Instructions for setting up a cube-sphere integration with sea-ice.

##########################################################################
# Get forcing files, etc.
# Example below is for cube94 on pleiades

mkdir cube94
cd cube94
ln -sf /nobackupp10/hzhang1/cs510/run_template .
ln -sf /nobackupp10/hzhang1/forcing/jra25 .
ln -sf /nobackupp10/hzhang1/forcing/cube78_forcing .


##########################################################################
# getting the code from anonymous CVS server

cvs co MITgcm_contrib/high_res_cube/README.cs510
cvs co MITgcm_contrib/high_res_cube/code-mods
cvs co MITgcm_contrib/high_res_cube/input
cvs co MITgcm_code


##########################################################################
# 510*510*6*50, 450-cpu cube sphere on pleiades with ifort

cd MITgcm
mkdir build run
cd build
\rm *
\cp ../../MITgcm_contrib/high_res_cube/code-mods/* .
\cp ../../MITgcm_contrib/high_res_cube/code-mods/s450t_34x102/SIZE.h .
\rm README SIZE.h_mpi
../tools/genmake2 -of ../tools/build_options/linux_amd64_ifort+mpi_ice_nas
make depend
make -j 16
cd ../run
\rm *
\cp ../../MITgcm_contrib/high_res_cube/input/*data* .
\cp ../../MITgcm_contrib/high_res_cube/input/modpickup .
\cp ../../MITgcm_contrib/high_res_cube/input/job* .
\mv data.seaice_hr data.seaice
\mv data.exf_hr data.exf
\mv data_hr data
\ln -sf ../../run_template/tile* .
\ln -sf ../../run_template/G*dig* .
\ln -sf ../../run_template/*Init.cube78 .
\cp ../build/mitgcmuv .
qsub job_cs510_pleiades450

=================

UPDATES

March 19, 2012. Cube94 on pleiades
This integration is driven by JRA25 (as was cube92)
but it includes shelfice (as did cube86),
it is based on MITgcm > checkpoint63k (that is post ICE workshop code),
it uses optimized Arctic sea ice parameters from
http://ecco2.jpl.nasa.gov/data1/arctic/output/newcode_050109/JRA25_OPT3/input/data.seaice
http://ecco2.org/manuscripts/2011/NguyenJGR2011.pdf
it uses Southern Ocean ice and ice shelf parameters from JSO24
/data14/scratch/hzhang/CP/JSO24/input
(bathymetry and initial conditions tbd),
and it uses pkg/bbl and frazil instead of down_slope

July 27, 2010.  Cube88 on pleiades - same as cube84 but with:
   1. JRA25 instead of cube84 blend forcing
   2. useSALT_PLUME  = .TRUE., (off in Southern Ocean)
   3. useDOWN_SLOPE  = .TRUE.,
   4. split north/south data.sec17saice parameters from regional optimizations
   5. initialize from T/S/U/V/ETAN and sea ice from cube78 Jan 1992 pickup
   6. 3-day 3D diagnostics
   7. SEAICE_no_slip = .TRUE. to keep code stable

June 30, 2009.  Cube86 -same as cube85 but with:
   1. updated Southern OCean Bathymetry
   2. ice shelf cavities

June 16, 2009. Cube85 -same as cube84 but with:
   1. split north/south data.seaice parameters from regional optimizations
   2. includes pkg/salt_plume in the Arctic and pkg/down_slope globally
   3. initialize from T/S/U/V/ETAN and sea ice files
   4. 3-day 3D diagnostics
   5. SEAICE_no_slip=.TRUE. to keep code stable

June 13, 2008. Cube 81 - same as cube79 but with
   1. new values for data.seaice and data.exf
   2. DIFFKR_2_20_1_lat6070_cube81, which has diffKrS/T=3.55e-7 in Arctic
   3. GMRedi turned off

December 22, 2007. Cube80 - same as cube79 but with
   SEAICE_BREAKS_VERIFICATION (SST relaxation depends on SIarea)
   ALLOW_CLIMSST_RELAXATION to Reynold's daily 1/4-deg AVHRR analysis
   ALLOW_CLIMSST_RELAXATION to monthly 1-deg WOA05 analysis
December 2, 2007. Cube79 - same as cube78 (blend3) but with
   useRelativeWind=.TRUE. and SEAICE_gamma_t=259200
November 22, 2007. Cube 78 - blend 3
November 6, 2007. Cube 77 - same as cube75 but with SEAICE_SALINITY
                            and era40_ecmwf_blend/cube59_GPCP forcing
November 3, 2007. Cube 76 - same as cube77 but 1979-2006 integration
August 31, 2007.  Cube75 - the second blend.
August 9, 2007. Cube74
August 6, 2007. Cube73
July 24, 2007. Cube72
July 8, 2007. Cube66: SEAICE_MULTICATEGORY, SEAICE_VARIABLE_FREEZING_POINT,
   rhonil=1027.5, [temp/salt]AdvScheme=7, convertFW2Salt=-1, LSR_ERROR=1e-6
   useRealFreshWaterFlux=.TRUE., runoff_lat_inc=179*1, SEAICE_salinity=10
   bathyFile=GEBCO_510x6x510_ver06_dig.bin, HeffFile=heff_file8
   SEAICE_availHeatFrac=.5, useGMRedi=.TRUE.
April 24, 2007. Cube65: Bryan and Lewis 1979 diffusivity
   (cube67, cube68, and cube69 were carried out with cube65 code)
April 7 , 2007. Cube64: era40_fullres forcing

February 6, 2006: cube56, same as cube 50 with SEAICEuseFlooding

February 1, 2006: back to cube50 default (bottomDragQuadratic = 0.002)
                  removed UVEL and VVEL from diagnostics

January 5, 2006: cube51, like cube50 but with bottomDragQuadratic = 0.0012

January 5, 2006: cube50, like cube48 but with snow advection

December 30, 2006: updates for cube49, the first
"blend" integration.

December 11, 2006: preparing for cube47, same as cube43
but with Arctic monthly river runoff climatology.

December 5, 2006: 216-CPU code for cube46
Changed diagnostics to accomodate JMCs latest and some
changes to code-mods/CPP_EEOPTIONS.h and W2_OPTIONS.h
to speed up code.

November 7, 2006: 216-CPU code for cube43
Bug fixes in growth.F routine and new set of diagnostics

October 15, 2006: 216-CPU code for cube40

September 28, 2006: 216-CPU code for cube38

September 4, 2006
Modified 32*32*6*15 experiments to use grid_cs32.* files from
 verification/tutorial_held_suarez_cs/input instead of
 tile* files from verification/global_ocean.cs32x15/input

August 8, 2006: 216-CPU code and input used for cube37
using "June 10, 2006" MITgcm code.

for online T/S profile diagnostics all that is needed is
  profiles_init_fixed
  profiles_inloop
see pkg/ecco/ecco_cost_init_fixed.F
    pkg/ecco/cost_averagesfields.F