/[MITgcm]/MITgcm_contrib/ocean_inversion_project/README
ViewVC logotype

Diff of /MITgcm_contrib/ocean_inversion_project/README

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.6 by dimitri, Thu Sep 25 03:01:59 2003 UTC revision 1.28 by dimitri, Mon Nov 22 23:47:01 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 MITgcm/../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 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    efc -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  ======================================================  ======================================================
270    
271  % some matlab code for looking at fort.10 debug files  % some matlab code for looking at fort.10 debug files
# Line 115  mypcolor( Line 295  mypcolor(
295  % tracer uptake is approximately 1e18 mols.  % tracer uptake is approximately 1e18 mols.
296  lon=2:4:360; lat=-78:4:78;  lon=2:4:360; lat=-78:4:78;
297  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];
298  tracer=zeros(90,40,15,30); sumtracer1=zeros(30,1);  mask=readbin('hFacC.001.001.data',[90 40 15],1);
299    tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
300  for i=1:30, mydisp(i)  for i=1:30, mydisp(i)
301   fn=['PTRACER' myint2str(i) '.0000000180.001.001.data'];   fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
302   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
303   for x=1:length(lon)   for j=1:length(lat)
304    for y=1:length(lat)    for k=1:length(thk)
305     for z=1:length(thk)     sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
306      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  
307    end    end
308   end   end
309  end  end
310    plot(1:30,0*sumtracer,1:30,sumtracer)
311    
312  % some matlab code for checking that one year's worth of  
313  % tracer uptake is approximately 1e18 mols.  % check that tracer flux is 1e18 mols / year
314    nb_seconds_per_year=31556880;
315  lon=2:4:360; lat=-78:4:78;  lon=2:4:360; lat=-78:4:78;
316  thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];  mask=readbin('hFacC.data',[90 40 15],1);
317  tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);  tracer=zeros(90,40,30); sumtracer=zeros(30,1);
318  for i=1:30, mydisp(i)  for i=1:30, mydisp(i)
319   fn=['PTRACER' myint2str(i) '.0000003600.001.001.data'];   fn=['PtrFlux' myint2str(i) '.0000000180.data'];
320   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,i)=readbin(fn,[90 40],1);
321   for j=1:length(lat)   for j=1:length(lat)
322    for k=1:length(thk)      sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
323     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);  
324    end    end
  end  
325  end  end
326  plot(1:30,0*sumtracer,1:30,sumtracer)  plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
Legend:
Removed from v.1.6  
changed lines
  Added in v.1.28
  ViewVC Help
Powered by ViewVC 1.1.22