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revision 1.1 by dimitri, Wed Sep 17 21:45:51 2003 UTC revision 1.20 by dimitri, Thu Dec 18 06:11:14 2003 UTC
# Line 3  Ocean Inversion Project Line 3  Ocean Inversion Project
3    
4  Instructions for using pkg/ptracers to compute tracer  Instructions for using pkg/ptracers to compute tracer
5  Green's functions for Gruber's ocean inversion project  Green's functions for Gruber's ocean inversion project
6  (http://quercus.igpp.ucla.edu/OceanInversion/).  (see quercus.igpp.ucla.edu/OceanInversion/ for details).
7    
8  =====================================  Preprocessed OceanInversion input files are available
9    under directories region_mask, takahashi, and
10    atm_co2 in this package.  All netcdf input files
11    have been converted to binary format in order to avoid
12    having to link netcdf library with MITgcm code.  See
13    respective README files in each directory for details.
14    
 To run a pkg/ptracers test case using salt initial and boundary conditions:  
15    
16    ===============================================
17    First check that pkg/ptracers works OK by using
18   cd MITgcm/bin  salinity initial and boundary conditions
19    ===============================================
20    
21    1 ===> get MITgcm code from cvs repository
22    
23     CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
24     cvs login ( CVS password: cvsanon )
25     cvs co -r checkpoint51n_branch MITgcm
26    
27    2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
28    
29     cd MITgcm
30     cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project
31    
32    3 ===> compile and link
33    
34     cd bin
35   cp ../verification/global_with_exf/code/* .   cp ../verification/global_with_exf/code/* .
36   cp ../code/.genmakerc .   cp ../ocean_inversion_project/code/* .
37   cp ../code/* .   rm ptracers_*.F PTRACERS_OPTIONS.h
38   cp ../code/ptracers_forcing.F.test ptracers_forcing.F   ../tools/genmake2
39   cp ../code/ptracers_init.F.test ptracers_init.F     (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
  cp ../code/ptracers_read_mask.F.test ptracers_read_mask.F  
  ../tools/genmake  
40   make depend   make depend
41   make   make
  cd ../exe  
  cp ../verification/global_with_exf/input/* .  
  cp ../input/* .  
  cp ../input/data.ptracers.test data.ptracers  
  mitgcmuv > output .txt  
   
 ===> check that PTRACER output is identical to salinity output  
   
  diff PTRACER30.0000000020.001.001.data PTRACER01.0000000020.001.001.data  
  diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data  
42    
43  ===> examine interpolation output for 30-region mask  4 ===> execute
44    
45   matlab   cd ../exe
46   mask=zeros(94,44,30);   cp ../verification/global_with_exf/input/eedata .
47   load fort.10   cp ../verification/global_with_exf/input/data.* .
48   for i=1:length(fort)   cp ../verification/global_with_exf/input/POLY3.COEFFS .
49    mask(fort(i,2)+2,fort(i,3)+2,fort(i,1))=fort(i,4);   ln -sf ../verification/global_with_exf/input/*.bin .
50   end   cp ../ocean_inversion_project/input/* .
51   for i=1:30   cp data.test data
52    mypcolor(mask(3:92,3:42,i)');   cp data.ptracers.test data.ptracers
53    colorbar,title(i),pause   mitgcmuv > output.txt
54   end    
55   mypcolor(sum(mask,3)'); colorbar  5 ===> check that PTRACER output and salinity output are identical.
56    
57  =====================================   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
58     diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data
59     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
60     diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data
61    
62    
63  Global ocean experiment with ptracers  ==========================================================
64  =====================================  MPI instructions for carrying out a 3000-year quasi-stationary
65    integration using the global_ocean.90x40x15 configuration.
66    ==========================================================
67    
68     cd MITgcm/exe
69     rm *
70     cd ../bin
71     rm *
72     cp ../verification/global_with_exf/code/* .
73     cp ../ocean_inversion_project/code/* .
74     rm PTRACERS_OPTIONS.h
75     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
76     cp SIZE.h_mpi SIZE.h
77     ../tools/genmake2
78       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
79     make depend
80     make
81     cd ../exe
82     cp ../verification/global_with_exf/input/eedata .
83     cp ../verification/global_with_exf/input/data.* .
84     cp ../verification/global_with_exf/input/POLY3.COEFFS .
85     ln -sf ../verification/global_with_exf/input/*.bin .
86     cp ../ocean_inversion_project/input/* .
87     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
88     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
89     cp data.stationary.1 data
90     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
91       (on orion: qsub job.orion)
92    
93    ==========================================================
94    MPI instructions for carrying out time-dependent, 1765-2005,
95    anthropogenic carbon perturbation tracer experiments using
96    the global_ocean.90x40x15 configuration.
97    ==========================================================
98    
99     cd MITgcm/exe
100     rm *
101     cd ../bin
102     rm *
103     cp ../verification/global_with_exf/code/* .
104     cp ../ocean_inversion_project/code/* .
105     cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h
106     cp SIZE.h_mpi SIZE.h
107     ../tools/genmake2
108       (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
109     make depend
110     make
111     cd ../exe
112     cp ../verification/global_with_exf/input/eedata .
113     cp ../verification/global_with_exf/input/data.* .
114     cp ../verification/global_with_exf/input/POLY3.COEFFS .
115     ln -sf ../verification/global_with_exf/input/*.bin .
116     cp ../ocean_inversion_project/input/* .
117     cp data.1765-2005 data
118     ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
119     ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
120     ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
121     mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
122       (on orion: qsub job.orion.td)
123    
124    
125    ==========================================================
126    Instructions for carrying out time-dependent, 1765-2005,
127    anthropogenic carbon perturbation tracer experiments using
128    global_ocean.90x40x15 configuration and netcdf output.
129    This assumes that the appropriate libnetcdf.a exists
130    and that it be specified in the genmake2 option file.
131    ==========================================================
132    
133     cd MITgcm/exe
134     rm *
135     cd ../bin
136     rm *
137     cp ../verification/global_with_exf/code/* .
138     cp ../ocean_inversion_project/code/* .
139     cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h
140     cp ../ocean_inversion_project/write_netCDF/*  .
141     \rm mk_output.F
142    
143  ===> set up and integrate 30-tracer computation  ### need customized option file; example below is for nireas
144     ../tools/genmake2 -of linux_ia32_g77_netcdf
145    
  cd MITgcm/bin  
  cp ../verification/global_with_exf/code/* .  
  cp ../code/.genmakerc .  
  cp ../code/* .  
  ../tools/genmake  
146   make depend   make depend
147   make   make
148   cd ../exe   cd ../exe
149   cp ../verification/global_with_exf/input/* .   cp ../verification/global_with_exf/input/eedata .
150   cp ../input/* .   cp ../verification/global_with_exf/input/data.* .
151   mitgcmuv > output .txt   cp ../verification/global_with_exf/input/POLY3.COEFFS .
152     ln -sf ../verification/global_with_exf/input/*.bin .
153  ===> look at output   cp ../ocean_inversion_project/input/* .
154     cp data.1765-2005.1 data
155   matlab   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
156   for i=1:30   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
157    tr=readbin(['PTRACER' myint2str(i) ...   ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat .
158                '.0000000020.001.001.data'],[90 40 15],1);   mitgcmuv > output .txt &
159    mypcolor(tr(:,:,2)'), colorbar, pause(1)  
160    
161    ======================================================
162    
163    ==========================================================
164    Instructions for generating netcdf output files on orion
165    ==========================================================
166    
167    cd ocean_inversion_project/write_netCDF
168    setenv F_UFMTENDIAN big
169    
170    (check that defaults in  mk_output.F are appropriate)
171    
172    efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \
173         handle_errors.F write_nc_basisfnctns.F \
174         write_nc_diag_0D.F write_nc_diag_2D.F \
175         -I/u2/dmenem/software/netcdf-3.5.0/include \
176         -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf
177    a.out
178    
179    
180    ======================================================
181    
182    % some matlab code for looking at fort.10 debug files
183    load fort.10
184    tak=zeros(90,40,12);
185    for n=1:length(fort)
186     m=fort(n,1); i=fort(n,2); j=fort(n,3);
187     if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end
188    end
189    lon=2:4:360; lat=-78:4:78;
190    clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10)
191    caxis([-6 6]), colorbar, plotland
192    
193    % some matlab code for looking at PTRACER output files
194    salt=readbin('S.0000000020.001.001.data',[90 40 15],1);
195    tracer=zeros(90,40,15,30);
196    for i=1:30
197     fn=['PTRACER' myint2str(i) '.0000000020.001.001.data'];
198     tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
199     clf, mypcolor(tracer(:,:,1,i)'); pause(1)
200    end
201    tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)')
202    mypcolor(
203    
204    
205    % some matlab code for checking that one year's worth of
206    % tracer uptake is approximately 1e18 mols.
207    lon=2:4:360; lat=-78:4:78;
208    thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690];
209    mask=readbin('hFacC.001.001.data',[90 40 15],1);
210    tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
211    for i=1:30, mydisp(i)
212     fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
213     tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
214     for j=1:length(lat)
215      for k=1:length(thk)
216       sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
217                      thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180);
218      end
219   end   end
220    end
221    plot(1:30,0*sumtracer,1:30,sumtracer)
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