make   make
151   cd ../exe   cd ../exe
152   cp ../verification/global_with_exf/input/* .   cp ../verification/global_with_exf/input/eedata .
153   cp ../input/* .   cp ../verification/global_with_exf/input/data.* .
154   mitgcmuv > output .txt   cp ../verification/global_with_exf/input/POLY3.COEFFS .
155     ln -sf ../verification/global_with_exf/input/*.bin .
156  ===> look at output   cp ../ocean_inversion_project/input/* .
157     cp data.1765-2005.1 data
158   matlab   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
159   for i=1:30   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
160    tr=readbin(['PTRACER' myint2str(i) ...   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
161                '.0000000020.001.001.data'],[90 40 15],1);   mitgcmuv > output .txt &
162    mypcolor(tr(:,:,2)'), colorbar, pause(1)  
163    
164    ==========================================================
165    Instructions for carrying out time-dependent, 1765-2005,
166    anthropogenic carbon perturbation tracer experiments using
167    the ecco1x1 configuration and netcdf output on columbia.
168    This assumes that the appropriate libnetcdf.a exists
169    and that it be specified in the genmake2 option file.
170    It also assumes that surface forcing files are available
171    in /nobackup2/menemenl/ocmip/iter69
172    ==========================================================
173    
174     cd MITgcm/exe
175     \rm *
176     cd ../bin
177     \rm *
178     \cp ../ocean_inversion_project/code_ecco1x1/* .
179     \cp ../ocean_inversion_project/write_netCDF/*  .
180     \rm mk_output.F
181     \cp SIZE.h.96 SIZE.h
182     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
183     make depend
184     make -j 16
185     cd ../exe
186     \cp ../ocean_inversion_project/input_ecco1x1/* .
187     ln -sf ../../iter69/* .
188     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
189     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
190     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
191     qsub job01
192    
193    
194    ==========================================================
195    Instructions for generating netcdf output files on columbia
196    ==========================================================
197    
198    cd ocean_inversion_project/write_netCDF
199    setenv F_UFMTENDIAN big
200    
201    (check that defaults in  mk_output.F are appropriate)
202    
203    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
204         handle_errors.F write_nc_basisfnctns.F \
205         write_nc_diag_0D.F write_nc_diag_2D.F \
206         -I/u/menemenl/software/netcdf-3.5.0/include \
207         -L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf
208    ./a.out
209    
210    
211    ==========================================================
212    Instructions for generating netcdf output files on orion
213    ==========================================================
214    
215    cd ocean_inversion_project/write_netCDF
216    setenv F_UFMTENDIAN big
217    
218    (check that defaults in  mk_output.F are appropriate)
219    
220    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
221         handle_errors.F write_nc_basisfnctns.F \
222         write_nc_diag_0D.F write_nc_diag_2D.F \
223         -I/u2/dmenem/software/netcdf-3.5.0/include \
224         -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
225    ./a.out
226    
227    
228    ======================================================
229    
230    % some matlab code for looking at fort.10 debug files
231    load fort.10
232    tak=zeros(90,40,12);
233    for n=1:length(fort)
234     m=fort(n,1); i=fort(n,2); j=fort(n,3);
235     if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end
236    end
237    lon=2:4:360; lat=-78:4:78;
238    clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10)
239    caxis([-6 6]), colorbar, plotland
240    
241    % some matlab code for looking at PTRACER output files
242    salt=readbin('S.0000000020.001.001.data',[90 40 15],1);
243    tracer=zeros(90,40,15,30);
244    for i=1:30
245     fn=['PTRACER' myint2str(i) '.0000000020.001.001.data'];
246     tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
247     clf, mypcolor(tracer(:,:,1,i)'); pause(1)
248    end
249    tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)')
250    mypcolor(
251    
252    
253    % some matlab code for checking that one year's worth of
254    % tracer uptake is approximately 1e18 mols.
255    lon=2:4:360; lat=-78:4:78;
256    thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];
257    mask=readbin('hFacC.001.001.data',[90 40 15],1);
258    tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
259    for i=1:30, mydisp(i)
260     fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
261     tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
262     for j=1:length(lat)
263      for k=1:length(thk)
264       sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
265                      thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
266      end
267   end   end
268    end
269    plot(1:30,0*sumtracer,1:30,sumtracer)
270    
271    
272    % check that tracer flux is 1e18 mols / year
273    nb_seconds_per_year=31556880;
274    lon=2:4:360; lat=-78:4:78;
275    mask=readbin('hFacC.data',[90 40 15],1);
276    tracer=zeros(90,40,30); sumtracer=zeros(30,1);
277    for i=1:30, mydisp(i)
278     fn=['PtrFlux' myint2str(i) '.0000000180.data'];
279     tracer(:,:,i)=readbin(fn,[90 40],1);
280     for j=1:length(lat)
281        sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
282            nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
283      end
284    end
285    plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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