25-Sep-2008 
heimbach@mit.edu, gforget@mit.edu, dmenemenlis@gmail.com, hzhang@caltech.edu

# The following is a description of the CS510
# adjoint-based state estimation setup.
# It is based on checkpoint61d.
# A prototype setup ran successfully in a 360-proc. config.
# on beagle.darwinproject.mit.edu
# Stable run for 10-days. sensitivity growth for 1 month
# (but not much tweaking with viscosity etc.)
#
# Default setup for columbia set up to use 450 processors of tile size 34x34.

# 0. Set some variables
set mitgcm_basedir = [ for example ~/MITgcm_c61d ]

# 1. Check out clean MITgcm checkpoint from CVS
cvs co -d MITgcm_c61d -r checkpoint61d MITgcm
#or latest code
#cvs co MITgcm_code 

# 2. Check out config. files for this setup:
cvs co MITgcm_contrib/high_res_cube/cs510_adjoint

# 3. (I prefer it that way, but a matter of taste),
\cp -r MITgcm_contrib/high_res_cube/cs510_adjoint $mitgcm_basedir/verification/.

# 4. Prepare build; we now need cyrus-makedepend
cd $mitgcm_basedir/tools/cyrus-imapd-makedepend
./configure
make

# 5.  Make sure to use default topology (or use different one)
cd $mitgcm_basedir/verification/cs510_adjoint/code_ad/
#no more topo needed
#\cp -f topol_360_85x51/* .
#level options: 50 levels
\cp -f SIZE.h_lev50 SIZE.h
#DIVA options: no_diva
\cp -f ECCO_CPPOPTIONS.h_nodiva ECCO_CPPOPTIONS.h
#Or DIVA
\cp -f ECCO_CPPOPTIONS.h_diva ECCO_CPPOPTIONS.h


# 6. Build model
cd $mitgcm_basedir/verification/cs510_adjoint/build_ad/
#DIVA options: no_diva
../../../tools/genmake2  "-of" "linux_ia64_ifort+mpi_altix_nas" \
   "-makedepend" "../../../tools/cyrus-imapd-makedepend/makedepend" \
   "-mods" "../code_ad"
#Or DIVA
#../../../tools/genmake2 -of linux_ia64_ifort+mpi_altix_nas \
#  -adof ../../../tools/adjoint_options/adjoint_diva_mpi \
#    -makedepend ../../../tools/cyrus-imapd-makedepend/makedepend -mods ../code_ad

make depend
make adtaf
make -j adall

 
# 7. Run model
cd ..
mkdir run
cd run
ln -sf ../build_ad/mitgcmuv_ad .
cp -pf ../input_ad/* .
#On Columbia
ln -sf /nobackup2a/menemenl/cs510_ad_test/MITgcm/verification/cs510_adjoint/input_fields/* .
ln -sf /nobackup2a/menemenl/forcing/cube78_forcing .
#Or on Pleiades
#ln -sf /nobackupp10/zhangh/cs510_ad_test/MITgcm/verification/cs510_adjoint/input_fields/* .
#ln -sf /nobackupp10/zhangh/forcing/cube78_forcing . 
#change data*...
#level 50
\cp -f data.err_lev50 data.err
\cp -f data.ecco_lev50 data.ecco
\cp -f data_lev50 data


#change jobfile: cs510_adj_run
#On Columbia
qsub cs510_adj_run_Columbia
#Or on Pleiades
#qsub cs510_adj_run_Pleiades