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revision 1.8 by dimitri, Sat Sep 27 07:45:51 2003 UTC revision 1.30 by dimitri, Wed Aug 24 20:59:54 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
17    MITgcm/verification/global_with_CFC11/README
18    
19    
20    Notes and problems:
21    ===================
22    
23    there is problem generating ECCO_MaskAreaBathy.nc on columbia
24    works OK on nireas
25    
26    variable global_mean_conc in 0D output from mk_output.F is
27    screwed up
28    
29    
30    
31  ===============================================  ===============================================
32  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 35  salinity initial and boundary conditions
35    
36  1 ===> get MITgcm code from cvs repository  1 ===> get MITgcm code from cvs repository
37    
38   CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack   cvs co -r checkpoint51n_branch MITgcm_code
39   cvs login ( CVS password: cvsanon )   cvs co -r checkpoint51n_branch MITgcm/verification/testreport
40   cvs co MITgcm   cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf
41    
42  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory  2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
43    
# Line 31  salinity initial and boundary conditions Line 46  salinity initial and boundary conditions
46    
47  3 ===> compile and link  3 ===> compile and link
48    
49     mkdir bin exe
50   cd bin   cd bin
51   cp ../verification/global_with_exf/code/* .   \cp ../verification/global_with_exf/code/* .
52   cp ../ocean_inversion_project/code/.genmakerc .   \cp ../ocean_inversion_project/code/* .
53   cp ../ocean_inversion_project/code/* .   \rm ptracers_*.F PTRACERS_OPTIONS.h
54   rm ptracers_*.F   ../tools/genmake2
55   ../tools/genmake     (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
56       (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
57   make depend   make depend
58   make   make -j 16
59    
60  4 ===> execute  4 ===> execute
61    
62   cd ../exe   cd ../exe
63   cp ../verification/global_with_exf/input/eedata .   \cp ../verification/global_with_exf/input/eedata .
64   cp ../verification/global_with_exf/input/data.* .   \cp ../verification/global_with_exf/input/data.* .
65   cp ../verification/global_with_exf/input/POLY3.COEFFS .   \cp ../verification/global_with_exf/input/POLY3.COEFFS .
66   ln -sf ../verification/global_with_exf/input/*.bin .   \ln -sf ../verification/global_with_exf/input/*.bin .
67   cp ../ocean_inversion_project/input/* .   \cp ../ocean_inversion_project/input/* .
68   cp data.test data   \cp data.test data
69   cp data.ptracers.test data.ptracers   \cp data.ptracers.test data.ptracers
70   mitgcmuv > output.txt   ./mitgcmuv >! output.txt
71      
72  5 ===> check that PTRACER output and salinity output are identical.  5 ===> check that PTRACER output and salinity output are identical.
73    
74   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
75   diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data   diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data
76     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
77     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
78    
79    
80  ==========================================================  ==========================================================
81  Instructions for carrying out a 3000-year quasi-stationary  MPI instructions for carrying out a 3000-year quasi-stationary
82  integration using the global_ocean.90x40x15 configuration.  integration using the global_ocean.90x40x15 configuration.
83  ==========================================================  ==========================================================
84    
 1 ===> compile, link, and execute  
   
85   cd MITgcm/exe   cd MITgcm/exe
86   rm *   rm *
87   cd ../bin   cd ../bin
88   rm *   rm *
89   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
90   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
91   ../tools/genmake   rm PTRACERS_OPTIONS.h
92     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
93     cp SIZE.h_mpi SIZE.h
94     ../tools/genmake2
95       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
96   make depend   make depend
97   make   make
98   cd ../exe   cd ../exe
# Line 83  integration using the global_ocean.90x40 Line 103  integration using the global_ocean.90x40
103   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
104   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
105   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
106   mitgcmuv > output .txt &   cp data.stationary.1 data
107     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
108       (on orion: qsub job.orion)
109    
110    
111  ==========================================================  ==========================================================
112  MPI instructions for carrying out a 3000-year quasi-stationary  MPI instructions for carrying out time-dependent, 1765-2005,
113  integration using the global_ocean.90x40x15 configuration.  anthropogenic carbon perturbation tracer experiments using
114    the global_ocean.90x40x15 configuration.
115  ==========================================================  ==========================================================
116    
 1 ===> compile, link, and execute  
   
117   cd MITgcm/exe   cd MITgcm/exe
118   rm *   rm *
119   cd ../bin   cd ../bin
120   rm *   rm *
121   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
122   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
123   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h   cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
124   cp SIZE.h_mpi SIZE.h   cp SIZE.h_mpi SIZE.h
125   ../tools/genmake   ../tools/genmake2
126       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
127     make depend
128     make
129     cd ../exe
130     cp ../verification/global_with_exf/input/eedata .
131     cp ../verification/global_with_exf/input/data.* .
132     cp ../verification/global_with_exf/input/POLY3.COEFFS .
133     ln -sf ../verification/global_with_exf/input/*.bin .
134     cp ../ocean_inversion_project/input/* .
135     cp data.1765-2005 data
136     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
137     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
138     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
139     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
140       (on orion: qsub job.orion.td)
141    
142    
143    ==========================================================
144    Instructions for carrying out time-dependent, 1765-2005,
145    anthropogenic carbon perturbation tracer experiments using
146    global_ocean.90x40x15 configuration and netcdf output.
147    This assumes that the appropriate libnetcdf.a exists
148    and that it be specified in the genmake2 option file.
149    ==========================================================
150    
151     cd MITgcm/exe
152     rm *
153     cd ../bin
154     rm *
155     cp ../verification/global_with_exf/code/* .
156     cp ../ocean_inversion_project/code/* .
157     cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
158     cp ../ocean_inversion_project/write_netCDF/*  .
159     \rm mk_output.F
160    
161    ### need customized option file; example below is for nireas
162     ../tools/genmake2 -of linux_ia32_g77_netcdf
163    
164   make depend   make depend
165   make   make
166   cd ../exe   cd ../exe
# Line 111  integration using the global_ocean.90x40 Line 169  integration using the global_ocean.90x40
169   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
170   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
171   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
172     cp data.1765-2005.1 data
173     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
174     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
175     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
176     mitgcmuv > output .txt &
177    
178    
179    ==========================================================
180    Instructions for carrying out time-dependent, 1765-2005,
181    anthropogenic carbon perturbation tracer experiments using
182    the ecco1x1 configuration and netcdf output on columbia.
183    This assumes that the appropriate libnetcdf.a exists
184    and that it be specified in the genmake2 option file.
185    It also assumes that surface forcing files are available
186    in MITgcm/../iter69
187    ==========================================================
188    
189     cd MITgcm/exe
190     \rm *
191     cd ../bin
192     \rm *
193     \cp ../ocean_inversion_project/code_ecco1x1/* .
194     \cp ../ocean_inversion_project/write_netCDF/*  .
195     \rm mk_output.F
196     \cp SIZE.h.96 SIZE.h
197     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
198     make depend
199     make -j 16
200     cd ../exe
201     \cp ../ocean_inversion_project/input_ecco1x1/* .
202     ln -sf ../../iter69/* .
203   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
204   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
205   mpirun -np 36 dplace -s1 -c25-60 mitgcmuv < /dev/null > & ! errlog &   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
206     qsub job01
207    
208    
209    ==========================================================
210    Instructions for carrying out 3000-year quasi-stationary
211    integration using the ecco1x1 configuration and netcdf
212    output on columbia.
213    This assumes that the appropriate libnetcdf.a exists
214    and that it be specified in the genmake2 option file.
215    It also assumes that surface forcing files are available
216    in MITgcm/../iter69
217    ==========================================================
218    
219     cd MITgcm/exe
220     \rm *
221     cd ../bin
222     \rm *
223     \cp ../ocean_inversion_project/code_ecco1x1/* .
224     \cp ../ocean_inversion_project/write_netCDF/*  .
225     \rm mk_output.F
226     \cp SIZE.h.96 SIZE.h
227     \cp PTRACERS_OPTIONS.h.stationary PTRACERS_OPTIONS.h
228     ../tools/genmake2 -of linux_ia64_efc+mpi_altix
229     make depend
230     make -j 16
231     cd ../exe
232     \cp ../ocean_inversion_project/input_ecco1x1/* .
233     \ln -sf ../../iter69/* .
234     \ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
235     \ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
236     qsub job01s
237    
238    
239    ==========================================================
240    Instructions for generating netcdf output files on columbia
241    ==========================================================
242    
243    cd ocean_inversion_project/write_netCDF
244    setenv F_UFMTENDIAN big
245    
246    (check that defaults in  mk_output.F are appropriate)
247    
248    ifort -assume byterecl -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
249         handle_errors.F write_nc_basisfnctns.F \
250         write_nc_diag_0D.F write_nc_diag_2D.F \
251         -I/u/menemenl/software/netcdf-3.5.0/include \
252         -L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf
253    ./a.out
254    
255    
256    ==========================================================
257    Instructions for generating netcdf output files on orion
258    ==========================================================
259    
260    cd ocean_inversion_project/write_netCDF
261    setenv F_UFMTENDIAN big
262    
263    (check that defaults in  mk_output.F are appropriate)
264    
265    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
266         handle_errors.F write_nc_basisfnctns.F \
267         write_nc_diag_0D.F write_nc_diag_2D.F \
268         -I/u2/dmenem/software/netcdf-3.5.0/include \
269         -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
270    ./a.out
271    
272    
273  ======================================================  ======================================================
# Line 158  for i=1:30, mydisp(i) Line 312  for i=1:30, mydisp(i)
312   end   end
313  end  end
314  plot(1:30,0*sumtracer,1:30,sumtracer)  plot(1:30,0*sumtracer,1:30,sumtracer)
315    
316    
317    % check that tracer flux is 1e18 mols / year
318    nb_seconds_per_year=31556880;
319    lon=2:4:360; lat=-78:4:78;
320    mask=readbin('hFacC.data',[90 40 15],1);
321    tracer=zeros(90,40,30); sumtracer=zeros(30,1);
322    for i=1:30, mydisp(i)
323     fn=['PtrFlux' myint2str(i) '.0000000180.data'];
324     tracer(:,:,i)=readbin(fn,[90 40],1);
325     for j=1:length(lat)
326        sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
327            nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
328      end
329    end
330    plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))
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