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dimitri |
1.1 |
Ocean Inversion Project |
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======================= |
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Instructions for using pkg/ptracers to compute tracer |
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Green's functions for Gruber's ocean inversion project |
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dimitri |
1.3 |
(see quercus.igpp.ucla.edu/OceanInversion/ for details). |
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Preprocessed OceanInversion input files are available |
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under directories region_mask, takahashi, and |
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atm_co2 in this package. All netcdf input files |
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have been converted to binary format in order to avoid |
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having to link netcdf library with MITgcm code. See |
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respective README files in each directory for details. |
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dimitri |
1.1 |
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dimitri |
1.30 |
Instructions for CFC-11 computations are in |
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cvs co -r release1_50yr MITgcm |
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MITgcm/verification/global_with_CFC11/README |
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dimitri |
1.1 |
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dimitri |
1.27 |
Notes and problems: |
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=================== |
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there is problem generating ECCO_MaskAreaBathy.nc on columbia |
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works OK on nireas |
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variable global_mean_conc in 0D output from mk_output.F is |
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screwed up |
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dimitri |
1.2 |
=============================================== |
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First check that pkg/ptracers works OK by using |
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salinity initial and boundary conditions |
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=============================================== |
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1 ===> get MITgcm code from cvs repository |
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dimitri |
1.21 |
cvs co -r checkpoint51n_branch MITgcm_code |
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cvs co -r checkpoint51n_branch MITgcm/verification/testreport |
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cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf |
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dimitri |
1.2 |
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2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory |
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cd MITgcm |
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cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project |
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dimitri |
1.3 |
3 ===> compile and link |
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dimitri |
1.2 |
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dimitri |
1.21 |
mkdir bin exe |
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dimitri |
1.2 |
cd bin |
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dimitri |
1.22 |
\cp ../verification/global_with_exf/code/* . |
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\cp ../ocean_inversion_project/code/* . |
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\rm ptracers_*.F PTRACERS_OPTIONS.h |
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dimitri |
1.11 |
../tools/genmake2 |
| 55 |
dimitri |
1.22 |
(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi ) |
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(on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix ) |
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dimitri |
1.2 |
make depend |
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dimitri |
1.22 |
make -j 16 |
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dimitri |
1.2 |
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4 ===> execute |
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cd ../exe |
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dimitri |
1.22 |
\cp ../verification/global_with_exf/input/eedata . |
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\cp ../verification/global_with_exf/input/data.* . |
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\cp ../verification/global_with_exf/input/POLY3.COEFFS . |
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\ln -sf ../verification/global_with_exf/input/*.bin . |
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\cp ../ocean_inversion_project/input/* . |
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\cp data.test data |
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\cp data.ptracers.test data.ptracers |
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./mitgcmuv >! output.txt |
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dimitri |
1.5 |
5 ===> check that PTRACER output and salinity output are identical. |
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dimitri |
1.2 |
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diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data |
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diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data |
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dimitri |
1.14 |
diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data |
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diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data |
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dimitri |
1.3 |
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dimitri |
1.1 |
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dimitri |
1.8 |
========================================================== |
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MPI instructions for carrying out a 3000-year quasi-stationary |
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integration using the global_ocean.90x40x15 configuration. |
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========================================================== |
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cd MITgcm/exe |
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rm * |
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cd ../bin |
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rm * |
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cp ../verification/global_with_exf/code/* . |
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cp ../ocean_inversion_project/code/* . |
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dimitri |
1.12 |
rm PTRACERS_OPTIONS.h |
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dimitri |
1.8 |
cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h |
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cp SIZE.h_mpi SIZE.h |
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dimitri |
1.11 |
../tools/genmake2 |
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(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) |
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dimitri |
1.8 |
make depend |
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make |
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cd ../exe |
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cp ../verification/global_with_exf/input/eedata . |
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cp ../verification/global_with_exf/input/data.* . |
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cp ../verification/global_with_exf/input/POLY3.COEFFS . |
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ln -sf ../verification/global_with_exf/input/*.bin . |
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cp ../ocean_inversion_project/input/* . |
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ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
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ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
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dimitri |
1.17 |
cp data.stationary.1 data |
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mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & |
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dimitri |
1.19 |
(on orion: qsub job.orion) |
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dimitri |
1.12 |
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dimitri |
1.22 |
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dimitri |
1.12 |
========================================================== |
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dimitri |
1.19 |
MPI instructions for carrying out time-dependent, 1765-2005, |
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dimitri |
1.12 |
anthropogenic carbon perturbation tracer experiments using |
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the global_ocean.90x40x15 configuration. |
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========================================================== |
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cd MITgcm/exe |
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rm * |
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cd ../bin |
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rm * |
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cp ../verification/global_with_exf/code/* . |
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cp ../ocean_inversion_project/code/* . |
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dimitri |
1.19 |
cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h |
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cp SIZE.h_mpi SIZE.h |
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dimitri |
1.12 |
../tools/genmake2 |
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(on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) |
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dimitri |
1.13 |
make depend |
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make |
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cd ../exe |
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cp ../verification/global_with_exf/input/eedata . |
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cp ../verification/global_with_exf/input/data.* . |
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cp ../verification/global_with_exf/input/POLY3.COEFFS . |
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ln -sf ../verification/global_with_exf/input/*.bin . |
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cp ../ocean_inversion_project/input/* . |
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cp data.1765-2005 data |
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ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
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ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
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ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
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dimitri |
1.19 |
mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & |
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(on orion: qsub job.orion.td) |
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dimitri |
1.13 |
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========================================================== |
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Instructions for carrying out time-dependent, 1765-2005, |
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anthropogenic carbon perturbation tracer experiments using |
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global_ocean.90x40x15 configuration and netcdf output. |
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This assumes that the appropriate libnetcdf.a exists |
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and that it be specified in the genmake2 option file. |
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========================================================== |
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cd MITgcm/exe |
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rm * |
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cd ../bin |
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rm * |
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cp ../verification/global_with_exf/code/* . |
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cp ../ocean_inversion_project/code/* . |
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cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h |
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cp ../ocean_inversion_project/write_netCDF/* . |
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dimitri |
1.20 |
\rm mk_output.F |
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dimitri |
1.13 |
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### need customized option file; example below is for nireas |
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../tools/genmake2 -of linux_ia32_g77_netcdf |
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dimitri |
1.12 |
make depend |
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make |
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cd ../exe |
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cp ../verification/global_with_exf/input/eedata . |
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cp ../verification/global_with_exf/input/data.* . |
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cp ../verification/global_with_exf/input/POLY3.COEFFS . |
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ln -sf ../verification/global_with_exf/input/*.bin . |
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cp ../ocean_inversion_project/input/* . |
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dimitri |
1.18 |
cp data.1765-2005.1 data |
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dimitri |
1.12 |
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
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ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
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ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
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mitgcmuv > output .txt & |
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dimitri |
1.19 |
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dimitri |
1.22 |
========================================================== |
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Instructions for carrying out time-dependent, 1765-2005, |
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anthropogenic carbon perturbation tracer experiments using |
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the ecco1x1 configuration and netcdf output on columbia. |
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This assumes that the appropriate libnetcdf.a exists |
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and that it be specified in the genmake2 option file. |
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It also assumes that surface forcing files are available |
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dimitri |
1.28 |
in MITgcm/../iter69 |
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dimitri |
1.22 |
========================================================== |
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cd MITgcm/exe |
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\rm * |
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cd ../bin |
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\rm * |
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\cp ../ocean_inversion_project/code_ecco1x1/* . |
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\cp ../ocean_inversion_project/write_netCDF/* . |
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\rm mk_output.F |
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dimitri |
1.24 |
\cp SIZE.h.96 SIZE.h |
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dimitri |
1.22 |
../tools/genmake2 -of linux_ia64_efc+mpi_altix |
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make depend |
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make -j 16 |
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cd ../exe |
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\cp ../ocean_inversion_project/input_ecco1x1/* . |
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dimitri |
1.23 |
ln -sf ../../iter69/* . |
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dimitri |
1.22 |
ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
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ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
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ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . |
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qsub job01 |
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dimitri |
1.19 |
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========================================================== |
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dimitri |
1.28 |
Instructions for carrying out 3000-year quasi-stationary |
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integration using the ecco1x1 configuration and netcdf |
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output on columbia. |
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This assumes that the appropriate libnetcdf.a exists |
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and that it be specified in the genmake2 option file. |
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It also assumes that surface forcing files are available |
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in MITgcm/../iter69 |
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========================================================== |
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cd MITgcm/exe |
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\rm * |
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cd ../bin |
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\rm * |
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\cp ../ocean_inversion_project/code_ecco1x1/* . |
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\cp ../ocean_inversion_project/write_netCDF/* . |
| 225 |
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\rm mk_output.F |
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\cp SIZE.h.96 SIZE.h |
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\cp PTRACERS_OPTIONS.h.stationary PTRACERS_OPTIONS.h |
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../tools/genmake2 -of linux_ia64_efc+mpi_altix |
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make depend |
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make -j 16 |
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cd ../exe |
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\cp ../ocean_inversion_project/input_ecco1x1/* . |
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\ln -sf ../../iter69/* . |
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\ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . |
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\ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . |
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qsub job01s |
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========================================================== |
| 240 |
dimitri |
1.25 |
Instructions for generating netcdf output files on columbia |
| 241 |
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========================================================== |
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| 243 |
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cd ocean_inversion_project/write_netCDF |
| 244 |
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setenv F_UFMTENDIAN big |
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| 246 |
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(check that defaults in mk_output.F are appropriate) |
| 247 |
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dimitri |
1.29 |
ifort -assume byterecl -W0 -WB mk_output.F write_nc_phys.F nc_util.F \ |
| 249 |
dimitri |
1.25 |
handle_errors.F write_nc_basisfnctns.F \ |
| 250 |
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write_nc_diag_0D.F write_nc_diag_2D.F \ |
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-I/u/menemenl/software/netcdf-3.5.0/include \ |
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-L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf |
| 253 |
dimitri |
1.26 |
./a.out |
| 254 |
dimitri |
1.25 |
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| 256 |
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========================================================== |
| 257 |
dimitri |
1.19 |
Instructions for generating netcdf output files on orion |
| 258 |
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========================================================== |
| 259 |
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| 260 |
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cd ocean_inversion_project/write_netCDF |
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setenv F_UFMTENDIAN big |
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| 263 |
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(check that defaults in mk_output.F are appropriate) |
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| 265 |
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efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \ |
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handle_errors.F write_nc_basisfnctns.F \ |
| 267 |
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write_nc_diag_0D.F write_nc_diag_2D.F \ |
| 268 |
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-I/u2/dmenem/software/netcdf-3.5.0/include \ |
| 269 |
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-L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf |
| 270 |
dimitri |
1.26 |
./a.out |
| 271 |
dimitri |
1.8 |
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dimitri |
1.3 |
====================================================== |
| 274 |
dimitri |
1.1 |
|
| 275 |
dimitri |
1.3 |
% some matlab code for looking at fort.10 debug files |
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load fort.10 |
| 277 |
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tak=zeros(90,40,12); |
| 278 |
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for n=1:length(fort) |
| 279 |
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m=fort(n,1); i=fort(n,2); j=fort(n,3); |
| 280 |
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if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end |
| 281 |
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end |
| 282 |
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lon=2:4:360; lat=-78:4:78; |
| 283 |
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clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10) |
| 284 |
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caxis([-6 6]), colorbar, plotland |
| 285 |
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| 286 |
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% some matlab code for looking at PTRACER output files |
| 287 |
dimitri |
1.4 |
salt=readbin('S.0000000020.001.001.data',[90 40 15],1); |
| 288 |
dimitri |
1.3 |
tracer=zeros(90,40,15,30); |
| 289 |
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for i=1:30 |
| 290 |
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fn=['PTRACER' myint2str(i) '.0000000020.001.001.data']; |
| 291 |
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tracer(:,:,:,i)=readbin(fn,[90 40 15],1); |
| 292 |
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clf, mypcolor(tracer(:,:,1,i)'); pause(1) |
| 293 |
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end |
| 294 |
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tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)') |
| 295 |
dimitri |
1.4 |
mypcolor( |
| 296 |
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dimitri |
1.3 |
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% some matlab code for checking that one year's worth of |
| 299 |
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% tracer uptake is approximately 1e18 mols. |
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lon=2:4:360; lat=-78:4:78; |
| 301 |
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thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690]; |
| 302 |
dimitri |
1.7 |
mask=readbin('hFacC.001.001.data',[90 40 15],1); |
| 303 |
dimitri |
1.3 |
tracer=zeros(90,40,15,30); sumtracer=zeros(30,1); |
| 304 |
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for i=1:30, mydisp(i) |
| 305 |
dimitri |
1.7 |
fn=['PTRACER' myint2str(i) '.0000001800.001.001.data']; |
| 306 |
dimitri |
1.3 |
tracer(:,:,:,i)=readbin(fn,[90 40 15],1); |
| 307 |
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for j=1:length(lat) |
| 308 |
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for k=1:length(thk) |
| 309 |
dimitri |
1.7 |
sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ... |
| 310 |
dimitri |
1.3 |
thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180); |
| 311 |
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end |
| 312 |
dimitri |
1.1 |
end |
| 313 |
dimitri |
1.3 |
end |
| 314 |
dimitri |
1.4 |
plot(1:30,0*sumtracer,1:30,sumtracer) |
| 315 |
dimitri |
1.21 |
|
| 316 |
|
|
|
| 317 |
|
|
% check that tracer flux is 1e18 mols / year |
| 318 |
|
|
nb_seconds_per_year=31556880; |
| 319 |
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lon=2:4:360; lat=-78:4:78; |
| 320 |
|
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mask=readbin('hFacC.data',[90 40 15],1); |
| 321 |
|
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tracer=zeros(90,40,30); sumtracer=zeros(30,1); |
| 322 |
|
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for i=1:30, mydisp(i) |
| 323 |
|
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fn=['PtrFlux' myint2str(i) '.0000000180.data']; |
| 324 |
|
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tracer(:,:,i)=readbin(fn,[90 40],1); |
| 325 |
|
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for j=1:length(lat) |
| 326 |
|
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sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ... |
| 327 |
|
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nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180); |
| 328 |
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end |
| 329 |
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end |
| 330 |
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plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer)) |
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