| 1 |
dimitri |
1.1 |
Ocean Inversion Project |
| 2 |
|
|
======================= |
| 3 |
|
|
|
| 4 |
|
|
Instructions for using pkg/ptracers to compute tracer |
| 5 |
|
|
Green's functions for Gruber's ocean inversion project |
| 6 |
dimitri |
1.3 |
(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 |
dimitri |
1.1 |
|
| 15 |
|
|
|
| 16 |
dimitri |
1.27 |
Notes and problems: |
| 17 |
|
|
=================== |
| 18 |
|
|
|
| 19 |
|
|
there is problem generating ECCO_MaskAreaBathy.nc on columbia |
| 20 |
|
|
works OK on nireas |
| 21 |
|
|
|
| 22 |
|
|
variable global_mean_conc in 0D output from mk_output.F is |
| 23 |
|
|
screwed up |
| 24 |
|
|
|
| 25 |
|
|
|
| 26 |
|
|
|
| 27 |
dimitri |
1.2 |
=============================================== |
| 28 |
|
|
First check that pkg/ptracers works OK by using |
| 29 |
|
|
salinity initial and boundary conditions |
| 30 |
|
|
=============================================== |
| 31 |
|
|
|
| 32 |
|
|
1 ===> get MITgcm code from cvs repository |
| 33 |
|
|
|
| 34 |
dimitri |
1.21 |
cvs co -r checkpoint51n_branch MITgcm_code |
| 35 |
|
|
cvs co -r checkpoint51n_branch MITgcm/verification/testreport |
| 36 |
|
|
cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf |
| 37 |
dimitri |
1.2 |
|
| 38 |
|
|
2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory |
| 39 |
|
|
|
| 40 |
|
|
cd MITgcm |
| 41 |
|
|
cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project |
| 42 |
|
|
|
| 43 |
dimitri |
1.3 |
3 ===> compile and link |
| 44 |
dimitri |
1.2 |
|
| 45 |
dimitri |
1.21 |
mkdir bin exe |
| 46 |
dimitri |
1.2 |
cd bin |
| 47 |
dimitri |
1.22 |
\cp ../verification/global_with_exf/code/* . |
| 48 |
|
|
\cp ../ocean_inversion_project/code/* . |
| 49 |
|
|
\rm ptracers_*.F PTRACERS_OPTIONS.h |
| 50 |
dimitri |
1.11 |
../tools/genmake2 |
| 51 |
dimitri |
1.22 |
(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi ) |
| 52 |
|
|
(on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix ) |
| 53 |
dimitri |
1.2 |
make depend |
| 54 |
dimitri |
1.22 |
make -j 16 |
| 55 |
dimitri |
1.2 |
|
| 56 |
|
|
4 ===> execute |
| 57 |
|
|
|
| 58 |
|
|
cd ../exe |
| 59 |
dimitri |
1.22 |
\cp ../verification/global_with_exf/input/eedata . |
| 60 |
|
|
\cp ../verification/global_with_exf/input/data.* . |
| 61 |
|
|
\cp ../verification/global_with_exf/input/POLY3.COEFFS . |
| 62 |
|
|
\ln -sf ../verification/global_with_exf/input/*.bin . |
| 63 |
|
|
\cp ../ocean_inversion_project/input/* . |
| 64 |
|
|
\cp data.test data |
| 65 |
|
|
\cp data.ptracers.test data.ptracers |
| 66 |
|
|
./mitgcmuv >! output.txt |
| 67 |
|
|
|
| 68 |
dimitri |
1.5 |
5 ===> check that PTRACER output and salinity output are identical. |
| 69 |
dimitri |
1.2 |
|
| 70 |
|
|
diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data |
| 71 |
|
|
diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data |
| 72 |
dimitri |
1.14 |
diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data |
| 73 |
|
|
diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data |
| 74 |
dimitri |
1.3 |
|
| 75 |
dimitri |
1.1 |
|
| 76 |
dimitri |
1.8 |
========================================================== |
| 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/* . |
| 86 |
|
|
cp ../ocean_inversion_project/code/* . |
| 87 |
dimitri |
1.12 |
rm PTRACERS_OPTIONS.h |
| 88 |
dimitri |
1.8 |
cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h |
| 89 |
|
|
cp SIZE.h_mpi SIZE.h |
| 90 |
dimitri |
1.11 |
../tools/genmake2 |
| 91 |
|
|
(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) |
| 92 |
dimitri |
1.8 |
make depend |
| 93 |
|
|
make |
| 94 |
|
|
cd ../exe |
| 95 |
|
|
cp ../verification/global_with_exf/input/eedata . |
| 96 |
|
|
cp ../verification/global_with_exf/input/data.* . |
| 97 |
|
|
cp ../verification/global_with_exf/input/POLY3.COEFFS . |
| 98 |
|
|
ln -sf ../verification/global_with_exf/input/*.bin . |
| 99 |
|
|
cp ../ocean_inversion_project/input/* . |
| 100 |
|
|
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
| 101 |
|
|
ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
| 102 |
dimitri |
1.17 |
cp data.stationary.1 data |
| 103 |
|
|
mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & |
| 104 |
dimitri |
1.19 |
(on orion: qsub job.orion) |
| 105 |
dimitri |
1.12 |
|
| 106 |
dimitri |
1.22 |
|
| 107 |
dimitri |
1.12 |
========================================================== |
| 108 |
dimitri |
1.19 |
MPI instructions for carrying out time-dependent, 1765-2005, |
| 109 |
dimitri |
1.12 |
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 |
dimitri |
1.19 |
cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h |
| 120 |
|
|
cp SIZE.h_mpi SIZE.h |
| 121 |
dimitri |
1.12 |
../tools/genmake2 |
| 122 |
|
|
(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) |
| 123 |
dimitri |
1.13 |
make depend |
| 124 |
|
|
make |
| 125 |
|
|
cd ../exe |
| 126 |
|
|
cp ../verification/global_with_exf/input/eedata . |
| 127 |
|
|
cp ../verification/global_with_exf/input/data.* . |
| 128 |
|
|
cp ../verification/global_with_exf/input/POLY3.COEFFS . |
| 129 |
|
|
ln -sf ../verification/global_with_exf/input/*.bin . |
| 130 |
|
|
cp ../ocean_inversion_project/input/* . |
| 131 |
|
|
cp data.1765-2005 data |
| 132 |
|
|
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
| 133 |
|
|
ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
| 134 |
|
|
ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
| 135 |
dimitri |
1.19 |
mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & |
| 136 |
|
|
(on orion: qsub job.orion.td) |
| 137 |
dimitri |
1.13 |
|
| 138 |
|
|
|
| 139 |
|
|
========================================================== |
| 140 |
|
|
Instructions for carrying out time-dependent, 1765-2005, |
| 141 |
|
|
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 |
|
|
|
| 147 |
|
|
cd MITgcm/exe |
| 148 |
|
|
rm * |
| 149 |
|
|
cd ../bin |
| 150 |
|
|
rm * |
| 151 |
|
|
cp ../verification/global_with_exf/code/* . |
| 152 |
|
|
cp ../ocean_inversion_project/code/* . |
| 153 |
|
|
cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h |
| 154 |
|
|
cp ../ocean_inversion_project/write_netCDF/* . |
| 155 |
dimitri |
1.20 |
\rm mk_output.F |
| 156 |
dimitri |
1.13 |
|
| 157 |
|
|
### need customized option file; example below is for nireas |
| 158 |
|
|
../tools/genmake2 -of linux_ia32_g77_netcdf |
| 159 |
|
|
|
| 160 |
dimitri |
1.12 |
make depend |
| 161 |
|
|
make |
| 162 |
|
|
cd ../exe |
| 163 |
|
|
cp ../verification/global_with_exf/input/eedata . |
| 164 |
|
|
cp ../verification/global_with_exf/input/data.* . |
| 165 |
|
|
cp ../verification/global_with_exf/input/POLY3.COEFFS . |
| 166 |
|
|
ln -sf ../verification/global_with_exf/input/*.bin . |
| 167 |
|
|
cp ../ocean_inversion_project/input/* . |
| 168 |
dimitri |
1.18 |
cp data.1765-2005.1 data |
| 169 |
dimitri |
1.12 |
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
| 170 |
|
|
ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
| 171 |
|
|
ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
| 172 |
|
|
mitgcmuv > output .txt & |
| 173 |
dimitri |
1.19 |
|
| 174 |
|
|
|
| 175 |
dimitri |
1.22 |
========================================================== |
| 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 |
dimitri |
1.28 |
in MITgcm/../iter69 |
| 183 |
dimitri |
1.22 |
========================================================== |
| 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 |
dimitri |
1.24 |
\cp SIZE.h.96 SIZE.h |
| 193 |
dimitri |
1.22 |
../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 |
dimitri |
1.23 |
ln -sf ../../iter69/* . |
| 199 |
dimitri |
1.22 |
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 |
dimitri |
1.19 |
|
| 205 |
|
|
========================================================== |
| 206 |
dimitri |
1.28 |
Instructions for carrying out 3000-year quasi-stationary |
| 207 |
|
|
integration using the ecco1x1 configuration and netcdf |
| 208 |
|
|
output on columbia. |
| 209 |
|
|
This assumes that the appropriate libnetcdf.a exists |
| 210 |
|
|
and that it be specified in the genmake2 option file. |
| 211 |
|
|
It also assumes that surface forcing files are available |
| 212 |
|
|
in MITgcm/../iter69 |
| 213 |
|
|
========================================================== |
| 214 |
|
|
|
| 215 |
|
|
cd MITgcm/exe |
| 216 |
|
|
\rm * |
| 217 |
|
|
cd ../bin |
| 218 |
|
|
\rm * |
| 219 |
|
|
\cp ../ocean_inversion_project/code_ecco1x1/* . |
| 220 |
|
|
\cp ../ocean_inversion_project/write_netCDF/* . |
| 221 |
|
|
\rm mk_output.F |
| 222 |
|
|
\cp SIZE.h.96 SIZE.h |
| 223 |
|
|
\cp PTRACERS_OPTIONS.h.stationary PTRACERS_OPTIONS.h |
| 224 |
|
|
../tools/genmake2 -of linux_ia64_efc+mpi_altix |
| 225 |
|
|
make depend |
| 226 |
|
|
make -j 16 |
| 227 |
|
|
cd ../exe |
| 228 |
|
|
\cp ../ocean_inversion_project/input_ecco1x1/* . |
| 229 |
|
|
\ln -sf ../../iter69/* . |
| 230 |
|
|
\ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
| 231 |
|
|
\ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
| 232 |
|
|
qsub job01s |
| 233 |
|
|
|
| 234 |
|
|
|
| 235 |
|
|
========================================================== |
| 236 |
dimitri |
1.25 |
Instructions for generating netcdf output files on columbia |
| 237 |
|
|
========================================================== |
| 238 |
|
|
|
| 239 |
|
|
cd ocean_inversion_project/write_netCDF |
| 240 |
|
|
setenv F_UFMTENDIAN big |
| 241 |
|
|
|
| 242 |
|
|
(check that defaults in mk_output.F are appropriate) |
| 243 |
|
|
|
| 244 |
|
|
efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \ |
| 245 |
|
|
handle_errors.F write_nc_basisfnctns.F \ |
| 246 |
|
|
write_nc_diag_0D.F write_nc_diag_2D.F \ |
| 247 |
|
|
-I/u/menemenl/software/netcdf-3.5.0/include \ |
| 248 |
|
|
-L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf |
| 249 |
dimitri |
1.26 |
./a.out |
| 250 |
dimitri |
1.25 |
|
| 251 |
|
|
|
| 252 |
|
|
========================================================== |
| 253 |
dimitri |
1.19 |
Instructions for generating netcdf output files on orion |
| 254 |
|
|
========================================================== |
| 255 |
|
|
|
| 256 |
|
|
cd ocean_inversion_project/write_netCDF |
| 257 |
|
|
setenv F_UFMTENDIAN big |
| 258 |
|
|
|
| 259 |
|
|
(check that defaults in mk_output.F are appropriate) |
| 260 |
|
|
|
| 261 |
|
|
efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \ |
| 262 |
|
|
handle_errors.F write_nc_basisfnctns.F \ |
| 263 |
|
|
write_nc_diag_0D.F write_nc_diag_2D.F \ |
| 264 |
|
|
-I/u2/dmenem/software/netcdf-3.5.0/include \ |
| 265 |
|
|
-L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf |
| 266 |
dimitri |
1.26 |
./a.out |
| 267 |
dimitri |
1.8 |
|
| 268 |
|
|
|
| 269 |
dimitri |
1.3 |
====================================================== |
| 270 |
dimitri |
1.1 |
|
| 271 |
dimitri |
1.3 |
% some matlab code for looking at fort.10 debug files |
| 272 |
|
|
load fort.10 |
| 273 |
|
|
tak=zeros(90,40,12); |
| 274 |
|
|
for n=1:length(fort) |
| 275 |
|
|
m=fort(n,1); i=fort(n,2); j=fort(n,3); |
| 276 |
|
|
if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end |
| 277 |
|
|
end |
| 278 |
|
|
lon=2:4:360; lat=-78:4:78; |
| 279 |
|
|
clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10) |
| 280 |
|
|
caxis([-6 6]), colorbar, plotland |
| 281 |
|
|
|
| 282 |
|
|
% some matlab code for looking at PTRACER output files |
| 283 |
dimitri |
1.4 |
salt=readbin('S.0000000020.001.001.data',[90 40 15],1); |
| 284 |
dimitri |
1.3 |
tracer=zeros(90,40,15,30); |
| 285 |
|
|
for i=1:30 |
| 286 |
|
|
fn=['PTRACER' myint2str(i) '.0000000020.001.001.data']; |
| 287 |
|
|
tracer(:,:,:,i)=readbin(fn,[90 40 15],1); |
| 288 |
|
|
clf, mypcolor(tracer(:,:,1,i)'); pause(1) |
| 289 |
|
|
end |
| 290 |
|
|
tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)') |
| 291 |
dimitri |
1.4 |
mypcolor( |
| 292 |
|
|
|
| 293 |
dimitri |
1.3 |
|
| 294 |
|
|
% some matlab code for checking that one year's worth of |
| 295 |
|
|
% tracer uptake is approximately 1e18 mols. |
| 296 |
|
|
lon=2:4:360; lat=-78:4:78; |
| 297 |
|
|
thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690]; |
| 298 |
dimitri |
1.7 |
mask=readbin('hFacC.001.001.data',[90 40 15],1); |
| 299 |
dimitri |
1.3 |
tracer=zeros(90,40,15,30); sumtracer=zeros(30,1); |
| 300 |
|
|
for i=1:30, mydisp(i) |
| 301 |
dimitri |
1.7 |
fn=['PTRACER' myint2str(i) '.0000001800.001.001.data']; |
| 302 |
dimitri |
1.3 |
tracer(:,:,:,i)=readbin(fn,[90 40 15],1); |
| 303 |
|
|
for j=1:length(lat) |
| 304 |
|
|
for k=1:length(thk) |
| 305 |
dimitri |
1.7 |
sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ... |
| 306 |
dimitri |
1.3 |
thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180); |
| 307 |
|
|
end |
| 308 |
dimitri |
1.1 |
end |
| 309 |
dimitri |
1.3 |
end |
| 310 |
dimitri |
1.4 |
plot(1:30,0*sumtracer,1:30,sumtracer) |
| 311 |
dimitri |
1.21 |
|
| 312 |
|
|
|
| 313 |
|
|
% check that tracer flux is 1e18 mols / year |
| 314 |
|
|
nb_seconds_per_year=31556880; |
| 315 |
|
|
lon=2:4:360; lat=-78:4:78; |
| 316 |
|
|
mask=readbin('hFacC.data',[90 40 15],1); |
| 317 |
|
|
tracer=zeros(90,40,30); sumtracer=zeros(30,1); |
| 318 |
|
|
for i=1:30, mydisp(i) |
| 319 |
|
|
fn=['PtrFlux' myint2str(i) '.0000000180.data']; |
| 320 |
|
|
tracer(:,:,i)=readbin(fn,[90 40],1); |
| 321 |
|
|
for j=1:length(lat) |
| 322 |
|
|
sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ... |
| 323 |
|
|
nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180); |
| 324 |
|
|
end |
| 325 |
|
|
end |
| 326 |
|
|
plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer)) |
Parent Directory
| 
Revision Log
| 
Revision Graph