instructions to perform the regridding to the cubed sphere:

1) Add new regridding routine for your needs
    * The regridding routines are in aux/inputLL2CS.f
    * in the program section of inputLL2CS.f you have to define the resolution of the source grid (e.g. ims_TOPO/jms_TOPO, replace TOPO by something else)
      the resolution of the target cubed sphere grid is defined in the IM, JM in the resolution file
      you then create a regridding object (e.g. xll2cs_TOPO) which will contain all coefficient and data to perform the interpolation. You do this using e.g. 
          call init_regrid_root(xll2cs_TOPO,ims_TOPO,jms_TOPO,ntilessource,imt,jmt,ntilestarget)   (replace TOPO by something else)
    * in the am_i_root section just below, add a call to your regridding routine, e.g. call regridTOPO
    * create a regridding routine. regridTOPO provides a good template
      the routine contains 3 sections:
        -reading the input file. It reads all records (in your case all months from january to december) using read(unit=iu_TOPO,END=30) TITLE(irec), tsourc4(:,:,:,irec). You can modify this for your needs. Make sure that the binary input file has been written using big endians.
        -regridding to the cubed sphere, for every record it calls root_regrid which is defined in an external library. 
        -writing the file on disk. It writes all records using write(unit=iu_TOPO) TITLE(ir), ttargr4(:,:,:,ir). You can modify this for your needs
2) to Compile/Run, 
     * you must use a cubed sphere compatible .modelErc file
       here is an example of such a file:
	# This file contains global options for modelE. By default they are
	# adjusted to the working environment of Ra.giss.nasa.gov .

	## Directory structure ##

	# DECKS_REPOSITORY - a directory for permanenet storage of run info.
	# All rundecks that you create will be copied to this directory.
	DECKS_REPOSITORY=/discover/nobackup/dgueyffi/decks

	# CMRUNDIR - directory to which all run directories will be linked.
	# This directory will be searched by most scripts for locations of
	# specific runs.
	CMRUNDIR=/discover/nobackup/projects/giss/prod_runs

	# GCMSEARCHPATH - directory to search for gcm input files.
	# All necessary input files should be copied or linked to this directory.
	GCMSEARCHPATH=/discover/nobackup/projects/giss/prod_input_files

	# EXECDIR - path to directory with modelE scripts and with some
	# executables. This directory should contain the scripts from modelE/exec.
	EXECDIR=/discover/nobackup/projects/giss/exec

	# NETCDFHOME - path to location of netcdf library. Leave blank if netcdf
	# is not installed on this computer
	NETCDFHOME=/usr/local/other_old/netcdf/3.6.1

        # SAVEDISK - a directory where all run directories (which will contain
        # all output files such as rsf, acc etc.) will be created. This should
        # be big enough to accomodate all model output.
        SAVEDISK=/discover/nobackup/dgueyffi
      
        ## Customizable setings for Makefile ##

        # MAILTO - email address of the user. When the program ends/crashes
        # all notifications will be sent to this address. If not specified
        # `whoami` will be used.
        MAILTO=

	# OVERWRITE - can "gmake rundeck" overwrite files already in repository?
	# (i.e. in the directory DECKS_REPOSITORY)
	OVERWRITE=NO

	# OUTPUT_TO_FILES - if set to YES all errors and warnings will be sent
	# to files with the names <source_name>.ERR
	OUTPUT_TO_FILES=YES

	# VERBOSE_OUTPUT - if set to YES gmake will show compilation commands
	# and some other information. Otherwise most of the output will be
	# suppressed
	VERBOSE_OUTPUT=YES

	# MP - multiprocessing support. If set to YES gmake will compile the
	# code with OpenMP instructions. This option has effect only on SGI.
	MP=NO

	# ESMF variables
	ESMF=YES
	# ESMF_DIR=/discover/nobackup/projects/giss/esmf_2_2_ifort_9.1.042
	ESMF_BOPT=O

	#FV variablesdd following entries to .modelErc:
	FVCORE_ROOT=/discover/nobackup/projects/map/GEOSGCM
	FVCUBED_ROOT=/discover/nobackup/projects/map/GEOSagcm-cubed
	MPPDIR=/discover/nobackup/projects/map/MPP/mpp_intel-9.1.052_scali-5
	BASELIBDIR=/usr/local/other/baselibs/ESMF222rp3_NetCDF362b6_9.1.052/Linux

	QSUB_STRING="qsub -V -l select=2:ncpus=4:scali=true -l walltime=00:05:00 -W block=true -W group_list=a940a"

     * create rundeck from an existing cubed sphere template rundeck, e.g. gmake rundeck RUNSRC=E1CS32L20 RUN=your_deck

     * compile using gmake -j aux RUN=your_deck NPES=6 CUBE_GRID=YES FVCUBED=YES

     * copy inputll2cs in your run directory 

     * copy the input files you want to regrid (fox example vegtype.global4X5.bin, lai01.global.bin...) from e.g.
         /discover/nobackup/projects/giss/prod_input_files/ to your run directory

     * copy the remap file containing the coefficients for the regridding (e.g. remap360-180C32-32.nc for regridding from 360x160 resolution on latlon grid to CS32 grid) from /discover/nobackup/projects/giss/prod_input_files/ to your run directory

     * run inputll2cs using PBS script 
       Here is an example of such a pbs script:
	#!/bin/ksh
	#PBS -S /bin/ksh
	#PBS -N tst
	#PBS -l walltime=00:10:00
	#PBS -l select=2:ncpus=4:scali=true
	#PBS -W group_list=a940a
	#PBS -W umask=002
	#PBS -A "a940a"
	#PBS -j oe 
	#PBS -o /home/dgueyffi/mE-FVcubed/decks/your_deck/
	#PBS -V

	#ulimit -s unlimited
	#ulimit -c  0

	. /usr/share/modules/init/bash
	module purge
	module load comp/intel-9.1.052
	module load mpi/scali-5

	cd /home/dgueyffi/mE-FVcubed/decks/your_deck/

	#echo ${LD_LIBRARY_PATH}
	#export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/other/hdf/5-1.8.0_parallel/lib
	umask 2
	mpirun -np 6 -inherit_limits ./inputll2cs > log