--- MITgcm_contrib/ocean_inversion_project/README	2003/10/21 03:25:30	1.12
+++ MITgcm_contrib/ocean_inversion_project/README	2003/12/18 06:11:14	1.20
@@ -22,7 +22,7 @@
 
  CVSROOT=:pserver:cvsanon@mitgcm.org:/u/u0/gcmpack
  cvs login ( CVS password: cvsanon )
- cvs co -P MITgcm
+ cvs co -r checkpoint51n_branch MITgcm
 
 2 ===> put MITgcm_contrib/ocean_inversion_project in MITgcm directory
 
@@ -56,10 +56,12 @@
 
  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.
 ==========================================================
 
@@ -68,9 +70,10 @@
  cd ../bin
  rm *
  cp ../verification/global_with_exf/code/* .
- cp ../ocean_inversion_project/code/.genmakerc .
  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
@@ -83,12 +86,14 @@
  cp ../ocean_inversion_project/input/* .
  ln -sf ../ocean_inversion_project/region_mask/30reg_regionmask.bin .
  ln -sf ../ocean_inversion_project/takahashi/taka02_montlhy.bin .
- mitgcmuv > output .txt &
-
+ cp data.stationary.1 data
+ mpirun -np 24 dplace -s1 mitgcmuv < /dev/null > & ! errlog &
+   (on orion: qsub job.orion)
 
 ==========================================================
-MPI instructions for carrying out a 3000-year quasi-stationary
-integration using the global_ocean.90x40x15 configuration.
+MPI instructions for carrying out time-dependent, 1765-2005,
+anthropogenic carbon perturbation tracer experiments using
+the global_ocean.90x40x15 configuration.
 ==========================================================
 
  cd MITgcm/exe
@@ -96,9 +101,7 @@
  cd ../bin
  rm *
  cp ../verification/global_with_exf/code/* .
- cp ../ocean_inversion_project/code/.genmakerc .
  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
@@ -111,15 +114,20 @@
  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 .
- mpirun -np 36 dplace -s1 -c3-38 mitgcmuv < /dev/null > & ! errlog &
+ 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
-the global_ocean.90x40x15 configuration.
+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
@@ -127,10 +135,14 @@
  cd ../bin
  rm *
  cp ../verification/global_with_exf/code/* .
- cp ../ocean_inversion_project/code/.genmakerc .
  cp ../ocean_inversion_project/code/* .
- ../tools/genmake2
-   (on orion: ../tools/genmake2 -of linux_ia64_efc+mpi)
+ 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
@@ -139,7 +151,7 @@
  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 .
@@ -147,6 +159,25 @@
 
 
 ======================================================
+
+==========================================================
+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