sette.rst

######################
A guide to using SETTE
######################

.. contents::
   :local:

Overview
======== 

``SETTE`` is a suite of bash scripts that automates the building, running and
basic validation and verification of a broad spectrum of NEMO reference and
test configurations. Because compilation and batch running environments differ
wildly, automation is only achieved after some effort by the user for each new test
platform. However, examples are provided for all the major systems used by the NEMO
System team and many new platforms can be incorporated simply by adapting these
templates.

When configured correctly, a single command will:

* Compile multiple reference and test configurations
* Run restartability and reproducibility tests with each configuration
* Run additional conformance checks with any AGRIF-based configurations
* Archive sufficient output measures for meaningful comparsion between future 
  tests at different revisions
* On completion, run a secondary script to table the successes or failures of each test

Many namelist-controlled options can be varied using command line arguments to the
main sette script and test results can be compared across different innvocations. Thus,
by chaining sette innvocations with different options, more complex and comprehensive
testing can be achieved.

Installation
============

``SETTE`` is provided within the main NEMO git repository and will be found in the
subdirectory ``sette`` below the top-level of a checked out (cloned) copy (at the same
level as ``src/`` or ``cfgs/``).

.. _Initial setup:

Initial setup
=============

Assuming, for now, that you are intending to run ``SETTE`` on one of the platforms
already supported then there are only a few settings required to setup for each
individual user. These settings are all to be found in the ``sette/param.default`` file:

.. code-block:: bash

     NEMO_VALIDATION_REF=/path/to/reference/sette/results
     NEMO_REV_REF=0000
     COMPILER=${SETTE_COMPILER:-XXXXXXXX}
     BATCH_CMD=${SETTE_BATCH_CMD:-llsubmit}
     BATCH_STAT=${SETTE_BATCH_STAT:-llq}
     FORCING_DIR=${SETTE_FORCING_DIR:-$WORKDIR/FORCING}
     NEMO_VALIDATION_DIR=${SETTE_NEMO_VALIDATION_DIR:-$MAIN_DIR}/NEMO_VALIDATION
     JOB_PREFIX_NOMPMD=${SETTE_JOB_PREFIX_NOMPMD:-batch}
     JOB_PREFIX_MPMD=${SETTE_JOB_PREFIX_MPMD:-batch-mpmd}

and each can be set either in a ``param.cfg`` file (created by copying ``param.default``
to ``param.cfg`` and editing) or through the corresponding environment variable. For
example, changing the contents of a ``param.cfg`` to include:

.. code-block:: bash

     NEMO_VALIDATION_REF=/work/n01/n01/acc/NEMO/2024/5.0.0/sette/NEMO_VALIDATION
     NEMO_REV_REF=24335_c1604aac
     COMPILER=X86_ARCHER2-Cray
     BATCH_CMD=sbatch
     BATCH_STAT=squeue
     FORCING_DIR=/work/n01/n01/acc/FORCING/SETTE_inputs/5.0.0
     NEMO_VALIDATION_DIR=/work/n01/n01/acc/NEMO/2024/5.0.0/sette/NEMO_VALIDATION
     JOB_PREFIX_NOMPMD=batch
     JOB_PREFIX_MPMD=batch

or settings:

.. code-block:: bash

     export SETTE_COMPILER=X86_ARCHER2-Cray
     export SETTE_BATCH_CMD=sbatch
     export SETTE_BATCH_STAT=squeue
     export SETTE_FORCING_DIR=/work/n01/n01/acc/FORCING/SETTE_inputs/5.0.0
     export SETTE_NEMO_VALIDATION_DIR=/work/n01/n01/acc/NEMO/2024/5.0.0/sette/NEMO_VALIDATION
     export SETTE_JOB_PREFIX_NOMPMD=batch
     export SETTE_JOB_PREFIX_MPMD=batch

in your runtime environment will achieve the same result. The requirement to create a
``param.cfg`` from ``param.default`` for each installation protects against developers
accidentally returning a local ``param.cfg`` to the main repository. The ``param.default``
file should only be altered by ``SETTE`` developers.

.. note:: 
     Apart from ``NEMO_VALIDATION_REF`` and ``NEMO_REV_REF`` which do not have an equivalent environment variable - TO BE FIXED

The purposes of these settings should be clear:

* ``NEMO_VALIDATION_REF`` points to a ``SETTE``-generated directory of previous archived results to be used 
  optionally as a reference set.
* ``NEMO_REV_REF`` defines the reference tag (since raw git commit hashes do not list chronologically, they are prepended with a string constructed from the year and year-day)
* ``COMPILER`` names the architecture file to be used to compile NEMO
* ``BATCH_CMD``  names the command used to submit jobs to the batch system
* ``BATCH_STAT`` names the command used to query the batch system and return a list of queued and running jobs
* ``FORCING_DIR`` points to a directory containing the input files required by the reference configurations. 
  Details of how to obtain the files with which to populate this directory are provided 
  in the `Obtaining configuration input files`_ section.  Note that this directory must be in a part of 
  the filesystem that is visible to the back-end compute nodes.
* ``NEMO_VALIDATION_DIR`` points to a directory under which ``SETTE`` will archive its results.
* ``JOB_PREFIX_NOMPMD`` A prefix for the template batch file if running in SPMD mode (e,g. with attached XIOS servers)
* ``JOB_PREFIX_MPMD`` An alternative prefix for the template batch file if running in MPMD mode (i.e. with detached
  XIOS servers). This isn't necessarily different to the SPMD setting since some of the templates provided are written to
  handle both modes. See the `Template batch files`_ section for details.

.. _`Obtaining configuration input files`:

Obtaining configuration input files
===================================

Many of the reference configurations require domain files, initial conditions and surface
forcing fields. The exceptions are the GYRE_PISCES configurations and the simpler,
test-cases. It is possible to limit ``SETTE`` to a subset of tests to avoid the need for
downloading data files but far less of the code will be covered by the tests in this case.
All the required files are available from the `SETTE inputs site`_ .

The entire set of inputs can be downloaded using the ``./sette_fetch_inputs.sh`` script
which uses ``wget`` to retrieve the files and populate the ``FORCING_DIR`` directory.
I.e.:

.. code-block:: bash

  sette_fetch_inputs.sh -h
  sette_fetch_inputs.sh :
       Fetch 5.0.0 input files from remote store

.. _`SETTE inputs site`: https://gws-access.jasmin.ac.uk/public/nemo/sette_inputs/

.. _Template batch files:

Template batch files
====================

If you have previously compiled NEMO successfully on your test platform then you can have
confidence that providing the same environment and arch file to ``SETTE`` will allow SETTE
to compile successfully (barring any compile-time bugs in previously untested code).
However, ``SETTE`` also needs to configure and run a series of batch jobs with varying
resource requirements. To do this, you must provide ``SETTE`` with a means to generate valid
job submission scripts. There are essentially two ways of doing this:

* Provide a template batch file with known strings that ``SETTE`` can replace with 
  settings based on the needs of each job.
* Provide an external script that can accept those settings and generate a new batch file.

If you are working on a test platform already supported by ``SETTE``, a solution will already
be in place and you can skip to the `Component scripts`_ section. 

If you are commissioning a new platform then you will need to provide either a template
batch file or an external generating script. Batch file templates are located in the
``sette/BATCH_TEMPLATE`` subdirectory. They are named with the ``COMPILER`` setting
prefixed by the ``JOB_PREFIX_NOMPMD`` (or ``JOB_PREFIX_NOMPMD``) setting and separated by
a hyphen. To use the first method, the batch template should be a version of a working
submission script with the following strings in place of their corresponding numerical
values:

.. code-block:: bash

        NODES                  The total number of nodes required
        TOTAL_NPROCS           The total number of cores required
        NPROCS                 The number of ocean cores
        NXIOPROCS              The number of XIOS cores
        MPI_FLAG               A logical to declare if MPI is being used
        DEF_EXE_DIR            The test execution directory
                               Paths and names that have to be passed through 
                               to the post-run tidy-up script:
        DEF_SETTE_DIR
        DEF_INPUT_DIR
        DEF_CONFIG_DIR
        DEF_TOOLS_DIR
        DEF_NEMO_VALIDATION
        DEF_NEW_CONF
        DEF_CMP_NAM
        DEF_TEST_NAME

Not all of these need to used and if your particular system needs additional information then this
can be added as a case statement (dependent on ``COMPILER``) in the ``prepare_job.sh`` script

An example template file is given in the sette_batch_template file:

.. code-block:: bash

     cat BATCH_TEMPLATE/sette_batch_template
     #!/bin/bash
     #!
     # @ job_name = MPI_config
     # standard output file
     # @ output = $(job_name).$(jobid)
     # standard error file
     # @ error =  $(job_name).$(jobid)
     # job type
     # @ job_type = parallel
     # Number of procs
     # @ total_tasks = NPROCS
     # time
     # @ wall_clock_limit = 0:30:00
     # @ queue
     
     #
     # Test specific settings. Do not hand edit these lines; the prepare_job.sh script will set these
     # (via sed operating on this template job file).
     #
       OCEANCORES=NPROCS
       export SETTE_DIR=DEF_SETTE_DIR
     
     ###############################################################
     #
     # set up mpp computing environment
     #
     # Local settings for machine IBM Power6 (VARGAS at IDRIS France)
     #
     export MPIRUN="mpiexec -n $OCEANCORES"
     
     #
     # load sette functions (only post_test_tidyup needed)
     #
       . ${SETTE_DIR}/all_functions.sh
     
     # Do not remove or change the following comment line
     # BODY
     
     
     #
     # These variables are needed by post_test_tidyup function in all_functions.sh
     #
       export EXE_DIR=DEF_EXE_DIR
       export INPUT_DIR=DEF_INPUT_DIR
       export CONFIG_DIR=DEF_CONFIG_DIR
       export TOOLS_DIR=DEF_TOOLS_DIR
       export NEMO_VALIDATION_DIR=DEF_NEMO_VALIDATION
       export NEW_CONF=DEF_NEW_CONF
       export CMP_NAM=DEF_CMP_NAM
       export TEST_NAME=DEF_TEST_NAME
     #
     # end of set up
     
     
     ###############################################################
     #
     # change to the working directory
     #
     cd ${EXE_DIR}
     
       echo Running on host `hostname`
       echo Time is `date`
       echo Directory is `pwd`
     #
     #  Run the parallel MPI executable
     #
       if [ MPI_FLAG == "yes" ]; then
       echo "Running time ${MPIRUN} ./nemo"
          time ${MPIRUN} ./nemo
       else
       echo "Running time./nemo"
          time ./nemo
       fi
     
     
     #
       post_test_tidyup
     
     # END_BODY
     # Do not remove or change the previous comment line
     
       exit

But commamds and environments are most likely different on every test platform so it may 
require some effort to produce an equivalent template for new platforms.

For cases where the calculation and declaration of resources is more complex (for example,
in hetrogeneous computing environments requiring het-job declarations), in may be easier to
provide an external script to generate the job script. An example is included in the case
of X86_ARCHER2-Cray where the batch template is simply a placeholder:

.. code-block:: bash

    #!/bin/bash
    #
    # A batch script will be generated using:
    # /work/n01/shared/acc/mkslurm_settejob -S $NXIO_PROC -s 8 -m 4 -C $NB_PROC -g 2 -a n01-CLASS -j sette_job -t 20:00 > ${SETTE_DIR}/job_batch_template
    # by prepare_job.sh
    #

and the suggested script is executed by prepare_job.sh instead of editing the template:

.. code-block:: bash

     case ${COMPILER} in
        X64_MOBILIS*)
          .
          .
          ;;
        X86_ARCHER2*)
          MK_TEMPLATE=$( /work/n01/shared/acc/mkslurm_settejob_4.2 -S $NXIO_PROC -s 8 -m 4 -C $NB_PROC -g 2 -a n01-CLASS -j sette_job -t 20:00 > ${SETTE_DIR}/job_batch_template )
          ;;

Any such solutions should be fed back to the system team for incorporation into future releases.

.. _Component scripts:

Component scripts
=================

``SETTE`` consists of a suite of scripts and settings files. A complete list is given here but basic
use of ``SETTE`` only requires familiarisation with the first two listed:

+ **User scripts and settings**

  - ``param.cfg``
  - ``sette.sh``

    * ``sette_reference-configurations.sh``
    * ``sette_test-cases.sh``

  - ``sette_rpt.sh``
  - ``sette_eval.sh``
  - ``sette_fetch_inputs.sh``
  - ``sette_list_avail_cfg.sh``
  - ``sette_list_avail_rev.sh``

+ **Internal scripts and settings**

  - ``all_functions.sh``
  - ``fcm_job.sh``
  - ``prepare_exe_dir.sh``
  - ``prepare_job.sh``
  - ``input_<CONFIG>.cfg``

.. _Usage of main scripts:

Usage of main scripts
=====================

The purpose and contents of ``param.cfg`` were explained in the `Initial setup`_ section.
``sette.sh`` is the main utility script that, when executed without any arguments, will
compile, configure and submit a pre-set series of tests. After all the tests have completed,
a basic report is presented to the user which lists the various successes or failures.

.. code-block:: bash

     ./sette.sh

     <lots of progress information and compilation stages followed by:>

     
     SETTE validation report generated for :
     
            trunk @ c1604aac (with local changes)
     
            on X86_ARCHER2-Cray arch file
     
     
     !!---------------1st pass------------------!!
     
        !----restart----!
     GYRE_PISCES                  run.stat    restartability  passed :  24335_c1604aac+
     GYRE_PISCES                  tracer.stat restartability  passed :  24335_c1604aac+
     ORCA2_ICE_PISCES             run.stat    restartability  passed :  24335_c1604aac+
     ORCA2_ICE_PISCES             tracer.stat restartability  passed :  24335_c1604aac+
     ORCA2_OFF_PISCES             tracer.stat restartability  passed :  24335_c1604aac+
     AMM12                        run.stat    restartability  passed :  24335_c1604aac+
     ORCA2_SAS_ICE                run.stat    restartability  passed :  24335_c1604aac+
     AGRIF_DEMO                   run.stat    restartability  passed :  24335_c1604aac+
     AGRIF_DEMO                   tracer.stat restartability  passed :  24335_c1604aac+
     WED025                       run.stat    restartability  passed :  24335_c1604aac+
     ISOMIP+                      run.stat    restartability  passed :  24335_c1604aac+
     OVERFLOW                     run.stat    restartability  passed :  24335_c1604aac+
     LOCK_EXCHANGE                run.stat    restartability  passed :  24335_c1604aac+
     VORTEX                       run.stat    restartability  passed :  24335_c1604aac+
     ICE_AGRIF                    run.stat    restartability  passed :  24335_c1604aac+
     SWG                          run.stat    restartability  passed :  24335_c1604aac+
     
        !----repro----!
     GYRE_PISCES                  run.stat    reproducibility passed :  24335_c1604aac+
     GYRE_PISCES                  tracer.stat reproducibility passed :  24335_c1604aac+
     ORCA2_ICE_PISCES             run.stat    reproducibility passed :  24335_c1604aac+
     ORCA2_ICE_PISCES             tracer.stat reproducibility passed :  24335_c1604aac+
     ORCA2_OFF_PISCES             tracer.stat reproducibility passed :  24335_c1604aac+
     AMM12                        run.stat    reproducibility passed :  24335_c1604aac+
     ORCA2_SAS_ICE                run.stat    reproducibility passed :  24335_c1604aac+
     ORCA2_ICE_OBS                run.stat    reproducibility passed :  24335_c1604aac+
     AGRIF_DEMO                   run.stat    reproducibility passed :  24335_c1604aac+
     AGRIF_DEMO                   tracer.stat reproducibility passed :  24335_c1604aac+
     WED025                       run.stat    reproducibility passed :  24335_c1604aac+
     ISOMIP+                      run.stat    reproducibility passed :  24335_c1604aac+
     VORTEX                       run.stat    reproducibility passed :  24335_c1604aac+
     ICE_AGRIF                    run.stat    reproducibility passed :  24335_c1604aac+
     SWG                          run.stat    reproducibility passed :  24335_c1604aac+
     
        !----agrif check----!
     ORCA2 AGRIF vs ORCA2 NOAGRIF run.stat    unchanged  -    passed :  24335_c1604aac+ 15541
     
        !----result comparison check----!
     
     check result differences between :
     VALID directory : /work/n01/n01/acc/NEMO/4.2.0/sette/NEMO_VALIDATION/MAIN at rev 24335_c1604aac+
     and
     REFERENCE directory : /work/n01/n01/acc/NEMO/4.2.0/sette/NEMO_VALIDATION/MAIN at rev 15150
     
     GYRE_PISCES           run.stat    files are identical
     GYRE_PISCES           tracer.stat files are identical
     ORCA2_ICE_PISCES      run.stat    files are DIFFERENT (results are different after  1  time steps)
     ORCA2_ICE_PISCES      tracer.stat files are DIFFERENT (results are different after  1  time steps)
     ORCA2_OFF_PISCES      tracer.stat files are DIFFERENT (results are different after  1  time steps)
     AMM12                 run.stat    files are DIFFERENT (results are different after  1  time steps)
     ORCA2_SAS_ICE         run.stat    files are DIFFERENT (results are different after  3  time steps)
     AGRIF_DEMO            run.stat    files are DIFFERENT (results are different after  1  time steps)
     AGRIF_DEMO            tracer.stat files are DIFFERENT (results are different after  1  time steps)
     WED025                run.stat    files are DIFFERENT (results are different after  1  time steps)
     ISOMIP+               run.stat    files are DIFFERENT (results are different after  1  time steps)
     VORTEX                run.stat    files are DIFFERENT (results are different after  1  time steps)
     ICE_AGRIF             run.stat    files are DIFFERENT (results are different after  2  time steps)
     OVERFLOW              run.stat    files are identical
     LOCK_EXCHANGE         run.stat    files are identical
     SWG                   run.stat    files are identical
     
     Report timing differences between REFERENCE and VALID (if available) :
     GYRE_PISCES              ref. time:     22.805     cur. time:     40.126         diff.:     17.321
     ORCA2_ICE_PISCES         ref. time:    133.614     cur. time:     63.484         diff.:     -70.13
     ORCA2_OFF_PISCES         ref. time:    172.469     cur. time:    471.569         diff.:      299.1
     AMM12                    ref. time:    139.546     cur. time:    222.412         diff.:     82.866
     WED025                   ref. time:    462.350     cur. time:    913.722         diff.:    451.372
     ISOMIP+                  ref. time:     33.319     cur. time:     69.091         diff.:     35.772
     OVERFLOW                 ref. time:     16.864     cur. time:     35.474         diff.:      18.61
     LOCK_EXCHANGE            ref. time:     11.912     cur. time:     13.802         diff.:       1.89

The report shows the result of restartability and reproducibility tests on the whole range of test 
configurations. Passing these tests is a necessary and mandatory requirement for any official release
of NEMO. Note these tests are not sufficient to guarantee restartability and reproducibility in all
user-defined configrations and anyone running configurations, which are not close variants of the 
reference or test configurations, should conduct their own tests. 

This report ends by comparing the latest results against a reference set (as defined in ``param.cfg``).
In this case the comparison is between revisions that were known to introduce numerical differences and
between runs with different levels of compiler optimisation. This is confined by the comparsion but the
report is most useful when numerical results are not expected to change between revisions and when changes
are expected to provide a performance benefit. It is not shown here but, on many terminals, test failures or
performance drops are presented in red to highlight areas of concern.

The set of tests executed by default are set in ``param.cfg`` in the ``TEST_CONFIGS``
environment variable:

.. code-block:: bash
		
  grep TEST_CONFIGS= param.cfg
  export TEST_CONFIGS=(${SETTE_TEST_CONFIGS[@]:-"ORCA2_ICE_PISCES ORCA2_OFF_PISCES AMM12 AGRIF WED025 GYRE_PISCES SAS ORCA2_ICE_OBS SWG ICE_AGRIF OVERFLOW LOCK_EXCHANGE VORTEX ISOMIP+"})

Note this set can be overridden by externally setting the ``SETTE_TEST_CONFIGS``
environment variable but individual or sub-sets of tests can also be selected by arguments
to the ``-n`` option to sette.sh. This is more explicit and the recommended method since
release 4.2.

Other options to ``sette.sh`` can be listed using the ``-h`` argument:

.. code-block:: bash

    ./sette.sh -h
    sette.sh with no arguments (in this case all configuration will be tested with default options)
      -T to set ln_timing false for configurations (default: true)
      -t set ln_tile false in all tests that support it (default: true)
      -e set nn_hls=3 but it is not yet supported (default: nn_hls=2)
      -i set ln_icebergs false (default: true)
      -a set ln_abl true (default: false)
      -C set nn_comm=1 (default: nn_comm=2 ==> use MPI3 collective comms)
      -N set ln_nnogather false for ORCA2 configurations (default: true)
      -q to remove the key_qco key (default: added)
      -X to remove the key_xios key (default: added)
      -Q to remove the key_RK3 key
      -A to run tests in attached (SPMD) mode (default: MPMD with key_xios)
      -n "CFG1_to_test CFG2_to_test ..." to test some specific configurations
      -x "TEST_type TEST_type ..." to specify particular type(s) of test(s) to run after compilation
                    TEST_type choices are: COMPILE RESTART REPRO CORRUPT PHYOPTS TRANSFORM
      -v "subdir" optional validation record subdirectory to be created below NEMO_VALIDATION_DIR
      -g "group_suffix" single character suffix to be appended to the standard _ST suffix used
                        for SETTE-built configurations (needed if sette.sh invocations may overlap)
      -r to execute without waiting to run sette_rpt.sh at the end (useful for chaining sette.sh invocations)
      -y to perform a dryrun to simply report what settings will be used
      -b to compile Nemo with debug options (only if %DEBUG_FCFLAGS if defined in your arch file)
      -c to clean each configuration
      -s to synchronise the sette MY_SRC and EXP00 with the reference MY_SRC and EXPREF
      -w to wait for Sette jobs to finish
      -r to print Sette report after Sette jobs completion
      -u to run sette.sh without any user interaction. This means no checks on creating
                directories etc. i.e. no safety net!

The first 11 options are switches to toggle commonly used namelist options or compile time
keys. The default setting is to have the option set ``.true.`` or the corresponding key
added. Thus, for example, running:

.. code-block:: bash

   ./sette.sh -i -Q

will run the full suite without icebergs (i.e. ``ln_icebergs=.false.``) and without
``key_RK3`` added at compile time. Some of these options (``-i``, for example)
will only affect those configurations that activate the related code option by default.
The ``-n`` option allows a sub-set of tests to be named on the command line. Testing will
be restricted to the named tests; multiple tests can be listed as a quoted,
space-separated string. For example:

.. code-block:: bash

   ./sette.sh
    and
   ./sette.sh -n "ORCA2_ICE_PISCES ORCA2_OFF_PISCES AMM12 AGRIF_DEMO WED025 GYRE_PISCES ORCA2_SAS_ICE ORCA2_ICE_OBS C1D_PAPA SWG ICE_AGRIF OVERFLOW LOCK_EXCHANGE VORTEX ISOMIP+ IWAVE"

are equivalent. As a point of interest, it is good practise to list tests in decreasing
order of their expected execution time. This will enable compilation time to overlap
run-time as much as possible and should minimise time to completion

The default operation is to perform all ``RESTART``, ``REPRO`` and agrif-processed,
``CORRUPT`` checks. The checks performed can be limited to a sub-set of these by supplying
arguments to the ``-x`` option. The combination of ``-n`` and ``-x`` is particularly
useful when working to solve a specific issue with a single configuration.  There is also
a ``PHYOPTS`` check which is not currently used but has been implemented, as a
demonstration, to run the ``OVERFLOW`` and ``LOCK_EXCHANGE`` test cases with a selection
of different physical schemes. Any other string supplied as an argument to the ``-x``
option will force a compilation only. This is useful for quickly checking for compile-time
errors. Although any non-recognised string will trigger this, it is good practise to be
explicit, i.e.:

.. code-block:: bash

   ./sette.sh -x COMPILE

The ``-s`` option forces a synchronisation of ``MY_SRC`` contents and input files from the 
EXREF directory of the reference configuration on which the test is based. This is useful
if you know these contents have been changed but do not wish to enforce a complete rebuild.
The ``-c`` option forces a clean rebuild from scratch of the test configuration. The 
``*_ST?`` directory will be deleted and recreated before a complete compilation and run is
performed. Finally, the ``-u`` option disables any interaction with the user. By default,
``sette.sh`` will request confirmation from the user for actions such as: creating the
base ``NEMO_VALIDATION_DIR`` or disabling options when incompatible choices are selected.
This interaction can be problematic with continuous integration systems and the ``-u``
option should always be used in these applications. It is the responsibility of the user
to ensure that the correct information is provided to sette.sh in these cases.
 
.. _The test results archive:

The test results archive
========================

This latest version of ``SETTE`` (released with NEMO v4.2) changes the organisation of the
records kept under the ``NEMO_VALIDATION_DIR``. This is partly to accommodate the fact
that the new command-line options provide so much flexibility for running a series of
tests on any one revision of the code with different options. To facilitate such testing,
two new command-line options have been introduced: ``-v <subdir>`` and 
``-g <sub-group_suffix>``. 

``-v`` names a sub-directory to create (or re-use) beneath ``NEMO_VALIDATION_DIR``
as the root of the records tree. If the ``-v`` option is not used then root of the
directory tree will be the branch name as returned by the:

.. code-block:: bash

  git branch --show-current

command (or ``MAIN`` if this command fails for any reason). 

``-g`` names a single character suffix that will be appended to the traditional ``_ST``
suffix that is added to the configurations built for testing. I.e.:
 
.. code-block:: bash

   ./sette.sh -e -v HALO1 -g 0

will compile and run the full suite with ``nn_hls=1``. The configurations will be
constructed with names such as: ``GYRE_PISCES_ST0`` and the directory structure
eventually populated with the test records would be similar to:

.. code-block:: bash

   ./NEMO_VALIDATION
      |-HALO1
        |---X86_ARCHER2-Cray
          |-----21334_a2c5986+
            |-------AGRIF_DEMO
              |---------LONG
              |---------ORCA2
              |---------REPRO_2_8
              |---------REPRO_4_4
              |---------SHORT
            |-------AGRIF_DEMO_NOAGRIF
              |---------ORCA2
            |-------AMM12
              |---------LONG
              |---------REPRO_4_8
              |---------REPRO_8_4
              |---------SHORT
            |-------GYRE_PISCES
              |---------LONG
              |---------REPRO_2_4
              |---------REPRO_4_2
              |---------SHORT
   .
   .
   .

Use of the ``-g`` option isn't always necessary. In this case, for example, ``-e``
only triggers a namelist changes so there is no difference in the compiled code between
this set and the default set (which will use names such as ``GYRE_PISCES_ST`` and would
have records stored under ``branch-name``). Thus, running tests sequentially such as:

.. code-block:: bash

   ./sette.sh 
   ./sette.sh -e -v HALO1

will reuse the same run-time directories and only require one set of compilations.
However, it will not be possible to diagnose any issues with the first set after the
second has run. The use of ``-g`` is recommended when running multiple tests with
different compilation keys since future tests with updated code may only need to
recompile changed modules and dependencies.

Note also that the move from ``subversion`` to ``git`` forces a change in the revision
tag used to identify the code base being tested. Whereas, with subversion, the revision
number was a integer that increased monotonically in the time-order of commits, ``git``
identifies its commits with long, hexadecimal hash strings that are not necessarily
correctly time-ordered when listed alphanumerically. The:

.. code-block:: bash

 git rev-list --abbrev-commit -1 origin

command can be used to obtain a abbreviated commit hash that still provides a unique
identifier but extra steps are required to provide a revision_tag that retains some
indication of time-order. The current solution is to prepend the abbreviated hash string
with a representation of the date on which the commit was made. This information can
be obtained from the ``git log`` response as follows:

.. code-block:: bash

  git log -1 | grep Date | sed -e 's/.*Date: *//' -e's/ +.*$//'
  Mon Dec 6 15:24:36 2021

Condensing this string into something usable requires use of the unix ``date`` command
which can vary in different flavours of the OS. Two examples are currently supported,
one for MacOSX and one, more general, POSIX variety. More can be added in ``param.cfg``
as required. Each supported style is tested in param.cfg to determine which form to use:

.. code-block:: bash

  # command for converting date (from git log -1) into 2-digit year + yearday
  #
  date -j -f "%a %b %d %H:%M:%S %Y" "Tue Nov 30 17:10:53 2021" +"%y%j" >& /dev/null
  if [ $? == 0 ] ; then DATE_CONV='date -j -f "%a %b %d %H:%M:%S %Y" ' ;fi
  #
  date --date="Tue Nov 30 17:10:53 2021" +"%y%j" >& /dev/null
  if [ $? == 0 ] ; then DATE_CONV='date --date=' ;fi

In both cases, the output format is a 2-digit year + a 3-digit year-day resulting
in a 5-digit string to prepend to the short hash. There is still scope for slight
mis-ordering between commits committed on the same day but this compromise avoids
over-long revision tags.

In the example directory listing above the revision tag is shown as: ``21334_a2c5986+``
which displays a typical 5-digit date and 7-digit short hash separated by an underscore.
In this case a ``+`` has been appended because ``sette`` has detected local changes to
the base commit. The output of:

.. code-block:: bash

  git status --short -uno

is used to check for local modifications when making this decision.



Super-sized SETTE
=================

The idea of chaining a series of tests to test various options leads to the possibility of
a ``super_sette.sh`` script. For example, this content:

.. code-block:: bash

    #!/bin/bash
    # set -vx
    # Simple script to robustly run a full suite of SETTE tests
    #
    ########################################
    # Start of main script
    ########################################
    FULLSET=( ORCA2_ICE_PISCES ORCA2_OFF_PISCES AMM12 AGRIF WED025 GYRE_PISCES SAS ORCA2_ICE_OBS SWG ICE_AGRIF OVERFLOW LOCK_EXCHANGE VORTEX ISOMIP+ )
    #
    GROUP_SETS=( "-g 0 -r -v MAIN" "-e -F -t -g 1 -v HALO1 -r" "-q -g 2 -v NO_QCO -r" "-i -e -F -t -g 3 -v NO_ICB1 -r" "-i -g 4 -v NO_ICB2 -r" "-C -g 5 -v NO_COLL -r" )
    #
    # These groups sets correspond to the following test regimes:
    #
    # A. Three complete sets with various combinations of options:
    #
      printf "%-93s %s\n" "Full tests - MAIN with default options (using *_ST0 config dirs) : "  "${GROUP_SETS[0]}"
      printf "%-93s %s\n" "Full tests - HALO1 with nn_hls=1 (no tiling or loop fusion) (using *_ST1 config dirs) : " "${GROUP_SETS[1]}"
      printf "%-93s %s\n" "Full tests - NO_QCO without qco (using *_ST2 config dirs) : " "${GROUP_SETS[2]}"
    #
    # B. Three different option choices with ORCA2_ICE_PISCES only:
    #
      printf "%-93s %s\n" "ORCA2_ICE_PISCES tests - NO_ICB1 without icebergs, with nn_hls=1 (using *_ST3 config dirs) : " "${GROUP_SETS[3]}"
      printf "%-93s %s\n" "ORCA2_ICE_PISCES tests - NO_ICB2 without icebergs, with nn_hls=2 (using *_ST4 config dirs) : " "${GROUP_SETS[4]}"
      printf "%-93s %s\n" "ORCA2_ICE_PISCES tests - NO_COLL without collective comms (using *_ST5 config dirs) : " "${GROUP_SETS[5]}"
    #
    # A. Full tests
    for gs in 0 1 2
    do
     for n in `seq 0 1 $(( ${#FULLSET[@]} - 1 ))`
     do
       confstr="${FULLSET[$n]}"
       # run the test
       echo ./sette.sh ${GROUP_SETS[$gs]} -x "RESTART REPRO CORRUPT" -n "$confstr"
            ./sette.sh ${GROUP_SETS[$gs]} -x "RESTART REPRO CORRUPT" -n "$confstr"
     done
    done
    #
    # B. ORCA2_ICE_PISCES special tests
    for gs in 3 4 5
    do
     # run the test
     echo ./sette.sh ${GROUP_SETS[$gs]} -x "RESTART REPRO" -n ORCA2_ICE_PISCES
          ./sette.sh ${GROUP_SETS[$gs]} -x "RESTART REPRO" -n ORCA2_ICE_PISCES
    done
    exit

will perform all these tests:

.. code-block:: bash

    Full tests - MAIN with default options (using *_ST0 config dirs) :                            -g 0 -r
    Full tests - HALO1 with nn_hls=1 (no tiling or loop fusion) (using *_ST1 config dirs) :       -e -F -t -g 1 -v HALO1 -r
    Full tests - NO_QCO without qco (using *_ST2 config dirs) :                                   -q -g 2 -v NO_QCO -r
    ORCA2_ICE_PISCES tests - NO_ICB1 without icebergs, with nn_hls=1 (using *_ST3 config dirs) :  -i -e -F -t -g 3 -v NO_ICB1 -r
    ORCA2_ICE_PISCES tests - NO_ICB2 without icebergs, with nn_hls=2 (using *_ST4 config dirs) :  -i -g 4 -v NO_ICB2 -r
    ORCA2_ICE_PISCES tests - NO_COLL without collective comms (using *_ST5 config dirs) :         -C -g 5 -v NO_COLL -r

and create archive structures under: ``MAIN``, ``HALO1``, ``NO_QCO``, ``NO_ICB1``,
``NO_ICB2``, ``NO_COLL`` subdirectories. An new command-line option: ``-r`` has been
introduced and used here. It simply prevents the ``sette.sh`` from generating a report on
completion. Normally, ``sette.sh`` waits until all jobs have completed and then runs the
``sette_rpt.sh`` script to produce the report. When chaining invocations like this there
is no requirement to produce a report between invocations and therefore no need to wait
for individual jobs to complete. ``sette_rpt.sh`` can always be invoked directly, see
section: `Reporting options`_ for more details.

.. _Archive contents:

Archive contents
================

``SETTE`` places copies of selected output files from each test within the relevant
subdirectory of the results directory structure. The selection of files is sufficient for
simple comparsions between equivalent tests carried out with different code revisions,
different run-time options or different compile-time keys. An example full set is:

.. code-block:: bash

    ls -1 NEMO_VALIDATION/HALO1/X86_ARCHER2-Cray/24335_c1604aac+/ORCA2_ICE_PISCES/LONG
    namelist_cfg
    namelist_ice_cfg
    namelist_pisces_cfg
    namelist_top_cfg
    ocean.output
    output.namelist.dyn
    output.namelist.ice
    output.namelist.pis
    output.namelist.top
    run.stat
    sette_config
    timing.output
    tracer.stat

but some tests may have fewer files (e.g. not all tests runs will produce a
``tracer.stat`` file and timing information may not have been requested).
NOTE: we should add the run.stat.nc files as well

The main comparison is performed between ``run.stat`` and ``tracer.stat`` files and
any differences will be highlighted. ``ocean.output`` files and the input namelists are
included to enable verification of the actual runtime conditions.  The output namelists
are also included so that accurate reading of the namelists can be verified. A new
addition at release 4.2 is the sette_config file which is a record on the options used
for this particular invocation of ``sette.sh``. For example:

.. code-block:: bash

    cat ./NEMO_VALIDATION/dev_main_halos/X86_ARCHER2-Cray/21336_0235f28+/GYRE_PISCES/LONG/sette_config
    Summary of sette environment
    ----------------------------
    requested by the command          : ./sette.sh -n GYRE_PISCES -u
    on branch                         : dev_main_halos
    USING_TIMING                      : yes
    USING_ICEBERGS                    : yes
    USING_EXTRA_HALO                  : yes
    USING_TILING                      : yes
    USING_COLLECTIVES                 : yes
    USING_QCO                         : yes
    USING_LOOP_FUSION                 : yes
    USING_XIOS                        : yes
    USING_MPMD                        : yes
    USING_RK3                         : no
    USER_INPUT                        : no
    Common compile keys added         : key_xios key_loop_fusion key_qco
    Common compile keys deleted       : key_RK3
    Compile keys actually used        : key_top key_linssh key_xios key_loop_fusion

.. _Reporting options:

Reporting options
=================

As mentioned previously, the reporting function is performed by the ``sette_rpt.sh``
script. This is normally invoked by ``sette.sh`` but can be run at anytime. The script
accepts several command-line options which makes it a versatile tool for comparing across
different sets of tests:

.. code-block:: bash

    ./sette_rpt.sh -h
    sette_rpt.sh :
         display result for the latest change
     -c COMPILER_name :
         display result for the specified compiler
     -r REVISION_number :
         display sette results for the specified revision (set old for the latest revision available for each config)
     -R REFERENCE REVISION_number :
         compare sette results against the specified revision (use to over-ride value set in param.cfg)
     -v sub_dir :
         validation sub-directory below NEMO_VALIDATION_DIR
     -V sub_dir2 :
         2nd validation sub-directory below NEMO_VALIDATION_DIR
         if set the comparison is between two subdirectory trees beneath NEMO_VALIDATION_DIR
     -u to run sette_rpt.sh without any user interaction


``sette_rpt.sh`` will check all restartability and reproducibility results as well as
comparing differences between sets. A stripped down version is available
named:``sette_eval.sh`` which can be used for a quick evaluation of differences only. For
example:

.. code-block:: bash

    ./sette_eval.sh -V MAIN -v HALO1 -R 14886
    
    Current code is : NEMO/trunk @ r14896  ( last change @ r14886 )
    
    SETTE evaluation for :
    
           NEMO/trunk @ r14886 (last changed revision)
    
           on X86_ARCHER2-Cray arch file
    
    
       !----result comparison check----!
    
    check result differences between :
    VALID directory : /work/n01/n01/acc/NEMO/2021/midmerge/dev_sette/NEMO_VALIDATION/HALO1 at rev 14886
    and
    REFERENCE directory : /work/n01/n01/acc/NEMO/2021/midmerge/dev_sette/NEMO_VALIDATION/MAIN at rev 14886
    
    GYRE_PISCES           run.stat    files are identical
    GYRE_PISCES           tracer.stat files are identical
    ORCA2_ICE_PISCES      run.stat    files are DIFFERENT (results are different after  71  time steps)
    ORCA2_ICE_PISCES      tracer.stat files are DIFFERENT (results are different after  73  time steps)
    ORCA2_OFF_PISCES      tracer.stat files are DIFFERENT (results are different after  17  time steps)
    AMM12                 run.stat    files are identical
    ORCA2_SAS_ICE         run.stat    files are identical
    AGRIF_DEMO            run.stat    files are identical
    WED025                run.stat    files are identical
    ISOMIP+               run.stat    files are identical
    VORTEX                run.stat    files are identical
    ICE_AGRIF             run.stat    files are identical
    OVERFLOW              run.stat    files are identical
    LOCK_EXCHANGE         run.stat    files are identical
    SWG                   run.stat    files are identical

This script also has a "quiet mode" for less verbose output (possibly, more suited
for regular monitoring appliactions):
    
.. code-block:: bash

    ./sette_eval.sh -V MAIN -v HALO1 -R 14886 -q
    3  differences from 13 matches.


It is also useful when tests have only been run with a few configurations. Take the
``ORCA2_ICE_PISCES`` only tests suggested by ``super_sette.sh``, for example:
    
.. code-block:: bash

    ./sette_eval.sh -V MAIN -v NO_ICB2 -R 14886 -q
    2  differences from 1 matches. 0 missing from REFERENCE 12 missing from VALID

The two differences here being some run.stat and tracer.stat differences for
``ORCA2_ICE_PISCES`` at that revision. Reassuringly:
    
.. code-block:: bash

    ./sette_eval.sh -V NO_ICB2 -v NO_ICB1 -R 14886 -q
    0  differences from 1 matches. 12 missing from REFERENCE 12 missing from VALID

and:
    
.. code-block:: bash

    ./sette_eval.sh -V MAIN -v NO_COLL -R 14886 -q
    0  differences from 1 matches. 0 missing from REFERENCE 12 missing from VALID

Keeping track of archived results
=================================

It is apparent that with all this flexibility comes the risk of losing track of which
revisions have been tested with which configurations. ``SETTE`` now includes a
helper script which can table the options available for comparison. E.g.:

.. code-block:: bash

     ./sette_list_avail_rev.sh

      Compiler used is : X86_ARCHER2-Cray

      List of all avail. rev. in   :/work/n01/n01/acc/NEMO/GIT/nemo/sette/NEMO_VALIDATION/MAIN/
                              is   : 21334_522ad4c+  21335_440ad90+  21336_0235f28+  21336_416860f+
      Availability for each config.:
      ------------------------------
      GYRE_PISCES                  : ------------    21335_440ad90+  21336_0235f28+  21336_416860f+
      ORCA2_ICE_PISCES             : ------------    21335_440ad90+  21336_0235f28+  21336_416860f+
      ORCA2_OFF_PISCES             : ------------    ------------    21336_0235f28+  ------------
      AMM12                        : ------------    ------------    21336_0235f28+  ------------
      WED025                       : ------------    ------------    21336_0235f28+  ------------
      ORCA2_ICE_OBS                : ------------    ------------    21336_0235f28+  ------------
      ORCA2_SAS_ICE                : ------------    ------------    21336_0235f28+  ------------
      AGRIF_DEMO                   : ------------    ------------    21336_0235f28+  ------------
      SWG                          : ------------    ------------    ------------    ------------
      ISOMIP+                      : 21334_522ad4c+  ------------    21336_0235f28+  ------------
      OVERFLOW                     : ------------    ------------    21336_0235f28+  ------------
      LOCK_EXCHANGE                : ------------    ------------    21336_0235f28+  ------------
      VORTEX                       : ------------    ------------    21336_0235f28+  ------------
      ICE_AGRIF                    : ------------    ------------    21336_0235f28+  ------------

By default, this lists the options in the MAIN sub-directory but other parts of the
directory tree can be examined using command-line arguments:

.. code-block:: bash

    sette_list_avail_rev.sh :
         list all sette directory and available revisions created with the compiler specified in param.cfg or in the startup file)
    -c COMPILER_name :
         list all sette directory and available revisions created with the compiler specified
     -v sub_dir :
         validation sub-directory below NEMO_VALIDATION_DIR

To add a new configuration
==========================
1. 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)
2. add a bloc in one of the ``sette_reference-configuration.sh`` or ``sette_test-cases.sh`` script 
3. add your configuration to the list in ``param.cfg``

.. image:: _static/sette_rpt.png
   :align: center