--- MITgcm_contrib/ocean_inversion_project/README 2003/09/17 21:45:51 1.1 +++ MITgcm_contrib/ocean_inversion_project/README 2004/10/08 06:21:29 1.23 @@ -3,75 +3,266 @@ Instructions for using pkg/ptracers to compute tracer Green's functions for Gruber's ocean inversion project -(http://quercus.igpp.ucla.edu/OceanInversion/). +(see quercus.igpp.ucla.edu/OceanInversion/ for details). -===================================== - -To run a pkg/ptracers test case using salt initial and boundary conditions: - - - - cd MITgcm/bin - cp ../verification/global_with_exf/code/* . - cp ../code/.genmakerc . - cp ../code/* . - cp ../code/ptracers_forcing.F.test ptracers_forcing.F - cp ../code/ptracers_init.F.test ptracers_init.F - cp ../code/ptracers_read_mask.F.test ptracers_read_mask.F - ../tools/genmake +Preprocessed OceanInversion input files are available +under directories region_mask, takahashi, and +atm_co2 in this package. All netcdf input files +have been converted to binary format in order to avoid +having to link netcdf library with MITgcm code. See +respective README files in each directory for details. + + +=============================================== +First check that pkg/ptracers works OK by using +salinity initial and boundary conditions +=============================================== + +1 ===> get MITgcm code from cvs repository + + cvs co -r checkpoint51n_branch MITgcm_code + cvs co -r checkpoint51n_branch MITgcm/verification/testreport + cvs co -r checkpoint51n_branch MITgcm/verification/global_with_exf + +2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory + + cd MITgcm + cvs co -d ocean_inversion_project MITgcm_contrib/ocean_inversion_project + +3 ===> compile and link + + mkdir bin exe + cd bin + \cp ../verification/global_with_exf/code/* . + \cp ../ocean_inversion_project/code/* . + \rm ptracers_*.F PTRACERS_OPTIONS.h + ../tools/genmake2 + (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi ) + (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix ) make depend - 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 + make -j 16 - diff PTRACER30.0000000020.001.001.data PTRACER01.0000000020.001.001.data - diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data +4 ===> execute -===> examine interpolation output for 30-region mask + cd ../exe + \cp ../verification/global_with_exf/input/eedata . + \cp ../verification/global_with_exf/input/data.* . + \cp ../verification/global_with_exf/input/POLY3.COEFFS . + \ln -sf ../verification/global_with_exf/input/*.bin . + \cp ../ocean_inversion_project/input/* . + \cp data.test data + \cp data.ptracers.test data.ptracers + ./mitgcmuv >! output.txt - matlab - mask=zeros(94,44,30); - load fort.10 - for i=1:length(fort) - mask(fort(i,2)+2,fort(i,3)+2,fort(i,1))=fort(i,4); - end - for i=1:30 - mypcolor(mask(3:92,3:42,i)'); - colorbar,title(i),pause - end - mypcolor(sum(mask,3)'); colorbar +5 ===> check that PTRACER output and salinity output are identical. -===================================== + diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data + diff PTRACER30.0000000020.001.001.data S.0000000020.001.001.data + diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data + diff PTRtave30.0000000020.001.001.data Stave.0000000020.001.001.data -Global ocean experiment with ptracers -===================================== +========================================================== +MPI instructions for carrying out a 3000-year quasi-stationary +integration using the global_ocean.90x40x15 configuration. +========================================================== + + cd MITgcm/exe + rm * + cd ../bin + rm * + cp ../verification/global_with_exf/code/* . + cp ../ocean_inversion_project/code/* . + rm PTRACERS_OPTIONS.h + cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h + cp SIZE.h_mpi SIZE.h + ../tools/genmake2 + (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) + make depend + make + cd ../exe + cp ../verification/global_with_exf/input/eedata . + cp ../verification/global_with_exf/input/data.* . + cp ../verification/global_with_exf/input/POLY3.COEFFS . + ln -sf ../verification/global_with_exf/input/*.bin . + cp ../ocean_inversion_project/input/* . + ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . + ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . + cp data.stationary.1 data + mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & + (on orion: qsub job.orion) + + +========================================================== +MPI instructions for carrying out time-dependent, 1765-2005, +anthropogenic carbon perturbation tracer experiments using +the global_ocean.90x40x15 configuration. +========================================================== + + cd MITgcm/exe + rm * + cd ../bin + rm * + cp ../verification/global_with_exf/code/* . + cp ../ocean_inversion_project/code/* . + cp CPP_EEOPTIONS.h_mpi CPP_EEOPTIONS.h + cp SIZE.h_mpi SIZE.h + ../tools/genmake2 + (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi) + make depend + make + cd ../exe + cp ../verification/global_with_exf/input/eedata . + cp ../verification/global_with_exf/input/data.* . + cp ../verification/global_with_exf/input/POLY3.COEFFS . + ln -sf ../verification/global_with_exf/input/*.bin . + cp ../ocean_inversion_project/input/* . + cp data.1765-2005 data + ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . + ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . + ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . + mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog & + (on orion: qsub job.orion.td) + + +========================================================== +Instructions for carrying out time-dependent, 1765-2005, +anthropogenic carbon perturbation tracer experiments using +global_ocean.90x40x15 configuration and netcdf output. +This assumes that the appropriate libnetcdf.a exists +and that it be specified in the genmake2 option file. +========================================================== + + cd MITgcm/exe + rm * + cd ../bin + rm * + cp ../verification/global_with_exf/code/* . + cp ../ocean_inversion_project/code/* . + cp PTRACERS_OPTIONS.h.netcdf PTRACERS_OPTIONS.h + cp ../ocean_inversion_project/write_netCDF/* . + \rm mk_output.F -===> set up and integrate 30-tracer computation +### need customized option file; example below is for nireas + ../tools/genmake2 -of linux_ia32_g77_netcdf - cd MITgcm/bin - cp ../verification/global_with_exf/code/* . - cp ../code/.genmakerc . - cp ../code/* . - ../tools/genmake make depend make cd ../exe - cp ../verification/global_with_exf/input/* . - cp ../input/* . - mitgcmuv > output .txt - -===> look at output - - matlab - for i=1:30 - tr=readbin(['PTRACER' myint2str(i) ... - '.0000000020.001.001.data'],[90 40 15],1); - mypcolor(tr(:,:,2)'), colorbar, pause(1) + cp ../verification/global_with_exf/input/eedata . + cp ../verification/global_with_exf/input/data.* . + cp ../verification/global_with_exf/input/POLY3.COEFFS . + ln -sf ../verification/global_with_exf/input/*.bin . + cp ../ocean_inversion_project/input/* . + cp data.1765-2005.1 data + ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . + ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . + ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . + mitgcmuv > output .txt & + + +========================================================== +Instructions for carrying out time-dependent, 1765-2005, +anthropogenic carbon perturbation tracer experiments using +the ecco1x1 configuration and netcdf output on columbia. +This assumes that the appropriate libnetcdf.a exists +and that it be specified in the genmake2 option file. +It also assumes that surface forcing files are available +in /nobackup2/menemenl/ocmip/iter69 +========================================================== + + cd MITgcm/exe + \rm * + cd ../bin + \rm * + \cp ../ocean_inversion_project/code_ecco1x1/* . + \cp ../ocean_inversion_project/write_netCDF/* . + \rm mk_output.F + \cp SIZE.h.144 SIZE.h + ../tools/genmake2 -of linux_ia64_efc+mpi_altix + make depend + make -j 16 + cd ../exe + \cp ../ocean_inversion_project/input_ecco1x1/* . + ln -sf ../../iter69/* . + ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin . + ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin . + ln -sf ../ocean_inversion_project/atm_co2/splco2_cis92a.dat . + qsub job01 + + +========================================================== +Instructions for generating netcdf output files on orion +========================================================== + +cd ocean_inversion_project/write_netCDF +setenv F_UFMTENDIAN big + +(check that defaults in mk_output.F are appropriate) + +efc -W0 -WB mk_output.F write_nc_phys.F nc_util.F \ + handle_errors.F write_nc_basisfnctns.F \ + write_nc_diag_0D.F write_nc_diag_2D.F \ + -I/u2/dmenem/software/netcdf-3.5.0/include \ + -L/u2/dmenem/software/netcdf-3.5.0/lib -lnetcdf +a.out + + +====================================================== + +% some matlab code for looking at fort.10 debug files +load fort.10 +tak=zeros(90,40,12); +for n=1:length(fort) + m=fort(n,1); i=fort(n,2); j=fort(n,3); + if i>0&i<91&j>0&j<41, tak(i,j,m)=fort(n,4); end +end +lon=2:4:360; lat=-78:4:78; +clf, contourf(lon,lat,mean(tak(:,:,1),3)',-10:10) +caxis([-6 6]), colorbar, plotland + +% some matlab code for looking at PTRACER output files +salt=readbin('S.0000000020.001.001.data',[90 40 15],1); +tracer=zeros(90,40,15,30); +for i=1:30 + fn=['PTRACER' myint2str(i) '.0000000020.001.001.data']; + tracer(:,:,:,i)=readbin(fn,[90 40 15],1); + clf, mypcolor(tracer(:,:,1,i)'); pause(1) +end +tmp=sum(tracer,4); clf, mypcolor(tmp(:,:,1)') +mypcolor( + + +% some matlab code for checking that one year's worth of +% tracer uptake is approximately 1e18 mols. +lon=2:4:360; lat=-78:4:78; +thk=[50 70 100 140 190 240 290 340 390 440 490 540 590 640 690]; +mask=readbin('hFacC.001.001.data',[90 40 15],1); +tracer=zeros(90,40,15,30); sumtracer=zeros(30,1); +for i=1:30, mydisp(i) + fn=['PTRACER' myint2str(i) '.0000001800.001.001.data']; + tracer(:,:,:,i)=readbin(fn,[90 40 15],1); + for j=1:length(lat) + for k=1:length(thk) + sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ... + thk(k) * (4*1.113195e+05)^2 * cos(pi*lat(j)/180); + end end +end +plot(1:30,0*sumtracer,1:30,sumtracer) + +% check that tracer flux is 1e18 mols / year +nb_seconds_per_year=31556880; +lon=2:4:360; lat=-78:4:78; +mask=readbin('hFacC.data',[90 40 15],1); +tracer=zeros(90,40,30); sumtracer=zeros(30,1); +for i=1:30, mydisp(i) + fn=['PtrFlux' myint2str(i) '.0000000180.data']; + tracer(:,:,i)=readbin(fn,[90 40],1); + for j=1:length(lat) + sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ... + nb_seconds_per_year* (4*1.113195e+05)^2 * cos(pi*lat(j)/180); + end +end +plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))