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revision 1.12 by dimitri, Tue Oct 21 03:25:30 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 -P 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/* .   \cp ../ocean_inversion_project/code/* .
53   rm ptracers_*.F PTRACERS_OPTIONS.h   \rm ptracers_*.F PTRACERS_OPTIONS.h
54   ../tools/genmake2   ../tools/genmake2
55     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)     (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    
# Line 68  integration using the global_ocean.90x40 Line 87  integration using the global_ocean.90x40
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   rm PTRACERS_OPTIONS.h   rm PTRACERS_OPTIONS.h
92     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
93     cp SIZE.h_mpi SIZE.h
94   ../tools/genmake2   ../tools/genmake2
95     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
96   make depend   make depend
# 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    
117   cd MITgcm/exe   cd MITgcm/exe
# Line 96  integration using the global_ocean.90x40 Line 119  integration using the global_ocean.90x40
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/* .
  rm PTRACERS_OPTIONS.h  
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/genmake2   ../tools/genmake2
# Line 111  integration using the global_ocean.90x40 Line 132  integration using the global_ocean.90x40
132   cp ../verification/global_with_exf/input/POLY3.COEFFS .   cp ../verification/global_with_exf/input/POLY3.COEFFS .
133   ln -sf ../verification/global_with_exf/input/*.bin .   ln -sf ../verification/global_with_exf/input/*.bin .
134   cp ../ocean_inversion_project/input/* .   cp ../ocean_inversion_project/input/* .
135     cp data.1765-2005 data
136   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
137   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
138   mpirun -np 36 dplace -s1 -c3-38 mitgcmuv < /dev/null > & ! errlog &   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,  Instructions for carrying out time-dependent, 1765-2005,
145  anthropogenic carbon perturbation tracer experiments using  anthropogenic carbon perturbation tracer experiments using
146  the global_ocean.90x40x15 configuration.  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   cd MITgcm/exe
# Line 127  the global_ocean.90x40x15 configuration. Line 153  the global_ocean.90x40x15 configuration.
153   cd ../bin   cd ../bin
154   rm *   rm *
155   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
  cp ../ocean_inversion_project/code/.genmakerc .  
156   cp ../ocean_inversion_project/code/* .   cp ../ocean_inversion_project/code/* .
157   ../tools/genmake2   cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
158     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)   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 139  the global_ocean.90x40x15 configuration. Line 169  the global_ocean.90x40x15 configuration.
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 data   cp data.1765-2005.1 data
173   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
174   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
175   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
176   mitgcmuv > output .txt &   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 .
204     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
205     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  ======================================================  ======================================================
274    
275  % some matlab code for looking at fort.10 debug files  % some matlab code for looking at fort.10 debug files
# Line 188  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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