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revision 1.9 by dimitri, Fri Oct 10 16:30:39 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/* .   \cp ../verification/global_with_exf/code/* .
53   cp ../ocean_inversion_project/code/.genmakerc .   \cp ../ocean_inversion_project/code/* .
54   cp ../ocean_inversion_project/code/* .   \rm ptracers_*.F PTRACERS_OPTIONS.h
55   rm ptracers_*.F   ../tools/genmake2
56   ../tools/genmake     (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
57       (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
58   make depend   make depend
59   make   make -j 16
60    
61  4 ===> execute  4 ===> execute
62    
63   cd ../exe   cd ../exe
64   cp ../verification/global_with_exf/input/eedata .   \cp ../verification/global_with_exf/input/eedata .
65   cp ../verification/global_with_exf/input/data.* .   \cp ../verification/global_with_exf/input/data.* .
66   cp ../verification/global_with_exf/input/POLY3.COEFFS .   \cp ../verification/global_with_exf/input/POLY3.COEFFS .
67   ln -sf ../verification/global_with_exf/input/*.bin .   \ln -sf ../verification/global_with_exf/input/*.bin .
68   cp ../ocean_inversion_project/input/* .   \cp ../ocean_inversion_project/input/* .
69   cp data.test data   \cp data.test data
70   cp data.ptracers.test data.ptracers   \cp data.ptracers.test data.ptracers
71   mitgcmuv > output.txt   ./mitgcmuv >! output.txt
72      
73  5 ===> check that PTRACER output and salinity output are identical.  5 ===> check that PTRACER output and salinity output are identical.
74    
75   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
76   diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data   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  Instructions for carrying out a 3000-year quasi-stationary  MPI instructions for carrying out a 3000-year quasi-stationary
83  integration using the global_ocean.90x40x15 configuration.  integration using the global_ocean.90x40x15 configuration.
84  ==========================================================  ==========================================================
85    
 1 ===> compile, link, and execute  
   
86   cd MITgcm/exe   cd MITgcm/exe
87   rm *   rm *
88   cd ../bin   cd ../bin
89   rm *   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   ../tools/genmake   rm PTRACERS_OPTIONS.h
93     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
94     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   cd ../exe
# Line 83  integration using the global_ocean.90x40 Line 104  integration using the global_ocean.90x40
104   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
105   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
106   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
107   mitgcmuv > output .txt &   cp data.stationary.1 data
108     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
109       (on orion: qsub job.orion)
110    
111    
112  ==========================================================  ==========================================================
113  MPI instructions for carrying out a 3000-year quasi-stationary  MPI instructions for carrying out time-dependent, 1765-2005,
114  integration using the global_ocean.90x40x15 configuration.  anthropogenic carbon perturbation tracer experiments using
115    the global_ocean.90x40x15 configuration.
116  ==========================================================  ==========================================================
117    
 1 ===> compile, link, and execute  
   
118   cd MITgcm/exe   cd MITgcm/exe
119   rm *   rm *
120   cd ../bin   cd ../bin
121   rm *   rm *
122   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
123   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
124   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
125   cp SIZE.h_mpi SIZE.h   cp SIZE.h_mpi SIZE.h
126   ../tools/genmake   ../tools/genmake2
127       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
128     make depend
129     make
130     cd ../exe
131     cp ../verification/global_with_exf/input/eedata .
132     cp ../verification/global_with_exf/input/data.* .
133     cp ../verification/global_with_exf/input/POLY3.COEFFS .
134     ln -sf ../verification/global_with_exf/input/*.bin .
135     cp ../ocean_inversion_project/input/* .
136     cp data.1765-2005 data
137     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
138     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
139     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
140     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
141       (on orion: qsub job.orion.td)
142    
143    
144    ==========================================================
145    Instructions for carrying out time-dependent, 1765-2005,
146    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    
152     cd MITgcm/exe
153     rm *
154     cd ../bin
155     rm *
156     cp ../verification/global_with_exf/code/* .
157     cp ../ocean_inversion_project/code/* .
158     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 111  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 .
175     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
176     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
177     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 .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
205   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
206   mpirun -np 36 dplace -s1 -c3-38 mitgcmuv < /dev/null > & ! errlog &   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  ======================================================  ======================================================
# Line 158  for i=1:30, mydisp(i) Line 313  for i=1:30, mydisp(i)
313   end   end
314  end  end
315  plot(1:30,0*sumtracer,1:30,sumtracer)  plot(1:30,0*sumtracer,1:30,sumtracer)
316    
317    
318    % check that tracer flux is 1e18 mols / year
319    nb_seconds_per_year=31556880;
320    lon=2:4:360; lat=-78:4:78;
321    mask=readbin('hFacC.data',[90 40 15],1);
322    tracer=zeros(90,40,30); sumtracer=zeros(30,1);
323    for i=1:30, mydisp(i)
324     fn=['PtrFlux' myint2str(i) '.0000000180.data'];
325     tracer(:,:,i)=readbin(fn,[90 40],1);
326     for j=1:length(lat)
327        sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
328            nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
329      end
330    end
331    plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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