To run on beagle.darwinproject.mit.edu :

#-- where executables have been built:
#   (see file 'utils/notes_bld' on how to build) 
BLD_DIR=~jmc/mitgcm/MITgcm/verification/nesting

#-- where to run:
RUN_DIR=/scratch/jmc/nesting
(mkdir $RUN_DIR)

#==== set-up: ====
Note: 1) driver is still using hard-coded absolute path
      (to /home/sannino/NESTING/ , subdir: PARENT/ & CHILD/ )
      to read parent and chilf grid files for parent <--> child interpolation
      2) forcing is over simplified to minimise Nb/size of input files.

cd $RUN_DIR

cvs co -P -d input  MITgcm_contrib/nesting_sannino/input
cvs co -P -d params MITgcm_contrib/nesting_sannino/params
cvs co -P -d utils  MITgcm_contrib/nesting_sannino/utils

( mkdir run_driv run_med run_gib )

cd run_driv
  ln -s $BLD_DIR/bld_driver/mitgcmuv .
cd ..

cd run_med
  ln -s $BLD_DIR/bld_parent/mitgcmuv .
  ln -s ../input/med/* .
  ln -s ../params/med/* .
cd ..

cd run_gib
  ln -s $BLD_DIR/bld_child/mitgcmuv .
  ln -s ../input/gib/* .
  ln -s ../params/gib/* .
cd ..

#==== running: ====
#-- on beagle:
> qrsh -pe mpich_mx 64

then do "qstat" to get the job number: JOB_IB

#-- on compute node:
> module load mitgcm
#- get the file which contains the list of nodes:
> ls -l /tmp/$JOB_ID.1.darwin/machines

> cd $RUN_DIR

#- to make "pgfile":
> utils/mk_pgfile.sh /tmp/$JOB_ID.1.darwin/machines

#- to run:
> mpirun -pg pgfile -np 64 $RUN_DIR/run_driv/mitgcmuv >& std_outp

# Note: Until now, this command will not finish since the driver does not know 
#       many iterations to do. Needs to kill (or Ctrl C) the mpirun process 
#       when parent and child are done.

#- to save all the output in new dir "res_new"
> utils/move_nest_outp res_new