mkdir cube92
cd cube92

# get code from anonymous CVS server
cvs co MITgcm_contrib/high_res_cube/cube92
cvs co -r checkpoint62h MITgcm_code
cd MITgcm
mkdir build run

# build executable
cd build
../tools/genmake2 -mo ../../MITgcm_contrib/high_res_cube/cube92/code -of ../tools/build_options/linux_amd64_ifort+mpi_ice_nas
make depend
make -j 16

# integrate model
cd ../run
cp ../../MITgcm_contrib/high_res_cube/cube92/input/* .
ln -sf /nobackup/hzhang1/cs510/run_template/*cube78 .
ln -sf /nobackup/hzhang1/cs510/run_template/tile* .
ln -sf /nobackup/hzhang1/cs510/run_template/GEBCO* .
mv pickup.0000000216.cube78 pickup.0000000216
mv pickup.0000000216.meta.cube78 pickup.0000000216.meta
mv pickup_seaice.0000000216.cube78 pickup_seaice.0000000216
mv pickup_seaice.0000000216.meta.cube78 pickup_seaice.0000000216.meta       
ln -sf /nobackup/hzhang1/forcing/cube78_forcing .
ln -sf /nobackup/hzhang1/forcing/jra25 .
ln -sf ../build/mitgcmuv .
qsub run_cube92


#update on 06/10/2013 regarding file location of initial conditions, forcing and building options
Initial condition and bathymetry files can be found here:
http://ecco2.jpl.nasa.gov/data1/cube/run_template/
for run_template/, need
*cube78
tile*
GEBCO*

Forcing files are here:
There are 2 sets of forcing fields. Basically we use JRA25 now.
http://ecco2.jpl.nasa.gov/data2/data/atmos/blend_forcing/cube78_forcing/
So for cube78_foring/, need
DIFFKR*
runoff*

http://ecco2.jpl.nasa.gov/data2/data/atmos/jra25/
for jra25/, download
jra25*_19??
jra25*_20??

put three folders (run_template/, cube78_forcing/, and jra25/) aywhere.
Then look at http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/high_res_cube/cube92/README.cs510?view=markup
need to change line 19-21, line 26-27 (link those three folders or files therein to work directory)

The build option above
http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/linux_amd64_ifort+mpi_ice_nas
in line 12 of http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/high_res_cube/cube92/README.cs510?view=markup
is tailored for NASA supercompuer Pleiades.
A particular option file is needed for other computer.
A generic one is
http://mitgcm.org/viewvc/MITgcm/MITgcm/tools/build_options/linux_amd64_gfortran?view=markup&sortby=date
but one still needs to load some modules or export some environmnet variables before compiling
as shown by line 16-45.