/[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 1.27 by dimitri, Sat Nov 20 14:40:47 2004 UTC
# Line 13  having to link netcdf library with MITgc Line 13  having to link netcdf library with MITgc
13  respective README files in each directory for details.  respective README files in each directory for details.
14    
15    
16    Notes and problems:
17    ===================
18    
19    there is problem generating ECCO_MaskAreaBathy.nc on columbia
20    works OK on nireas
21    
22    variable global_mean_conc in 0D output from mk_output.F is
23    screwed up
24    
25    
26    
27  ===============================================  ===============================================
28  First check that pkg/ptracers works OK by using  First check that pkg/ptracers works OK by using
29  salinity initial and boundary conditions  salinity initial and boundary conditions
# Line 20  salinity initial and boundary conditions Line 31  salinity initial and boundary conditions
31    
32  1 ===> get MITgcm code from cvs repository  1 ===> get MITgcm code from cvs repository
33    
34   CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack   cvs co -r checkpoint51n_branch MITgcm_code
35   cvs login ( CVS password: cvsanon )   cvs co -r checkpoint51n_branch MITgcm/verification/testreport
36   cvs co MITgcm   cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf
37    
38  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
39    
# Line 31  salinity initial and boundary conditions Line 42  salinity initial and boundary conditions
42    
43  3 ===> compile and link  3 ===> compile and link
44    
45     mkdir bin exe
46   cd bin   cd bin
47     \cp ../verification/global_with_exf/code/* .
48     \cp ../ocean_inversion_project/code/* .
49     \rm ptracers_*.F PTRACERS_OPTIONS.h
50     ../tools/genmake2
51       (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
52       (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
53     make depend
54     make -j 16
55    
56    4 ===> execute
57    
58     cd ../exe
59     \cp ../verification/global_with_exf/input/eedata .
60     \cp ../verification/global_with_exf/input/data.* .
61     \cp ../verification/global_with_exf/input/POLY3.COEFFS .
62     \ln -sf ../verification/global_with_exf/input/*.bin .
63     \cp ../ocean_inversion_project/input/* .
64     \cp data.test data
65     \cp data.ptracers.test data.ptracers
66     ./mitgcmuv >! output.txt
67    
68    5 ===> check that PTRACER output and salinity output are identical.
69    
70     diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
71     diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data
72     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
73     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
74    
75    
76    ==========================================================
77    MPI instructions for carrying out a 3000-year quasi-stationary
78    integration using the global_ocean.90x40x15 configuration.
79    ==========================================================
80    
81     cd MITgcm/exe
82     rm *
83     cd ../bin
84     rm *
85   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
86   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
87   rm ptracers_*.F   rm PTRACERS_OPTIONS.h
88   ../tools/genmake   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
89     cp SIZE.h_mpi SIZE.h
90     ../tools/genmake2
91       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
92   make depend   make depend
93   make   make
94     cd ../exe
95     cp ../verification/global_with_exf/input/eedata .
96     cp ../verification/global_with_exf/input/data.* .
97     cp ../verification/global_with_exf/input/POLY3.COEFFS .
98     ln -sf ../verification/global_with_exf/input/*.bin .
99     cp ../ocean_inversion_project/input/* .
100     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
101     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
102     cp data.stationary.1 data
103     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
104       (on orion: qsub job.orion)
105    
 4 ===> execute  
106    
107    ==========================================================
108    MPI instructions for carrying out time-dependent, 1765-2005,
109    anthropogenic carbon perturbation tracer experiments using
110    the global_ocean.90x40x15 configuration.
111    ==========================================================
112    
113     cd MITgcm/exe
114     rm *
115     cd ../bin
116     rm *
117     cp ../verification/global_with_exf/code/* .
118     cp ../ocean_inversion_project/code/* .
119     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
120     cp SIZE.h_mpi SIZE.h
121     ../tools/genmake2
122       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
123     make depend
124     make
125   cd ../exe   cd ../exe
126   cp ../verification/global_with_exf/input/eedata .   cp ../verification/global_with_exf/input/eedata .
127   cp ../verification/global_with_exf/input/data.* .   cp ../verification/global_with_exf/input/data.* .
128   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
129   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
130   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
131   cp data.test data   cp data.1765-2005 data
132   cp data.ptracers.test data.ptracers   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
133   mitgcmuv > output.txt   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
134       ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
135  5 ===> check that PTRACER output and salinity output are identical.   mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
136       (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  
137    
138    
139  ==========================================================  ==========================================================
140  Instructions for carrying out a 3000-year quasi-stationary  Instructions for carrying out time-dependent, 1765-2005,
141  integration using the global_ocean.90x40x15 configuration.  anthropogenic carbon perturbation tracer experiments using
142    global_ocean.90x40x15 configuration and netcdf output.
143    This assumes that the appropriate libnetcdf.a exists
144    and that it be specified in the genmake2 option file.
145  ==========================================================  ==========================================================
146    
 1 ===> compile, link, and execute  
   
147   cd MITgcm/exe   cd MITgcm/exe
148   rm *   rm *
149   cd ../bin   cd ../bin
150   rm *   rm *
151   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
152   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
153   ../tools/genmake   cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
154     cp ../ocean_inversion_project/write_netCDF/*  .
155     \rm mk_output.F
156    
157    ### need customized option file; example below is for nireas
158     ../tools/genmake2 -of linux_ia32_g77_netcdf
159    
160   make depend   make depend
161   make   make
162   cd ../exe   cd ../exe
# Line 81  integration using the global_ocean.90x40 Line 165  integration using the global_ocean.90x40
165   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
166   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
167   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
168     cp data.1765-2005.1 data
169   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
170   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
171     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
172   mitgcmuv > output .txt &   mitgcmuv > output .txt &
173    
174    
175    ==========================================================
176    Instructions for carrying out time-dependent, 1765-2005,
177    anthropogenic carbon perturbation tracer experiments using
178    the ecco1x1 configuration and netcdf output on columbia.
179    This assumes that the appropriate libnetcdf.a exists
180    and that it be specified in the genmake2 option file.
181    It also assumes that surface forcing files are available
182    in /nobackup2/menemenl/ocmip/iter69
183    ==========================================================
184    
185     cd MITgcm/exe
186     \rm *
187     cd ../bin
188     \rm *
189     \cp ../ocean_inversion_project/code_ecco1x1/* .
190     \cp ../ocean_inversion_project/write_netCDF/*  .
191     \rm mk_output.F
192     \cp SIZE.h.96 SIZE.h
193     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
194     make depend
195     make -j 16
196     cd ../exe
197     \cp ../ocean_inversion_project/input_ecco1x1/* .
198     ln -sf ../../iter69/* .
199     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
200     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
201     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
202     qsub job01
203    
204    
205    ==========================================================
206    Instructions for generating netcdf output files on columbia
207    ==========================================================
208    
209    cd ocean_inversion_project/write_netCDF
210    setenv F_UFMTENDIAN big
211    
212    (check that defaults in  mk_output.F are appropriate)
213    
214    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
215         handle_errors.F write_nc_basisfnctns.F \
216         write_nc_diag_0D.F write_nc_diag_2D.F \
217         -I/u/menemenl/software/netcdf-3.5.0/include \
218         -L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf
219    ./a.out
220    
221    
222    ==========================================================
223    Instructions for generating netcdf output files on orion
224    ==========================================================
225    
226    cd ocean_inversion_project/write_netCDF
227    setenv F_UFMTENDIAN big
228    
229    (check that defaults in  mk_output.F are appropriate)
230    
231    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
232         handle_errors.F write_nc_basisfnctns.F \
233         write_nc_diag_0D.F write_nc_diag_2D.F \
234         -I/u2/dmenem/software/netcdf-3.5.0/include \
235         -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
236    ./a.out
237    
238    
239  ======================================================  ======================================================
240    
241  % some matlab code for looking at fort.10 debug files  % some matlab code for looking at fort.10 debug files
# Line 115  mypcolor( Line 265  mypcolor(
265  % tracer uptake is approximately 1e18 mols.  % tracer uptake is approximately 1e18 mols.
266  lon=2:4:360; lat=-78:4:78;  lon=2:4:360; lat=-78:4:78;
267  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];
268  tracer=zeros(90,40,15,30); sumtracer1=zeros(30,1);  mask=readbin('hFacC.001.001.data',[90 40 15],1);
269    tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
270  for i=1:30, mydisp(i)  for i=1:30, mydisp(i)
271   fn=['PTRACER' myint2str(i) '.0000000180.001.001.data'];   fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
272   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
273   for x=1:length(lon)   for j=1:length(lat)
274    for y=1:length(lat)    for k=1:length(thk)
275     for z=1:length(thk)     sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
276      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  
277    end    end
278   end   end
279  end  end
280    plot(1:30,0*sumtracer,1:30,sumtracer)
281    
282  % some matlab code for checking that one year's worth of  
283  % tracer uptake is approximately 1e18 mols.  % check that tracer flux is 1e18 mols / year
284    nb_seconds_per_year=31556880;
285  lon=2:4:360; lat=-78:4:78;  lon=2:4:360; lat=-78:4:78;
286  thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];  mask=readbin('hFacC.data',[90 40 15],1);
287  tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);  tracer=zeros(90,40,30); sumtracer=zeros(30,1);
288  for i=1:30, mydisp(i)  for i=1:30, mydisp(i)
289   fn=['PTRACER' myint2str(i) '.0000003600.001.001.data'];   fn=['PtrFlux' myint2str(i) '.0000000180.data'];
290   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,i)=readbin(fn,[90 40],1);
291   for j=1:length(lat)   for j=1:length(lat)
292    for k=1:length(thk)      sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
293     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);  
294    end    end
  end  
295  end  end
296  plot(1:30,0*sumtracer,1:30,sumtracer)  plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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