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revision 1.4 by dimitri, Wed Sep 24 04:52:38 2003 UTC revision 1.31 by dimitri, Wed Aug 24 21:12:01 2005 UTC
# Line 12  have been converted to binary format in Line 12  have been converted to binary format in
12  having to link netcdf library with MITgcm code.  See  having to link netcdf library with MITgcm code.  See
13  respective README files in each directory for details.  respective README files in each directory for details.
14    
15    Instructions for CFC-11 computations are in
16    cvs co -r release1_50yr MITgcm_code
17    cvs co -r release1_50yr MITgcm/verification/global_with_CFC11
18    MITgcm/verification/global_with_CFC11/README
19    
20    
21    Notes and problems:
22    ===================
23    
24    there is problem generating ECCO_MaskAreaBathy.nc on columbia
25    works OK on nireas
26    
27    variable global_mean_conc in 0D output from mk_output.F is
28    screwed up
29    
30    
31    
32  ===============================================  ===============================================
33  First check that pkg/ptracers works OK by using  First check that pkg/ptracers works OK by using
# Line 20  salinity initial and boundary conditions Line 36  salinity initial and boundary conditions
36    
37  1 ===> get MITgcm code from cvs repository  1 ===> get MITgcm code from cvs repository
38    
39   CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack   cvs co -r checkpoint51n_branch MITgcm_code
40   cvs login ( CVS password: cvsanon )   cvs co -r checkpoint51n_branch MITgcm/verification/testreport
41   cvs co MITgcm   cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf
42    
43  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
44    
# Line 31  salinity initial and boundary conditions Line 47  salinity initial and boundary conditions
47    
48  3 ===> compile and link  3 ===> compile and link
49    
50     mkdir bin exe
51   cd bin   cd bin
52     \cp ../verification/global_with_exf/code/* .
53     \cp ../ocean_inversion_project/code/* .
54     \rm ptracers_*.F PTRACERS_OPTIONS.h
55     ../tools/genmake2
56       (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
57       (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
58     make depend
59     make -j 16
60    
61    4 ===> execute
62    
63     cd ../exe
64     \cp ../verification/global_with_exf/input/eedata .
65     \cp ../verification/global_with_exf/input/data.* .
66     \cp ../verification/global_with_exf/input/POLY3.COEFFS .
67     \ln -sf ../verification/global_with_exf/input/*.bin .
68     \cp ../ocean_inversion_project/input/* .
69     \cp data.test data
70     \cp data.ptracers.test data.ptracers
71     ./mitgcmuv >! output.txt
72    
73    5 ===> check that PTRACER output and salinity output are identical.
74    
75     diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
76     diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data
77     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
78     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
79    
80    
81    ==========================================================
82    MPI instructions for carrying out a 3000-year quasi-stationary
83    integration using the global_ocean.90x40x15 configuration.
84    ==========================================================
85    
86     cd MITgcm/exe
87     rm *
88     cd ../bin
89     rm *
90   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
91   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
92   rm ptracers_init.F ptracers_forcing_surf.F PTRACERS.h   rm PTRACERS_OPTIONS.h
93   rm ptracers_read_mask.F ptracers_read_takahashi.F   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
94   ../tools/genmake   cp SIZE.h_mpi SIZE.h
95     ../tools/genmake2
96       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
97   make depend   make depend
98   make   make
99     cd ../exe
100     cp ../verification/global_with_exf/input/eedata .
101     cp ../verification/global_with_exf/input/data.* .
102     cp ../verification/global_with_exf/input/POLY3.COEFFS .
103     ln -sf ../verification/global_with_exf/input/*.bin .
104     cp ../ocean_inversion_project/input/* .
105     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
106     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
107     cp data.stationary.1 data
108     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
109       (on orion: qsub job.orion)
110    
 4 ===> execute  
111    
112    ==========================================================
113    MPI instructions for carrying out time-dependent, 1765-2005,
114    anthropogenic carbon perturbation tracer experiments using
115    the global_ocean.90x40x15 configuration.
116    ==========================================================
117    
118     cd MITgcm/exe
119     rm *
120     cd ../bin
121     rm *
122     cp ../verification/global_with_exf/code/* .
123     cp ../ocean_inversion_project/code/* .
124     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
125     cp SIZE.h_mpi SIZE.h
126     ../tools/genmake2
127       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
128     make depend
129     make
130   cd ../exe   cd ../exe
131   cp ../verification/global_with_exf/input/eedata .   cp ../verification/global_with_exf/input/eedata .
132   cp ../verification/global_with_exf/input/data.* .   cp ../verification/global_with_exf/input/data.* .
133   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
134   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
135   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
136   cp data.test data   cp data.1765-2005 data
137   cp data.ptracers.test data.ptracers   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
138   mitgcmuv > output.txt   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
139       ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
140  5 ===> check that PTRACER output and salinity output   mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
141    ===> are identical.     (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  
142    
143    
144  ==========================================================  ==========================================================
145  Instructions for carrying out a 3000-year quasi-stationary  Instructions for carrying out time-dependent, 1765-2005,
146  integration using the global_ocean.90x40x15 configuration.  anthropogenic carbon perturbation tracer experiments using
147    global_ocean.90x40x15 configuration and netcdf output.
148    This assumes that the appropriate libnetcdf.a exists
149    and that it be specified in the genmake2 option file.
150  ==========================================================  ==========================================================
151    
 1 ===> compile, link, and execute  
   
152   cd MITgcm/exe   cd MITgcm/exe
153   rm *   rm *
154   cd ../bin   cd ../bin
155   rm *   rm *
156   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
157   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
158   ../tools/genmake   cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
159     cp ../ocean_inversion_project/write_netCDF/*  .
160     \rm mk_output.F
161    
162    ### need customized option file; example below is for nireas
163     ../tools/genmake2 -of linux_ia32_g77_netcdf
164    
165   make depend   make depend
166   make   make
167   cd ../exe   cd ../exe
# Line 83  integration using the global_ocean.90x40 Line 170  integration using the global_ocean.90x40
170   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
171   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
172   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
173     cp data.1765-2005.1 data
174   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
175   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
176     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
177   mitgcmuv > output .txt &   mitgcmuv > output .txt &
178    
179    
180    ==========================================================
181    Instructions for carrying out time-dependent, 1765-2005,
182    anthropogenic carbon perturbation tracer experiments using
183    the ecco1x1 configuration and netcdf output on columbia.
184    This assumes that the appropriate libnetcdf.a exists
185    and that it be specified in the genmake2 option file.
186    It also assumes that surface forcing files are available
187    in MITgcm/../iter69
188    ==========================================================
189    
190     cd MITgcm/exe
191     \rm *
192     cd ../bin
193     \rm *
194     \cp ../ocean_inversion_project/code_ecco1x1/* .
195     \cp ../ocean_inversion_project/write_netCDF/*  .
196     \rm mk_output.F
197     \cp SIZE.h.96 SIZE.h
198     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
199     make depend
200     make -j 16
201     cd ../exe
202     \cp ../ocean_inversion_project/input_ecco1x1/* .
203     ln -sf ../../iter69/* .
204     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
205     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
206     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
207     qsub job01
208    
209    
210    ==========================================================
211    Instructions for carrying out 3000-year quasi-stationary
212    integration using the ecco1x1 configuration and netcdf
213    output on columbia.
214    This assumes that the appropriate libnetcdf.a exists
215    and that it be specified in the genmake2 option file.
216    It also assumes that surface forcing files are available
217    in MITgcm/../iter69
218    ==========================================================
219    
220     cd MITgcm/exe
221     \rm *
222     cd ../bin
223     \rm *
224     \cp ../ocean_inversion_project/code_ecco1x1/* .
225     \cp ../ocean_inversion_project/write_netCDF/*  .
226     \rm mk_output.F
227     \cp SIZE.h.96 SIZE.h
228     \cp PTRACERS_OPTIONS.h.stationary PTRACERS_OPTIONS.h
229     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
230     make depend
231     make -j 16
232     cd ../exe
233     \cp ../ocean_inversion_project/input_ecco1x1/* .
234     \ln -sf ../../iter69/* .
235     \ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
236     \ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
237     qsub job01s
238    
239    
240    ==========================================================
241    Instructions for generating netcdf output files on columbia
242    ==========================================================
243    
244    cd ocean_inversion_project/write_netCDF
245    setenv F_UFMTENDIAN big
246    
247    (check that defaults in  mk_output.F are appropriate)
248    
249    ifort -assume byterecl -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
250         handle_errors.F write_nc_basisfnctns.F \
251         write_nc_diag_0D.F write_nc_diag_2D.F \
252         -I/u/menemenl/software/netcdf-3.5.0/include \
253         -L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf
254    ./a.out
255    
256    
257    ==========================================================
258    Instructions for generating netcdf output files on orion
259    ==========================================================
260    
261    cd ocean_inversion_project/write_netCDF
262    setenv F_UFMTENDIAN big
263    
264    (check that defaults in  mk_output.F are appropriate)
265    
266    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
267         handle_errors.F write_nc_basisfnctns.F \
268         write_nc_diag_0D.F write_nc_diag_2D.F \
269         -I/u2/dmenem/software/netcdf-3.5.0/include \
270         -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
271    ./a.out
272    
273    
274  ======================================================  ======================================================
275    
276  % some matlab code for looking at fort.10 debug files  % some matlab code for looking at fort.10 debug files
# Line 117  mypcolor( Line 300  mypcolor(
300  % tracer uptake is approximately 1e18 mols.  % tracer uptake is approximately 1e18 mols.
301  lon=2:4:360; lat=-78:4:78;  lon=2:4:360; lat=-78:4:78;
302  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];
303  tracer=zeros(90,40,15,30); sumtracer1=zeros(30,1);  mask=readbin('hFacC.001.001.data',[90 40 15],1);
304    tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
305  for i=1:30, mydisp(i)  for i=1:30, mydisp(i)
306   fn=['PTRACER' myint2str(i) '.0000000180.001.001.data'];   fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
307   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
308   for x=1:length(lon)   for j=1:length(lat)
309    for y=1:length(lat)    for k=1:length(thk)
310     for z=1:length(thk)     sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
311      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  
312    end    end
313   end   end
314  end  end
315    plot(1:30,0*sumtracer,1:30,sumtracer)
316    
317  % some matlab code for checking that one year's worth of  
318  % tracer uptake is approximately 1e18 mols.  % check that tracer flux is 1e18 mols / year
319    nb_seconds_per_year=31556880;
320  lon=2:4:360; lat=-78:4:78;  lon=2:4:360; lat=-78:4:78;
321  thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];  mask=readbin('hFacC.data',[90 40 15],1);
322  tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);  tracer=zeros(90,40,30); sumtracer=zeros(30,1);
323  for i=1:30, mydisp(i)  for i=1:30, mydisp(i)
324   fn=['PTRACER' myint2str(i) '.0000003600.001.001.data'];   fn=['PtrFlux' myint2str(i) '.0000000180.data'];
325   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);   tracer(:,:,i)=readbin(fn,[90 40],1);
326   for j=1:length(lat)   for j=1:length(lat)
327    for k=1:length(thk)      sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
328     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);  
329    end    end
  end  
330  end  end
331  plot(1:30,0*sumtracer,1:30,sumtracer)  plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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