/[MITgcm]/MITgcm_contrib/ocean_inversion_project/README

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-revision 1.14 by dimitri,
Tue Oct 28 00:27:48 2003 UTC
+revision 1.27 by dimitri,
Sat Nov 20 14:40:47 2004 UTC
 Line 13 
 having to link netcdf library with MITgc
  respective README files in each directory for details.
+ Notes and problems:
+ ===================
+ there is problem generating ECCO_MaskAreaBathy.nc on columbia
+ works OK on nireas
+ variable global_mean_conc in 0D output from mk_output.F is
+ screwed up
  ===============================================
  First check that pkg/ptracers works OK by using
  salinity initial and boundary conditions
-Line 20 
 salinity initial and boundary conditions
+Line 31 
 salinity initial and boundary conditions
 ===> get MITgcm code from cvs repository
-  CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
+  cvs co -r checkpoint51n_branch MITgcm_code
-  cvs login ( CVS password: cvsanon )
+  cvs co -r checkpoint51n_branch MITgcm/verification/testreport
-  cvs co -P MITgcm
+  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 42 
 salinity initial and boundary conditions
 ===> compile and link
+  mkdir bin exe
   cd bin
-  cp ../verification/global_with_exf/code/* .
+  \cp ../verification/global_with_exf/code/* .
-  cp ../ocean_inversion_project/code/* .
+  \cp ../ocean_inversion_project/code/* .
-  rm ptracers_*.F PTRACERS_OPTIONS.h
+  \rm ptracers_*.F PTRACERS_OPTIONS.h
   ../tools/genmake2
-    (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
+    (on orion:    ../tools/genmake2 -of linux_ia64_efc+mpi       )
+    (on columbia: ../tools/genmake2 -of linux_ia64_efc+mpi_altix )
   make depend
-  make
+  make -j 16
 ===> execute
   cd ../exe
-  cp ../verification/global_with_exf/input/eedata .
+  \cp ../verification/global_with_exf/input/eedata .
-  cp ../verification/global_with_exf/input/data.* .
+  \cp ../verification/global_with_exf/input/data.* .
-  cp ../verification/global_with_exf/input/POLY3.COEFFS .
+  \cp ../verification/global_with_exf/input/POLY3.COEFFS .
-  ln -sf ../verification/global_with_exf/input/*.bin .
+  \ln -sf ../verification/global_with_exf/input/*.bin .
-  cp ../ocean_inversion_project/input/* .
+  \cp ../ocean_inversion_project/input/* .
-  cp data.test data
+  \cp data.test data
-  cp data.ptracers.test data.ptracers
+  \cp data.ptracers.test data.ptracers
-  mitgcmuv > output.txt
+  ./mitgcmuv >! output.txt
 ===> check that PTRACER output and salinity output are identical.
   diff PTRACER01.0000000020.001.001.data S.0000000020.001.001.data
-Line 86 
 integration using the global_ocean.90x40
+Line 99 
 integration using the global_ocean.90x40
   cp ../ocean_inversion_project/input/* .
   ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
   ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
-  mpirun -np 24 dplace -s1 -c3-38 mitgcmuv < /dev/null > & ! errlog &
+  cp data.stationary.1 data
+  mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
+    (on orion: qsub job.orion)
  ==========================================================
- Instructions for carrying out time-dependent, 1765-2005,
+ MPI instructions for carrying out time-dependent, 1765-2005,
  anthropogenic carbon perturbation tracer experiments using
  the global_ocean.90x40x15 configuration.
  ==========================================================
-Line 101 
 the global_ocean.90x40x15 configuration.
+Line 116 
 the global_ocean.90x40x15 configuration.
   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
-Line 115 
 the global_ocean.90x40x15 configuration.
+Line 132 
 the global_ocean.90x40x15 configuration.
   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 &
+  mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
+    (on orion: qsub job.orion.td)
  ==========================================================
-Line 134 
 and that it be specified in the genmake2
+Line 152 
 and that it be specified in the genmake2
   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
-Line 146 
 and that it be specified in the genmake2
+Line 165 
 and that it be specified in the genmake2
   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
+  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.96 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 columbia
+ ==========================================================
+ 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/u/menemenl/software/netcdf-3.5.0/include \
+      -L/u/menemenl/software/netcdf-3.5.0/lib -lnetcdf
+ ./a.out
+ ==========================================================
+ 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
-Line 195 
 for i=1:30, mydisp(i)
+Line 278 
 for i=1:30, mydisp(i)
   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))

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