/[MITgcm]/MITgcm_contrib/ocean_inversion_project/README

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-revision 1.3 by dimitri,
Tue Sep 23 04:34:23 2003 UTC
+revision 1.21 by dimitri,
Thu Sep 30 23:45:07 2004 UTC
 Line 20 
 salinity initial and boundary conditions
 ===> get MITgcm code from cvs repository
-  CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+  CVSROOT=:pserver:cvsanon@mitgcm.org:/u/gcmpack
   cvs login ( CVS password: cvsanon )
-  cvs co MITgcm
+  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
 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
-Line 31 
 salinity initial and boundary conditions
+Line 33 
 salinity initial and boundary conditions
 ===> compile and link
+  mkdir bin exe
   cd bin
   cp ../verification/global_with_exf/code/* .
-  cp ../ocean_inversion_project/code/.genmakerc .
   cp ../ocean_inversion_project/code/* .
-  cp ptracers_forcing.F.test ptracers_forcing.F
+  rm ptracers_*.F PTRACERS_OPTIONS.h
-  rm ptracers_init.F ptracers_forcing.F
+  ../tools/genmake2
-  ../tools/genmake
+    (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
   make depend
   make
-Line 51 
 salinity initial and boundary conditions
+Line 53 
 salinity initial and boundary conditions
   cp ../ocean_inversion_project/input/* .
   cp data.test data
   cp data.ptracers.test data.ptracers
-  mitgcmuv > output .txt
+  mitgcmuv > output.txt
-===> check that PTRACER output for tracer 1 and tracer 30
+===> check that PTRACER output and salinity output are identical.
-   ===> is identical to salinity output
   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
  ==========================================================
- Instructions for carrying out a 3000-year quasi-stationary
+ MPI instructions for carrying out a 3000-year quasi-stationary
  integration using the global_ocean.90x40x15 configuration.
  ==========================================================
-===> compile, link, and execute
+  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/.genmakerc .
   cp ../ocean_inversion_project/code/* .
-  ../tools/genmake
+  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
-Line 83 
 integration using the global_ocean.90x40
+Line 117 
 integration using the global_ocean.90x40
   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
+ ### need customized option file; example below is for nireas
+  ../tools/genmake2 -of linux_ia32_g77_netcdf
+  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.1765-2005.1 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 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);
-Line 102 
 clf, contourf(lon,lat,mean(tak(:,:,1),3)
+Line 194 
 clf, contourf(lon,lat,mean(tak(:,:,1),3)
  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'];
-Line 109 
 for i=1:30
+Line 202 
 for i=1:30
   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];
- tracer=zeros(90,40,15,30); sumtracer1=zeros(30,1);
+ 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) '.0000000180.001.001.data'];
+  fn=['PTRACER' myint2str(i) '.0000001800.001.001.data'];
   tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
-  for x=1:length(lon)
+  for j=1:length(lat)
-   for y=1:length(lat)
+   for k=1:length(thk)
-    for z=1:length(thk)
+    sumtracer(i) = sumtracer(i) + sum(tracer(:,j,k,i).*mask(:,j,k)) * ...
-     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
    end
   end
  end
+ plot(1:30,0*sumtracer,1:30,sumtracer)
- % some matlab code for checking that one year's worth of
- % tracer uptake is approximately 1e18 mols.
+ % check that tracer flux is 1e18 mols / year
+ nb_seconds_per_year=31556880;
  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.data',[90 40 15],1);
- tracer=zeros(90,40,15,30); sumtracer=zeros(30,1);
+ tracer=zeros(90,40,30); sumtracer=zeros(30,1);
  for i=1:30, mydisp(i)
-  fn=['PTRACER' myint2str(i) '.0000000180.001.001.data'];
+  fn=['PtrFlux' myint2str(i) '.0000000180.data'];
-  tracer(:,:,:,i)=readbin(fn,[90 40 15],1);
+  tracer(:,:,i)=readbin(fn,[90 40],1);
   for j=1:length(lat)
-   for k=1:length(thk)
+     sumtracer(i) = sumtracer(i) + sum(tracer(:,j,i).*mask(:,j,1)) * ...
-    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);
    end
-  end
  end
+ plot(1:30,0*sumtracer,1:30,sumtracer-mmean(sumtracer))

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