/[MITgcm]/MITgcm_contrib/ocean_inversion_project/README
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revision 1.13 by dimitri, Tue Oct 21 06:21:51 2003 UTC revision 1.29 by dimitri, Wed May 4 23:47:17 2005 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 -P 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/* .   \cp ../ocean_inversion_project/code/* .
49   rm ptracers_*.F PTRACERS_OPTIONS.h   \rm ptracers_*.F PTRACERS_OPTIONS.h
50   ../tools/genmake2   ../tools/genmake2
51     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)     (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    
# Line 70  integration using the global_ocean.90x40 Line 85  integration using the global_ocean.90x40
85   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
86   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
87   rm PTRACERS_OPTIONS.h   rm PTRACERS_OPTIONS.h
88     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
89     cp SIZE.h_mpi SIZE.h
90   ../tools/genmake2   ../tools/genmake2
91     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
92   make depend   make depend
# Line 82  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    
113   cd MITgcm/exe   cd MITgcm/exe
# Line 96  integration using the global_ocean.90x40 Line 116  integration using the global_ocean.90x40
116   rm *   rm *
117   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
118   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
  rm PTRACERS_OPTIONS.h  
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/genmake2   ../tools/genmake2
# Line 109  integration using the global_ocean.90x40 Line 128  integration using the global_ocean.90x40
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.1765-2005 data
132   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
133   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
134   mpirun -np 36 dplace -s1 -c3-38 mitgcmuv < /dev/null > & ! errlog &   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,  Instructions for carrying out time-dependent, 1765-2005,
141  anthropogenic carbon perturbation tracer experiments using  anthropogenic carbon perturbation tracer experiments using
142  the global_ocean.90x40x15 configuration.  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   cd MITgcm/exe
# Line 126  the global_ocean.90x40x15 configuration. Line 150  the global_ocean.90x40x15 configuration.
150   rm *   rm *
151   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
152   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
153   ../tools/genmake2   cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
154     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)   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 136  the global_ocean.90x40x15 configuration. Line 165  the global_ocean.90x40x15 configuration.
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 data   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 .   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
# Line 146  the global_ocean.90x40x15 configuration. Line 175  the global_ocean.90x40x15 configuration.
175  ==========================================================  ==========================================================
176  Instructions for carrying out time-dependent, 1765-2005,  Instructions for carrying out time-dependent, 1765-2005,
177  anthropogenic carbon perturbation tracer experiments using  anthropogenic carbon perturbation tracer experiments using
178  global_ocean.90x40x15 configuration and netcdf output.  the ecco1x1 configuration and netcdf output on columbia.
179  This assumes that the appropriate libnetcdf.a exists  This assumes that the appropriate libnetcdf.a exists
180  and that it be specified in the genmake2 option file.  and that it be specified in the genmake2 option file.
181    It also assumes that surface forcing files are available
182    in MITgcm/../iter69
183  ==========================================================  ==========================================================
184    
185   cd MITgcm/exe   cd MITgcm/exe
186   rm *   \rm *
187   cd ../bin   cd ../bin
188   rm *   \rm *
189   cp ../verification/global_with_exf/code/* .   \cp ../ocean_inversion_project/code_ecco1x1/* .
190   cp ../ocean_inversion_project/code/* .   \cp ../ocean_inversion_project/write_netCDF/*  .
191   cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h   \rm mk_output.F
192   cp ../ocean_inversion_project/write_netCDF/*  .   \cp SIZE.h.96 SIZE.h
193     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
 ### need customized option file; example below is for nireas  
  ../tools/genmake2 -of linux_ia32_g77_netcdf  
   
194   make depend   make depend
195   make   make -j 16
196   cd ../exe   cd ../exe
197   cp ../verification/global_with_exf/input/eedata .   \cp ../ocean_inversion_project/input_ecco1x1/* .
198   cp ../verification/global_with_exf/input/data.* .   ln -sf ../../iter69/* .
  cp ../verification/global_with_exf/input/POLY3.COEFFS .  
  ln -sf ../verification/global_with_exf/input/*.bin .  
  cp ../ocean_inversion_project/input/* .  
  cp data.1765-2005 data  
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   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
202   mitgcmuv > output .txt &   qsub job01
203    
204    
205    ==========================================================
206    Instructions for carrying out 3000-year quasi-stationary
207    integration using the ecco1x1 configuration and netcdf
208    output on columbia.
209    This assumes that the appropriate libnetcdf.a exists
210    and that it be specified in the genmake2 option file.
211    It also assumes that surface forcing files are available
212    in MITgcm/../iter69
213    ==========================================================
214    
215     cd MITgcm/exe
216     \rm *
217     cd ../bin
218     \rm *
219     \cp ../ocean_inversion_project/code_ecco1x1/* .
220     \cp ../ocean_inversion_project/write_netCDF/*  .
221     \rm mk_output.F
222     \cp SIZE.h.96 SIZE.h
223     \cp PTRACERS_OPTIONS.h.stationary PTRACERS_OPTIONS.h
224     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
225     make depend
226     make -j 16
227     cd ../exe
228     \cp ../ocean_inversion_project/input_ecco1x1/* .
229     \ln -sf ../../iter69/* .
230     \ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
231     \ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
232     qsub job01s
233    
234    
235    ==========================================================
236    Instructions for generating netcdf output files on columbia
237    ==========================================================
238    
239    cd ocean_inversion_project/write_netCDF
240    setenv F_UFMTENDIAN big
241    
242    (check that defaults in  mk_output.F are appropriate)
243    
244    ifort -assume byterecl -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
245         handle_errors.F write_nc_basisfnctns.F \
246         write_nc_diag_0D.F write_nc_diag_2D.F \
247         -I/u/menemenl/software/netcdf-3.5.0/include \
248         -L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf
249    ./a.out
250    
251    
252    ==========================================================
253    Instructions for generating netcdf output files on orion
254    ==========================================================
255    
256    cd ocean_inversion_project/write_netCDF
257    setenv F_UFMTENDIAN big
258    
259    (check that defaults in  mk_output.F are appropriate)
260    
261    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
262         handle_errors.F write_nc_basisfnctns.F \
263         write_nc_diag_0D.F write_nc_diag_2D.F \
264         -I/u2/dmenem/software/netcdf-3.5.0/include \
265         -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
266    ./a.out
267    
268    
269  ======================================================  ======================================================
# Line 220  for i=1:30, mydisp(i) Line 308  for i=1:30, mydisp(i)
308   end   end
309  end  end
310  plot(1:30,0*sumtracer,1:30,sumtracer)  plot(1:30,0*sumtracer,1:30,sumtracer)
311    
312    
313    % check that tracer flux is 1e18 mols / year
314    nb_seconds_per_year=31556880;
315    lon=2:4:360; lat=-78:4:78;
316    mask=readbin('hFacC.data',[90 40 15],1);
317    tracer=zeros(90,40,30); sumtracer=zeros(30,1);
318    for i=1:30, mydisp(i)
319     fn=['PtrFlux' myint2str(i) '.0000000180.data'];
320     tracer(:,:,i)=readbin(fn,[90 40],1);
321     for j=1:length(lat)
322        sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
323            nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
324      end
325    end
326    plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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