source: branches/2015/dev_r5092_CNRS_SETTE/NEMOGCM/SETTE/README @ 5095

Last change on this file since 5095 was 5095, checked in by nicolasmartin, 6 years ago

Global reorganisation of directory

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1usage of SETTE package:
2
3principal script is sette.sh (usage: ./sette.sh)
4
5VERY IMPORTANT : for a verbose debug do:
6./sette.sh 2>&1 | tee out.sette
7this create out.sette file in ${SETTE_DIR}
8
9USER MODIFICATIONS
10 in sette.sh script :
11               COMPILER    : compiler among those available in NEMOGCM/ARCH, needed for makenemo (see below)
12                             can also be pass as an argument, e.g. ./sette.sh ifort_osx
13          BATCH_COMMAND_PAR : command for job submission in batch mode parallel (MMIÂ)
14          BATCH_COMMAND_SEQ : command for job submission in batch mode sequential (NB_PROC = 1)
15          INTERACT_FLAG : "yes" if you want to run in interactive mode
16                      "no" if you want to run in batch mode
17          MPIRUN_FLAG   : "yes" if you want to run in parallel (MPI)
18                "no" if you want to run in sequential mode (NB_PROC = 1)
19
20               makenemo -m : machine (compilator); see ./makenemo -m help (in NEMOGCM/CONFIG directory)
21                        -n : config name (in examples config_name_nproci_nprocj), see ./makenemo -n help
22                        -r : reference configuration (if you don't give it you have to choise directories to install)
23                        add_key : to add list of keys (for example to test reproductibility: add_key mpp_rep)
24                        del_key : to del list of keys
25               and for more details and options of makenemo see ./makenemo -h
26
27          set_namelist : to set namelist values
28         (example : to set 75 time steps for one test : namelist nn_itend 75)
29         (        : to change cn_icerst_in name : namelist_ice cn_icerst_in  \"test_00101231_restart_icemod\")
30         (      : to activate control print : namelist ln_ctl false )
31          prepare_exe_dir.sh creates execution directory for each test
32                    : NOTE for EACH JOB EXECUTION it is needed to set TEST_NAME variable
33                TEST_NAME variable gives name to execution directory (created in prepare_exe_dir.sh)
34                IT is mandatory to have different TEST_NAME for each job run if not existing files are re-written (for example namelist)
35
36               prepare_job.sh generates the script to be executed
37         input: INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPIRUN_FLAG JOB_FILE
38
39               fcm_job.sh needs input: TOTAL_NUMBER_OF_PROCS_used JOB_FILE_NAME INTERACT_FLAG MPIRUN_FLAG
40         (for example if you run with 4 procs JOB_FILE batch parallel
41         and only run short test ===> ./fcm_job 4 SHORT no    yes   )
42
43 in param.cfg :
44               FORCING_DIR       : directory in which will be found input.tar file (same name in input_CONFIG_NAME.cfg)
45               INPUT_DIR         : directory in which store input files (tar file)
46               TMPDIR            : temporary directory NEEDED ONLY FOR IBM machines (put EXP00 directory)
47          NEMO_VALIDATION_DIR : directory in which create NEMO_VALIDATION tree, and store restart, solver.stat, tracer.stat and ocean.output files in
48                            tree NEMO_VALIDATION_DIR/WCONFIG_NAME/WCOMPILER_NAME/TEST_NAME/REVISION_NUMBER(or DATE)
49 in fcm_job.sh :
50               IMPORTANT : control that name of tar file in FORCING directory
51               is the same of that in input_REF_CONFIG.cfg, if not change one.
52
53               change in "RUN OPA" if [ ${INTERACT_FLAG} == "yes" ] mpirun command line (some examples are already written)
54          NOTE: if INTERACT_FLAG="no" it is needed a batch_file (see below to create a new one)
55
56NOTE:
57in case of error you can remove you NEW_CONF directory and all files doing :
58./makenemo -n MY_CONFIG clean_config
59
60if you want recompile nemo but before you want to clean compiled code do :
61./makenemo clean
62
63and if you have already compiled you can re-run all sette.sh and compilation part will be by-passed.
64
65NOTE 2:
66if you want a completly verbose makenemo you can uncomment "set -x" in makenemo script
67and then launch ./sette.sh 2>&1 | tee out.sette
68
69TO ADD NEW CONFIGURATION:
701. makenemo -n NEW_CONFIG (see makenemo -h for help) OR
712. makenemo -n NEW_CONFIG -r REF_CONFIG (if it is based on another reference configuration)
723. for fcm_job.sh creates a new input_NEW_CONFIG.cfg if you need tar file (if you use same tar file of GYRE, ORCA2_LIM or ORCA2_LIM_PISCES you can use it)
73
74TO ADD NEW MACHINE:
751. add arch-compiler.fcm in NEMOGCM/ARCH directory
762. makenemo -m new_compiler  (see makenemo -h for help)
77
78TO ADD NEW BATCH-FILE:
791. see in SETTE/BATCH_TEMPLATE directory existing examples
802. create you own batch file like: batch-${COMPILER}
81(note: sette.sh will copy it in job_batch_template if you run tests in INTERACT_FLAG="no")
82
83# Variables to be checked by user:
84#
85# COMPILER          : name of compiler as defined in NEMOGCM/ARCH directory
86# BATCH_COMMAND_PAR :  name of the command for submitting parallel batch jobs
87# BATCH_COMMAND_SEQ :  name of the command for submitting sequential batch jobs 
88# INTERACT_FLAG     : flag to run in interactive mode "yes"
89#                           to run in batch mode "no"
90# MPIRUN_FLAG       : flag to run in parallel (MPI) "yes"
91#                           to run in sequential mode (NB_PROC = 1) "no"
92# USING_XIOS        : flag to control the activation of key_iomput
93#                      "yes" to compile using key_iomput and link to the external XIOS library
94#                      "no"  to compile without key_iomput and link to the old IOIPSL library
95# USING_MPMD        : flag to control the use of stand-alone IO servers
96#                     requires USING_XIOS="yes"
97#                      "yes" to run in MPMD (detached) mode with stand-alone IO servers
98#                      "no"  to run in SPMD (attached) mode without separate IO servers
99# NUM_XIOSERVERS    : number of stand-alone IO servers to employ
100#                     set to zero if USING_MPMD="no"
101#
102# Principal script is sette.sh, that calls
103#
104#  makenemo  : to create successive exectuables in ${CONFIG_NAME}/BLD/bin/nemo.exe
105#              and links to opa in ${CONFIG_NAME}/EXP00)
106#
107#  param.cfg : sets and loads following directories:
108#
109#   FORCING_DIR         : is the directory for forcing files (tarfile)
110#   INPUT_DIR           : is the directory for input files storing
111#   TMPDIR              : is the temporary directory (if needed)
112#   NEMO_VALIDATION_DIR : is the validation directory
113#
114#   (NOTE: this file is the same for all configrations to be tested with sette)
115#
116#   all_functions.sh : loads functions used by sette (note: new functions can be added here)
117#   set_namelist     : function declared in all_functions that sets namelist parameters
118#   post_test_tidyup : creates validation storage directory and copies required output files
119#                      (solver.stat and ocean.output) in it after execution of test.
120#
121#  VALIDATION tree is:
122#
123#   NEMO_VALIDATION_DIR/WCONFIG_NAME/WCOMPILER_NAME/TEST_NAME/REVISION_NUMBER(or DATE)
124#
125#  prepare_exe_dir.sh : defines and creates directory where the test is executed
126#                       execution directory takes name of TEST_NAME defined for every test
127#                       in sette.sh. (each test in executed in its own directory)
128#
129#  prepare_job.sh     : to generate the script run_job.sh
130#
131#  fcm_job.sh         : run in batch (INTERACT_FLAG="no") or interactive (INTERACT_FLAG="yes")
132#                        see sette.sh and BATCH_TEMPLATE directory
133#
134#  NOTE: jobs requiring initial or forcing data need to have an input_CONFIG.cfg in which
135#        can be found paths to the input tar file)
136#  NOTE: if job is not launched for any reason you have the executable ready in ${EXE_DIR}
137#        directory
138#  NOTE: the changed namelists are left in ${EXE_DIR} directory whereas original namelists
139#        remain in ${NEW_CONF}/EXP00
140#
141#  NOTE: a log file, output.sette, is created in ${SETTE_DIR} with the echoes of
142#        executed commands
143#
144#  NOTE: if sette.sh is stopped in output.sette there is written the last command
145#        executed by sette.sh
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