/[MITgcm]/MITgcm_contrib/ocean_inversion_project/README
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revision 1.8 by dimitri, Sat Sep 27 07:45:51 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/* .   \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   rm ptracers_*.F   ../tools/genmake2
51   ../tools/genmake     (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
52       (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
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/eedata .   \cp ../verification/global_with_exf/input/eedata .
60   cp ../verification/global_with_exf/input/data.* .   \cp ../verification/global_with_exf/input/data.* .
61   cp ../verification/global_with_exf/input/POLY3.COEFFS .   \cp ../verification/global_with_exf/input/POLY3.COEFFS .
62   ln -sf ../verification/global_with_exf/input/*.bin .   \ln -sf ../verification/global_with_exf/input/*.bin .
63   cp ../ocean_inversion_project/input/* .   \cp ../ocean_inversion_project/input/* .
64   cp data.test data   \cp data.test data
65   cp data.ptracers.test data.ptracers   \cp data.ptracers.test data.ptracers
66   mitgcmuv > output.txt   ./mitgcmuv >! output.txt
67      
68  5 ===> check that PTRACER output and salinity output are identical.  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  Instructions for carrying out a 3000-year quasi-stationary  MPI instructions for carrying out a 3000-year quasi-stationary
78  integration using the global_ocean.90x40x15 configuration.  integration using the global_ocean.90x40x15 configuration.
79  ==========================================================  ==========================================================
80    
 1 ===> compile, link, and execute  
   
81   cd MITgcm/exe   cd MITgcm/exe
82   rm *   rm *
83   cd ../bin   cd ../bin
84   rm *   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   ../tools/genmake   rm PTRACERS_OPTIONS.h
88     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   cd ../exe
# Line 83  integration using the global_ocean.90x40 Line 99  integration using the global_ocean.90x40
99   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
100   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
101   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
102   mitgcmuv > output .txt &   cp data.stationary.1 data
103     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
104       (on orion: qsub job.orion)
105    
106    
107  ==========================================================  ==========================================================
108  MPI instructions for carrying out a 3000-year quasi-stationary  MPI instructions for carrying out time-dependent, 1765-2005,
109  integration using the global_ocean.90x40x15 configuration.  anthropogenic carbon perturbation tracer experiments using
110    the global_ocean.90x40x15 configuration.
111  ==========================================================  ==========================================================
112    
 1 ===> compile, link, and execute  
   
113   cd MITgcm/exe   cd MITgcm/exe
114   rm *   rm *
115   cd ../bin   cd ../bin
116   rm *   rm *
117   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
118   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
119   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
120   cp SIZE.h_mpi SIZE.h   cp SIZE.h_mpi SIZE.h
121   ../tools/genmake   ../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    ### 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 111  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 .
170     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
171     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
172     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 .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
200   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
201   mpirun -np 36 dplace -s1 -c25-60 mitgcmuv < /dev/null > & ! errlog &   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  ======================================================  ======================================================
# Line 158  for i=1:30, mydisp(i) Line 278  for i=1:30, mydisp(i)
278   end   end
279  end  end
280  plot(1:30,0*sumtracer,1:30,sumtracer)  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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