usage of SETTE package:

principal script is sette.sh (usage: ./sette.sh) 

VERY IMPORTANT : for a verbose debug do:
./sette.sh 2>&1 | tee out.sette
this create out.sette file in ${SETTE_DIR}

USER MODIFICATIONS
 in sette.sh script :
               COMPILER    : compiler among those available in NEMOGCM/ARCH, needed for makenemo (see below)
                             can also be pass as an argument, e.g. ./sette.sh ifort_osx
	       BATCH_COMMAND_PAR : command for job submission in batch mode parallel (MMIÂ)
	       BATCH_COMMAND_SEQ : command for job submission in batch mode sequential (NB_PROC = 1)
	       INTERACT_FLAG : "yes" if you want to run in interactive mode 
	       		       "no" if you want to run in batch mode
	       MPIRUN_FLAG   : "yes" if you want to run in parallel (MPI)
			       "no" if you want to run in sequential mode (NB_PROC = 1)

               makenemo -m : machine (compilator); see ./makenemo -m help (in NEMOGCM/CONFIG directory)
                        -n : config name (in examples config_name_nproci_nprocj), see ./makenemo -n help
                        -r : reference configuration (if you don't give it you have to choise directories to install)
                        add_key : to add list of keys (for example to test reproductibility: add_key mpp_rep)
                        del_key : to del list of keys
               and for more details and options of makenemo see ./makenemo -h

	       set_namelist : to set namelist values 
			(example : to set 75 time steps for one test : namelist nn_itend 75)
			(        : to change cn_icerst_in name : namelist_ice cn_icerst_in  \"test_00101231_restart_icemod\")
			(  	 : to activate control print : namelist ln_ctl false )
	       prepare_exe_dir.sh creates execution directory for each test
	       			  : NOTE for EACH JOB EXECUTION it is needed to set TEST_NAME variable
				    TEST_NAME variable gives name to execution directory (created in prepare_exe_dir.sh)
				    IT is mandatory to have different TEST_NAME for each job run if not existing files are re-written (for example namelist)

               prepare_job.sh generates the script to be executed 
			input: INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPIRUN_FLAG JOB_FILE

               fcm_job.sh needs input: TOTAL_NUMBER_OF_PROCS_used JOB_FILE_NAME INTERACT_FLAG MPIRUN_FLAG 
			(for example if you run with 4 procs JOB_FILE batch parallel 
			and only run short test ===> ./fcm_job 4 SHORT no    yes   )

 in param.cfg :
               FORCING_DIR 	   : directory in which will be found input.tar file (same name in input_CONFIG_NAME.cfg)
               INPUT_DIR   	   : directory in which store input files (tar file)
               TMPDIR      	   : temporary directory NEEDED ONLY FOR IBM machines (put EXP00 directory)
	       NEMO_VALIDATION_DIR : directory in which create NEMO_VALIDATION tree, and store restart, solver.stat, tracer.stat and ocean.output files in
      			             tree NEMO_VALIDATION_DIR/WCONFIG_NAME/WCOMPILER_NAME/TEST_NAME/REVISION_NUMBER(or DATE)
 in fcm_job.sh :
               IMPORTANT : control that name of tar file in FORCING directory
               is the same of that in input_REF_CONFIG.cfg, if not change one.

               change in "RUN OPA" if [ ${INTERACT_FLAG} == "yes" ] mpirun command line (some examples are already written)
	       NOTE: if INTERACT_FLAG="no" it is needed a batch_file (see below to create a new one)

NOTE:
in case of error you can remove you NEW_CONF directory and all files doing :
./makenemo -n MY_CONFIG clean_config

if you want recompile nemo but before you want to clean compiled code do :
./makenemo clean

and if you have already compiled you can re-run all sette.sh and compilation part will be by-passed.

NOTE 2: 
if you want a completly verbose makenemo you can uncomment "set -x" in makenemo script
and then launch ./sette.sh 2>&1 | tee out.sette

TO ADD NEW CONFIGURATION:
1. makenemo -n NEW_CONFIG (see makenemo -h for help) OR
2. makenemo -n NEW_CONFIG -r REF_CONFIG (if it is based on another reference configuration)
3. for fcm_job.sh creates a new input_NEW_CONFIG.cfg if you need tar file (if you use same tar file of GYRE, ORCA2_LIM or ORCA2_LIM_PISCES you can use it)

TO ADD NEW MACHINE:
1. add arch-compiler.fcm in NEMOGCM/ARCH directory
2. makenemo -m new_compiler  (see makenemo -h for help)

TO ADD NEW BATCH-FILE:
1. see in SETTE/BATCH_TEMPLATE directory existing examples
2. create you own batch file like: batch-${COMPILER}
(note: sette.sh will copy it in job_batch_template if you run tests in INTERACT_FLAG="no")

# Variables to be checked by user:
#
# COMPILER          : name of compiler as defined in NEMOGCM/ARCH directory 
# BATCH_COMMAND_PAR :  name of the command for submitting parallel batch jobs
# BATCH_COMMAND_SEQ :  name of the command for submitting sequential batch jobs  
# INTERACT_FLAG     : flag to run in interactive mode "yes"
#                           to run in batch mode "no"
# MPIRUN_FLAG       : flag to run in parallel (MPI) "yes"
#                           to run in sequential mode (NB_PROC = 1) "no"
# USING_XIOS        : flag to control the activation of key_iomput
#                      "yes" to compile using key_iomput and link to the external XIOS library
#                      "no"  to compile without key_iomput and link to the old IOIPSL library
# USING_MPMD        : flag to control the use of stand-alone IO servers
#                     requires USING_XIOS="yes"
#                      "yes" to run in MPMD (detached) mode with stand-alone IO servers
#                      "no"  to run in SPMD (attached) mode without separate IO servers 
# NUM_XIOSERVERS    : number of stand-alone IO servers to employ
#                     set to zero if USING_MPMD="no"
#
# Principal script is sette.sh, that calls 
#
#  makenemo  : to create successive exectuables in ${CONFIG_NAME}/BLD/bin/nemo.exe 
#              and links to opa in ${CONFIG_NAME}/EXP00)
#
#  param.cfg : sets and loads following directories:
#
#   FORCING_DIR         : is the directory for forcing files (tarfile)
#   INPUT_DIR           : is the directory for input files storing 
#   TMPDIR              : is the temporary directory (if needed)
#   NEMO_VALIDATION_DIR : is the validation directory
#
#   (NOTE: this file is the same for all configrations to be tested with sette)
#
#   all_functions.sh : loads functions used by sette (note: new functions can be added here)
#   set_namelist     : function declared in all_functions that sets namelist parameters 
#   post_test_tidyup : creates validation storage directory and copies required output files 
#                      (solver.stat and ocean.output) in it after execution of test.
#
#  VALIDATION tree is:
#
#   NEMO_VALIDATION_DIR/WCONFIG_NAME/WCOMPILER_NAME/TEST_NAME/REVISION_NUMBER(or DATE)
#
#  prepare_exe_dir.sh : defines and creates directory where the test is executed
#                       execution directory takes name of TEST_NAME defined for every test 
#                       in sette.sh. (each test in executed in its own directory)
#
#  prepare_job.sh     : to generate the script run_job.sh
#
#  fcm_job.sh         : run in batch (INTERACT_FLAG="no") or interactive (INTERACT_FLAG="yes")
#                        see sette.sh and BATCH_TEMPLATE directory
#
#  NOTE: jobs requiring initial or forcing data need to have an input_CONFIG.cfg in which 
#        can be found paths to the input tar file)
#  NOTE: if job is not launched for any reason you have the executable ready in ${EXE_DIR} 
#        directory
#  NOTE: the changed namelists are left in ${EXE_DIR} directory whereas original namelists 
#        remain in ${NEW_CONF}/EXP00
# 
#  NOTE: a log file, output.sette, is created in ${SETTE_DIR} with the echoes of 
#        executed commands
#
#  NOTE: if sette.sh is stopped in output.sette there is written the last command 
#        executed by sette.sh