/[MITgcm]/MITgcm_contrib/ocean_inversion_project/README
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revision 1.6 by dimitri, Thu Sep 25 03:01:59 2003 UTC revision 1.26 by dimitri, Thu Nov 4 13:22:09 2004 UTC
# Line 20  salinity initial and boundary conditions Line 20  salinity initial and boundary conditions
20    
21  1 ===> get MITgcm code from cvs repository  1 ===> get MITgcm code from cvs repository
22    
23   CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack   cvs co -r checkpoint51n_branch MITgcm_code
24   cvs login ( CVS password: cvsanon )   cvs co -r checkpoint51n_branch MITgcm/verification/testreport
25   cvs co MITgcm   cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf
26    
27  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
28    
# Line 31  salinity initial and boundary conditions Line 31  salinity initial and boundary conditions
31    
32  3 ===> compile and link  3 ===> compile and link
33    
34     mkdir bin exe
35   cd bin   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
43     make -j 16
44    
45    4 ===> execute
46    
47     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    5 ===> check that PTRACER output and salinity output are identical.
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    ==========================================================
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/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
75   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
76   rm ptracers_*.F   rm PTRACERS_OPTIONS.h
77   ../tools/genmake   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   make depend
82   make   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    
 4 ===> execute  
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   cd ../exe
115   cp ../verification/global_with_exf/input/eedata .   cp ../verification/global_with_exf/input/eedata .
116   cp ../verification/global_with_exf/input/data.* .   cp ../verification/global_with_exf/input/data.* .
117   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
118   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
119   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
120   cp data.test data   cp data.1765-2005 data
121   cp data.ptracers.test data.ptracers   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
122   mitgcmuv > output.txt   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
123       ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
124  5 ===> check that PTRACER output and salinity output are identical.   mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
125       (on orion: qsub job.orion.td)
  diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data  
  diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data  
126    
127    
128  ==========================================================  ==========================================================
129  Instructions for carrying out a 3000-year quasi-stationary  Instructions for carrying out time-dependent, 1765-2005,
130  integration using the global_ocean.90x40x15 configuration.  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    
 1 ===> compile, link, and execute  
   
136   cd MITgcm/exe   cd MITgcm/exe
137   rm *   rm *
138   cd ../bin   cd ../bin
139   rm *   rm *
140   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
141   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
142   ../tools/genmake   cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
143     cp ../ocean_inversion_project/write_netCDF/*  .
144     \rm mk_output.F
145    
146    ### need customized option file; example below is for nireas
147     ../tools/genmake2 -of linux_ia32_g77_netcdf
148    
149   make depend   make depend
150   make   make
151   cd ../exe   cd ../exe
# Line 81  integration using the global_ocean.90x40 Line 154  integration using the global_ocean.90x40
154   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
155   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
156   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
157     cp data.1765-2005.1 data
158   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
159   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
160     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
161   mitgcmuv > output .txt &   mitgcmuv > output .txt &
162    
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  % some matlab code for looking at fort.10 debug files
# Line 115  mypcolor( Line 254  mypcolor(
254  % tracer uptake is approximately 1e18 mols.  % tracer uptake is approximately 1e18 mols.
255  lon=2:4:360; lat=-78:4:78;  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];  thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];
257  tracer=zeros(90,40,15,30); sumtracer1=zeros(30,1);  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)  for i=1:30, mydisp(i)
260   fn=['PTRACER' myint2str(i) '.0000000180.001.001.data'];   fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
261   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
262   for x=1:length(lon)   for j=1:length(lat)
263    for y=1:length(lat)    for k=1:length(thk)
264     for z=1:length(thk)     sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
265      sumtracer1(i) = sumtracer1(i) + tracer(x,y,z,i) * ...                    thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
                     thk(z) * (4*1.113195e+05)^2 * cos(pi*lat(y)/180);  
    end  
266    end    end
267   end   end
268  end  end
269    plot(1:30,0*sumtracer,1:30,sumtracer)
270    
271  % some matlab code for checking that one year's worth of  
272  % tracer uptake is approximately 1e18 mols.  % check that tracer flux is 1e18 mols / year
273    nb_seconds_per_year=31556880;
274  lon=2:4:360; lat=-78:4:78;  lon=2:4:360; lat=-78:4:78;
275  thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];  mask=readbin('hFacC.data',[90 40 15],1);
276  tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);  tracer=zeros(90,40,30); sumtracer=zeros(30,1);
277  for i=1:30, mydisp(i)  for i=1:30, mydisp(i)
278   fn=['PTRACER' myint2str(i) '.0000003600.001.001.data'];   fn=['PtrFlux' myint2str(i) '.0000000180.data'];
279   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,i)=readbin(fn,[90 40],1);
280   for j=1:length(lat)   for j=1:length(lat)
281    for k=1:length(thk)      sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
282     sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i)) * ...          nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
                   thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180);  
283    end    end
  end  
284  end  end
285  plot(1:30,0*sumtracer,1:30,sumtracer)  plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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