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revision 1.2 by dimitri, Thu Sep 18 02:33:38 2003 UTC revision 1.27 by dimitri, Sat Nov 20 14:40:47 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    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    
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  ===============================================  ===============================================
# Line 13  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    
40   cd MITgcm   cd MITgcm
41   cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project   cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project
42    
43  3 ===> compile  3 ===> compile and link
44    
45     mkdir bin exe
46   cd bin   cd bin
47   cp ../verification/global_with_exf/code/* .   \cp ../verification/global_with_exf/code/* .
48   cp ../ocean_inversion_project/code/.genmakerc .   \cp ../ocean_inversion_project/code/* .
49   cp ../ocean_inversion_project/code/* .   \rm ptracers_*.F PTRACERS_OPTIONS.h
50   cp ../ocean_inversion_project/code/ptracers_forcing.F.test ptracers_forcing.F   ../tools/genmake2
51   cp ../ocean_inversion_project/code/ptracers_init.F.test ptracers_init.F     (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
52   cp ../ocean_inversion_project/code/ptracers_read_mask.F.test ptracers_read_mask.F     (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
  ../tools/genmake  
53   make depend   make depend
54   make   make -j 16
55    
56  4 ===> execute  4 ===> execute
57    
58   cd ../exe   cd ../exe
59   cp ../verification/global_with_exf/input/* .   \cp ../verification/global_with_exf/input/eedata .
60   cp ../ocean_inversion_project/input/* .   \cp ../verification/global_with_exf/input/data.* .
61   cp ../ocean_inversion_project/input/data.ptracers.test data.ptracers   \cp ../verification/global_with_exf/input/POLY3.COEFFS .
62   mitgcmuv > output .txt   \ln -sf ../verification/global_with_exf/input/*.bin .
63       \cp ../ocean_inversion_project/input/* .
64  5 ===> check that PTRACER output for tracer 1 and tracer 30   \cp data.test data
65    ===> is identical to salinity output   \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   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
71   diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data   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  Second generate binary input files.  netcdf files are not OK  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   cd MITgcm/bin   rm *
85   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
86   cp ../code/.genmakerc .   cp ../ocean_inversion_project/code/* .
87   cp ../code/* .   rm PTRACERS_OPTIONS.h
88   cp ../code/ptracers_forcing.F.test ptracers_forcing.F   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
89   cp ../code/ptracers_init.F.test ptracers_init.F   cp SIZE.h_mpi SIZE.h
90   cp ../code/ptracers_read_mask.F.test ptracers_read_mask.F   ../tools/genmake2
91   ../tools/genmake     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
92   make depend   make depend
93   make   make
94   cd ../exe   cd ../exe
95   cp ../verification/global_with_exf/input/* .   cp ../verification/global_with_exf/input/eedata .
96   cp ../input/* .   cp ../verification/global_with_exf/input/data.* .
97   cp ../input/data.ptracers.test data.ptracers   cp ../verification/global_with_exf/input/POLY3.COEFFS .
98   mitgcmuv > output .txt   ln -sf ../verification/global_with_exf/input/*.bin .
99     cp ../ocean_inversion_project/input/* .
100  ===> examine interpolation output for 30-region mask   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
101     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
102   matlab   cp data.stationary.1 data
103   mask=zeros(94,44,30);   mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
104   load fort.10     (on orion: qsub job.orion)
105   for i=1:length(fort)  
106    mask(fort(i,2)+2,fort(i,3)+2,fort(i,1))=fort(i,4);  
107   end  ==========================================================
108   for i=1:30  MPI instructions for carrying out time-dependent, 1765-2005,
109    mypcolor(mask(3:92,3:42,i)');  anthropogenic carbon perturbation tracer experiments using
110    colorbar,title(i),pause  the global_ocean.90x40x15 configuration.
111   end  ==========================================================
112   mypcolor(sum(mask,3)'); colorbar  
113     cd MITgcm/exe
114  =====================================   rm *
115     cd ../bin
116     rm *
117  Global ocean experiment with ptracers   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
126     cp ../verification/global_with_exf/input/eedata .
127     cp ../verification/global_with_exf/input/data.* .
128     cp ../verification/global_with_exf/input/POLY3.COEFFS .
129     ln -sf ../verification/global_with_exf/input/*.bin .
130     cp ../ocean_inversion_project/input/* .
131     cp data.1765-2005 data
132     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
133     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
134     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
135     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
136       (on orion: qsub job.orion.td)
137    
138    
139    ==========================================================
140    Instructions for carrying out time-dependent, 1765-2005,
141    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    
147     cd MITgcm/exe
148     rm *
149     cd ../bin
150     rm *
151     cp ../verification/global_with_exf/code/* .
152     cp ../ocean_inversion_project/code/* .
153     cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
154     cp ../ocean_inversion_project/write_netCDF/*  .
155     \rm mk_output.F
156    
157  ===> set up and integrate 30-tracer computation  ### need customized option file; example below is for nireas
158     ../tools/genmake2 -of linux_ia32_g77_netcdf
159    
  cd MITgcm/bin  
  cp ../verification/global_with_exf/code/* .  
  cp ../code/.genmakerc .  
  cp ../code/* .  
  ../tools/genmake  
160   make depend   make depend
161   make   make
162   cd ../exe   cd ../exe
163   cp ../verification/global_with_exf/input/* .   cp ../verification/global_with_exf/input/eedata .
164   cp ../input/* .   cp ../verification/global_with_exf/input/data.* .
165   mitgcmuv > output .txt   cp ../verification/global_with_exf/input/POLY3.COEFFS .
166     ln -sf ../verification/global_with_exf/input/*.bin .
167  ===> look at output   cp ../ocean_inversion_project/input/* .
168     cp data.1765-2005.1 data
169   matlab   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
170   for i=1:30   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
171    tr=readbin(['PTRACER' myint2str(i) ...   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
172                '.0000000020.001.001.data'],[90 40 15],1);   mitgcmuv > output .txt &
173    mypcolor(tr(:,:,2)'), colorbar, pause(1)  
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
242    load fort.10
243    tak=zeros(90,40,12);
244    for n=1:length(fort)
245     m=fort(n,1); i=fort(n,2); j=fort(n,3);
246     if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end
247    end
248    lon=2:4:360; lat=-78:4:78;
249    clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10)
250    caxis([-6 6]), colorbar, plotland
251    
252    % some matlab code for looking at PTRACER output files
253    salt=readbin('S.0000000020.001.001.data',[90 40 15],1);
254    tracer=zeros(90,40,15,30);
255    for i=1:30
256     fn=['PTRACER' myint2str(i) '.0000000020.001.001.data'];
257     tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
258     clf, mypcolor(tracer(:,:,1,i)'); pause(1)
259    end
260    tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)')
261    mypcolor(
262    
263    
264    % some matlab code for checking that one year's worth of
265    % tracer uptake is approximately 1e18 mols.
266    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];
268    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)
271     fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
272     tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
273     for j=1:length(lat)
274      for k=1:length(thk)
275       sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
276                      thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
277      end
278   end   end
279    end
280    plot(1:30,0*sumtracer,1:30,sumtracer)
281    
282    
283    % check that tracer flux is 1e18 mols / year
284    nb_seconds_per_year=31556880;
285    lon=2:4:360; lat=-78:4:78;
286    mask=readbin('hFacC.data',[90 40 15],1);
287    tracer=zeros(90,40,30); sumtracer=zeros(30,1);
288    for i=1:30, mydisp(i)
289     fn=['PtrFlux' myint2str(i) '.0000000180.data'];
290     tracer(:,:,i)=readbin(fn,[90 40],1);
291     for j=1:length(lat)
292        sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
293            nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
294      end
295    end
296    plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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