13 |
respective README files in each directory for details. |
respective README files in each directory for details. |
14 |
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|
15 |
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|
16 |
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Notes and problems: |
17 |
|
=================== |
18 |
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|
19 |
|
there is problem generating ECCO_MaskAreaBathy.nc on columbia |
20 |
|
works OK on nireas |
21 |
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|
22 |
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variable global_mean_conc in 0D output from mk_output.F is |
23 |
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screwed up |
24 |
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|
25 |
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|
26 |
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|
27 |
=============================================== |
=============================================== |
28 |
First check that pkg/ptracers works OK by using |
First check that pkg/ptracers works OK by using |
29 |
salinity initial and boundary conditions |
salinity initial and boundary conditions |
31 |
|
|
32 |
1 ===> get MITgcm code from cvs repository |
1 ===> get MITgcm code from cvs repository |
33 |
|
|
34 |
CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack |
cvs co -r checkpoint51n_branch MITgcm_code |
35 |
cvs login ( CVS password: cvsanon ) |
cvs co -r checkpoint51n_branch MITgcm/verification/testreport |
36 |
cvs co MITgcm |
cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf |
37 |
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|
38 |
2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory |
2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory |
39 |
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|
42 |
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|
43 |
3 ===> compile and link |
3 ===> compile and link |
44 |
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|
45 |
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mkdir bin exe |
46 |
cd bin |
cd bin |
47 |
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\cp ../verification/global_with_exf/code/* . |
48 |
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\cp ../ocean_inversion_project/code/* . |
49 |
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\rm ptracers_*.F PTRACERS_OPTIONS.h |
50 |
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../tools/genmake2 |
51 |
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(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi ) |
52 |
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(on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix ) |
53 |
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make depend |
54 |
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make -j 16 |
55 |
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|
56 |
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4 ===> execute |
57 |
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|
58 |
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cd ../exe |
59 |
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\cp ../verification/global_with_exf/input/eedata . |
60 |
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\cp ../verification/global_with_exf/input/data.* . |
61 |
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\cp ../verification/global_with_exf/input/POLY3.COEFFS . |
62 |
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\ln -sf ../verification/global_with_exf/input/*.bin . |
63 |
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\cp ../ocean_inversion_project/input/* . |
64 |
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\cp data.test data |
65 |
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\cp data.ptracers.test data.ptracers |
66 |
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./mitgcmuv >! output.txt |
67 |
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|
68 |
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5 ===> check that PTRACER output and salinity output are identical. |
69 |
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|
70 |
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diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data |
71 |
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diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data |
72 |
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diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data |
73 |
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diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data |
74 |
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|
75 |
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|
76 |
|
========================================================== |
77 |
|
MPI instructions for carrying out a 3000-year quasi-stationary |
78 |
|
integration using the global_ocean.90x40x15 configuration. |
79 |
|
========================================================== |
80 |
|
|
81 |
|
cd MITgcm/exe |
82 |
|
rm * |
83 |
|
cd ../bin |
84 |
|
rm * |
85 |
cp ../verification/global_with_exf/code/* . |
cp ../verification/global_with_exf/code/* . |
|
cp ../ocean_inversion_project/code/.genmakerc . |
|
86 |
cp ../ocean_inversion_project/code/* . |
cp ../ocean_inversion_project/code/* . |
87 |
rm ptracers_*.F |
rm PTRACERS_OPTIONS.h |
88 |
../tools/genmake |
cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h |
89 |
|
cp SIZE.h_mpi SIZE.h |
90 |
|
../tools/genmake2 |
91 |
|
(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) |
92 |
make depend |
make depend |
93 |
make |
make |
94 |
|
cd ../exe |
95 |
|
cp ../verification/global_with_exf/input/eedata . |
96 |
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cp ../verification/global_with_exf/input/data.* . |
97 |
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cp ../verification/global_with_exf/input/POLY3.COEFFS . |
98 |
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ln -sf ../verification/global_with_exf/input/*.bin . |
99 |
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cp ../ocean_inversion_project/input/* . |
100 |
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ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
101 |
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ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
102 |
|
cp data.stationary.1 data |
103 |
|
mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & |
104 |
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(on orion: qsub job.orion) |
105 |
|
|
|
4 ===> execute |
|
106 |
|
|
107 |
|
========================================================== |
108 |
|
MPI instructions for carrying out time-dependent, 1765-2005, |
109 |
|
anthropogenic carbon perturbation tracer experiments using |
110 |
|
the global_ocean.90x40x15 configuration. |
111 |
|
========================================================== |
112 |
|
|
113 |
|
cd MITgcm/exe |
114 |
|
rm * |
115 |
|
cd ../bin |
116 |
|
rm * |
117 |
|
cp ../verification/global_with_exf/code/* . |
118 |
|
cp ../ocean_inversion_project/code/* . |
119 |
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cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h |
120 |
|
cp SIZE.h_mpi SIZE.h |
121 |
|
../tools/genmake2 |
122 |
|
(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) |
123 |
|
make depend |
124 |
|
make |
125 |
cd ../exe |
cd ../exe |
126 |
cp ../verification/global_with_exf/input/eedata . |
cp ../verification/global_with_exf/input/eedata . |
127 |
cp ../verification/global_with_exf/input/data.* . |
cp ../verification/global_with_exf/input/data.* . |
128 |
cp ../verification/global_with_exf/input/POLY3.COEFFS . |
cp ../verification/global_with_exf/input/POLY3.COEFFS . |
129 |
ln -sf ../verification/global_with_exf/input/*.bin . |
ln -sf ../verification/global_with_exf/input/*.bin . |
130 |
cp ../ocean_inversion_project/input/* . |
cp ../ocean_inversion_project/input/* . |
131 |
cp data.test data |
cp data.1765-2005 data |
132 |
cp data.ptracers.test data.ptracers |
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
133 |
mitgcmuv > output.txt |
ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
134 |
|
ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
135 |
5 ===> check that PTRACER output and salinity output are identical. |
mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & |
136 |
|
(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 |
|
137 |
|
|
138 |
|
|
139 |
========================================================== |
========================================================== |
140 |
Instructions for carrying out a 3000-year quasi-stationary |
Instructions for carrying out time-dependent, 1765-2005, |
141 |
integration using the global_ocean.90x40x15 configuration. |
anthropogenic carbon perturbation tracer experiments using |
142 |
|
global_ocean.90x40x15 configuration and netcdf output. |
143 |
|
This assumes that the appropriate libnetcdf.a exists |
144 |
|
and that it be specified in the genmake2 option file. |
145 |
========================================================== |
========================================================== |
146 |
|
|
|
1 ===> compile, link, and execute |
|
|
|
|
147 |
cd MITgcm/exe |
cd MITgcm/exe |
148 |
rm * |
rm * |
149 |
cd ../bin |
cd ../bin |
150 |
rm * |
rm * |
151 |
cp ../verification/global_with_exf/code/* . |
cp ../verification/global_with_exf/code/* . |
|
cp ../ocean_inversion_project/code/.genmakerc . |
|
152 |
cp ../ocean_inversion_project/code/* . |
cp ../ocean_inversion_project/code/* . |
153 |
../tools/genmake |
cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h |
154 |
|
cp ../ocean_inversion_project/write_netCDF/* . |
155 |
|
\rm mk_output.F |
156 |
|
|
157 |
|
### need customized option file; example below is for nireas |
158 |
|
../tools/genmake2 -of linux_ia32_g77_netcdf |
159 |
|
|
160 |
make depend |
make depend |
161 |
make |
make |
162 |
cd ../exe |
cd ../exe |
165 |
cp ../verification/global_with_exf/input/POLY3.COEFFS . |
cp ../verification/global_with_exf/input/POLY3.COEFFS . |
166 |
ln -sf ../verification/global_with_exf/input/*.bin . |
ln -sf ../verification/global_with_exf/input/*.bin . |
167 |
cp ../ocean_inversion_project/input/* . |
cp ../ocean_inversion_project/input/* . |
168 |
|
cp data.1765-2005.1 data |
169 |
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
170 |
ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
171 |
|
ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
172 |
mitgcmuv > output .txt & |
mitgcmuv > output .txt & |
173 |
|
|
174 |
|
|
175 |
|
========================================================== |
176 |
|
Instructions for carrying out time-dependent, 1765-2005, |
177 |
|
anthropogenic carbon perturbation tracer experiments using |
178 |
|
the ecco1x1 configuration and netcdf output on columbia. |
179 |
|
This assumes that the appropriate libnetcdf.a exists |
180 |
|
and that it be specified in the genmake2 option file. |
181 |
|
It also assumes that surface forcing files are available |
182 |
|
in /nobackup2/menemenl/ocmip/iter69 |
183 |
|
========================================================== |
184 |
|
|
185 |
|
cd MITgcm/exe |
186 |
|
\rm * |
187 |
|
cd ../bin |
188 |
|
\rm * |
189 |
|
\cp ../ocean_inversion_project/code_ecco1x1/* . |
190 |
|
\cp ../ocean_inversion_project/write_netCDF/* . |
191 |
|
\rm mk_output.F |
192 |
|
\cp SIZE.h.96 SIZE.h |
193 |
|
../tools/genmake2 -of linux_ia64_efc+mpi_altix |
194 |
|
make depend |
195 |
|
make -j 16 |
196 |
|
cd ../exe |
197 |
|
\cp ../ocean_inversion_project/input_ecco1x1/* . |
198 |
|
ln -sf ../../iter69/* . |
199 |
|
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
200 |
|
ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
201 |
|
ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
202 |
|
qsub job01 |
203 |
|
|
204 |
|
|
205 |
|
========================================================== |
206 |
|
Instructions for generating netcdf output files on columbia |
207 |
|
========================================================== |
208 |
|
|
209 |
|
cd ocean_inversion_project/write_netCDF |
210 |
|
setenv F_UFMTENDIAN big |
211 |
|
|
212 |
|
(check that defaults in mk_output.F are appropriate) |
213 |
|
|
214 |
|
efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \ |
215 |
|
handle_errors.F write_nc_basisfnctns.F \ |
216 |
|
write_nc_diag_0D.F write_nc_diag_2D.F \ |
217 |
|
-I/u/menemenl/software/netcdf-3.5.0/include \ |
218 |
|
-L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf |
219 |
|
./a.out |
220 |
|
|
221 |
|
|
222 |
|
========================================================== |
223 |
|
Instructions for generating netcdf output files on orion |
224 |
|
========================================================== |
225 |
|
|
226 |
|
cd ocean_inversion_project/write_netCDF |
227 |
|
setenv F_UFMTENDIAN big |
228 |
|
|
229 |
|
(check that defaults in mk_output.F are appropriate) |
230 |
|
|
231 |
|
efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \ |
232 |
|
handle_errors.F write_nc_basisfnctns.F \ |
233 |
|
write_nc_diag_0D.F write_nc_diag_2D.F \ |
234 |
|
-I/u2/dmenem/software/netcdf-3.5.0/include \ |
235 |
|
-L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf |
236 |
|
./a.out |
237 |
|
|
238 |
|
|
239 |
====================================================== |
====================================================== |
240 |
|
|
241 |
% some matlab code for looking at fort.10 debug files |
% some matlab code for looking at fort.10 debug files |
265 |
% tracer uptake is approximately 1e18 mols. |
% tracer uptake is approximately 1e18 mols. |
266 |
lon=2:4:360; lat=-78:4:78; |
lon=2:4:360; lat=-78:4:78; |
267 |
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]; |
268 |
tracer=zeros(90,40,15,30); sumtracer1=zeros(30,1); |
mask=readbin('hFacC.001.001.data',[90 40 15],1); |
269 |
|
tracer=zeros(90,40,15,30); sumtracer=zeros(30,1); |
270 |
for i=1:30, mydisp(i) |
for i=1:30, mydisp(i) |
271 |
fn=['PTRACER' myint2str(i) '.0000000180.001.001.data']; |
fn=['PTRACER' myint2str(i) '.0000001800.001.001.data']; |
272 |
tracer(:,:,:,i)=readbin(fn,[90 40 15],1); |
tracer(:,:,:,i)=readbin(fn,[90 40 15],1); |
273 |
for x=1:length(lon) |
for j=1:length(lat) |
274 |
for y=1:length(lat) |
for k=1:length(thk) |
275 |
for z=1:length(thk) |
sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ... |
276 |
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 |
|
277 |
end |
end |
278 |
end |
end |
279 |
end |
end |
280 |
|
plot(1:30,0*sumtracer,1:30,sumtracer) |
281 |
|
|
282 |
% some matlab code for checking that one year's worth of |
|
283 |
% tracer uptake is approximately 1e18 mols. |
% check that tracer flux is 1e18 mols / year |
284 |
|
nb_seconds_per_year=31556880; |
285 |
lon=2:4:360; lat=-78:4:78; |
lon=2:4:360; lat=-78:4:78; |
286 |
thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690]; |
mask=readbin('hFacC.data',[90 40 15],1); |
287 |
tracer=zeros(90,40,15,30); sumtracer=zeros(30,1); |
tracer=zeros(90,40,30); sumtracer=zeros(30,1); |
288 |
for i=1:30, mydisp(i) |
for i=1:30, mydisp(i) |
289 |
fn=['PTRACER' myint2str(i) '.0000003600.001.001.data']; |
fn=['PtrFlux' myint2str(i) '.0000000180.data']; |
290 |
tracer(:,:,:,i)=readbin(fn,[90 40 15],1); |
tracer(:,:,i)=readbin(fn,[90 40],1); |
291 |
for j=1:length(lat) |
for j=1:length(lat) |
292 |
for k=1:length(thk) |
sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ... |
293 |
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); |
|
294 |
end |
end |
|
end |
|
295 |
end |
end |
296 |
plot(1:30,0*sumtracer,1:30,sumtracer) |
plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer)) |