.. _xios3demo:

******************
XIOS3 demonstrator
******************

.. contents::
   :local:

Overview
========

NEMO version 5.0 includes a new configuration: ``cfgs/X3_ORCA2_ICE_PISCES`` which is a
variation on the ``ORCA2_ICE_PISCES`` reference configuration designed to illustrate the
XML changes required to utilise the new XIOS3 functionalities. This is in advance of any
detailed documentation on XIOS3 and is based mainly on material presented by the XIOS
developers at a coupling workshop in 2023. The slides from that presentation can be found
`here <http://forge.ipsl.fr/ioserver/raw-attachment/wiki/WikiStart/Coupling%20workshop-CW2023.pdf>`_ . 

The X3_ORCA2_ICE_PISCES demonstrator is based on the SETTE tests for ``ORCA2_ICE_PISCES``.
Traditionally, this is run with 32 Ocean cores and 4 XIOS servers producing one-file
output. This XIOS3 example has also been run with 32 ocean cores but has used 12 XIOS3
servers to produce one-file output via various pools and services. Whilst, in this case,
not much has been gained, the ability to control exactly how the xios resources are
deployed and employed should make for robust solutions in more demanding cases. This has
already been successfully tested in an eORCA025 configuration where 1019 ocean cores have
reliably produced one-file output via 52 xios servers. This latter example is illustrated
on a XIOS ticket at:
`XIOS forge ticket 190 <https://forge.ipsl.jussieu.fr/ioserver/ticket/190#comment:15>`_ . 
For now, this simpler example will be used to explain the options and highlight the XML 
changes required to make it happen. First, here is a schematic of the example:

.. figure:: _static/X3_O2IP_example.png
   :width: 100%
   :align: center

..

The idea is that, instead of all fields going to all xios servers, subsets of xios servers
are assigned to gather different groups of fields. These "gatherer" services then send the
collated fields to dedicated "writer" services. In this example, separate gatherer
services, with 2-cores each, are used for: T- and W-grid variables; ice fields; U- and
V-grid variables and passive tracer fields. These services are named: tgatherer,
igatherer, ugatherer and pgatherer. Larger configurations may elect to have separate
services for different output frequencies too to spread the memory footprint. Each of
these gatherer services has an associated writer service: twriter; iwriter; uwriter and
pwriter. Each writer service has only one server process assigned to it, thus guaranteeing
one-file output. With larger configurations, more writing processes may be required per
writing service but it is expected that numbers can be kept low enough for the "one_file"
activation of netcdf4 output to be suitably robust and efficient.

Changes to ``iodef.xml``
------------------------

All of this is set up via xml tags in the ``iodef.xml`` file, namely:

.. code-block:: xml

       <?xml version="1.0"?>
       <simulation>
       
       <!-- ============================================================================================ -->
       <!-- XIOS3 context                                                                                 -->
       <!-- ============================================================================================ -->
       
         <context id="xios" >
           <variable_definition>
             <variable_group id="buffer">
               <variable id="min_buffer_size" type="int">400000</variable>
               <variable id="optimal_buffer_size" type="string">performance</variable>
             </variable_group>
       
             <variable_group id="parameters" >
               <variable id="using_server" type="bool">true</variable>
               <variable id="info_level" type="int">0</variable>
               <variable id="print_file" type="bool">false</variable>
               <variable id="using_server2" type="bool">false</variable>
               <variable id="transport_protocol" type="string" >p2p</variable>
               <variable id="using_oasis"      type="bool">false</variable>
             </variable_group>
           </variable_definition>
           <pool_definition>
            <pool name="Opool" nprocs="12">
             <service name="tgatherer" nprocs="2" type="gatherer"/>
             <service name="igatherer" nprocs="2" type="gatherer"/>
             <service name="ugatherer" nprocs="2" type="gatherer"/>
             <service name="pgatherer" nprocs="2" type="gatherer"/>
             <service name="twriter" nprocs="1" type="writer"/>
             <service name="uwriter" nprocs="1" type="writer"/>
             <service name="iwriter" nprocs="1" type="writer"/>
             <service name="pwriter" nprocs="1" type="writer"/>
            </pool>
           </pool_definition>
         </context>
       
       <!-- ============================================================================================ -->
       <!-- NEMO  CONTEXT add and suppress the components you need                                       -->
       <!-- ============================================================================================ -->
       
         <context id="nemo" default_pool_writer="Opool" default_pool_gatherer="Opool" src="./context_nemo.xml"/>       <!--  NEMO       -->
       
       </simulation>

Much of this will be familiar and carries over from XIOS2. The new ``pool_definition`` tag
and the syntax of its contents is also straight-forward. There are a couple of subtleties
to point out:

.. code-block:: xml

       <variable id="transport_protocol" type="string" >p2p</variable>

This is a new transport_protocol using point to point communication and has proven to be 
the most reliable in these tests.

.. code-block:: xml

  <context id="nemo" default_pool_writer="Opool" default_pool_gatherer="Opool" src="./context_nemo.xml"/>

New attributes added to the context tag which declare the default pool from which named
gatherers and writers will be selected.

Changes to ``file_defs``
------------------------

Next, to make use of these services they have to be assigned at the file level. For example, 
here are the changes in the ``file_def_nemo-ice.xml``:

.. code-block:: diff

       --- ../../ORCA2_ICE_PISCES/EXPREF/file_def_nemo-ice.xml 2023-09-15 16:57:00.039299000 +0100
       +++ file_def_nemo-ice.xml       2023-09-21 13:10:36.750776000 +0100
       @@ -9,10 +9,10 @@
        ============================================================================================================
         -->
       
       - <file_definition type="one_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
       + <file_definition type="one_file" compression_level="1" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
       
           <file_group id="5d" output_freq="5d"  output_level="10" enabled=".TRUE.">  <!-- 5d files -->
       -     <file id="file21" name_suffix="_icemod" description="ice variables" enabled=".true." >
       +     <file id="file21" name_suffix="_icemod" mode="write" gatherer="igatherer" writer="iwriter" using_server2="true" description="ice variables" enabled=".true." >
       
               <!-- ice mask -->
               <field field_ref="icemask"          name="simsk"   />
       @@ -89,7 +89,7 @@
       
             </file>
       
       -     <file id="file22" name_suffix="_SBC_scalar" description="scalar variables" enabled=".true." >
       +     <file id="file22" compression_level="0" name_suffix="_SBC_scalar" mode="write" gatherer="igatherer" writer="iwriter" using_server2="true" description="scalar variables" enabled=".true." >
               <!-- global contents -->
               <field field_ref="ibgvol_tot"     name="ibgvol_tot"   />
               <field field_ref="sbgvol_tot"     name="sbgvol_tot"   />
       @@ -123,7 +123,7 @@
           <file_group id="4h"  output_freq="4h"  output_level="10" enabled=".TRUE."/> <!-- 4h files -->
           <file_group id="6h"  output_freq="6h"  output_level="10" enabled=".TRUE."/> <!-- 6h files -->
       
       -   <file_group id="1m"  output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
       +   <file_group id="1m"  compression_level="0" output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
       
             <!-- To compute transport through straits : need to read ice mask at ice iteration at freq_offset = 1mo - nn_fsbc
              <file id="file23" name_suffix="_strait_ice" description="transport variables through straits" >

with corresponding changes in the other file_def files. Note that ``compression_level``
attributes have also been added here, more about that to follow. 

Other XML changes
-----------------

A couple of other XML tags are transitioning to new names. To avoid generating warnings
concerning the use of the old names it is recommended to make the following changes before
testing this new capability:

.. code-block:: sh

        zoom_axis ---> extract_axis in axis_def_nemo.xml

and the change of all:

.. code-block:: sh

         zoom_domain ---> extract_domain in domain_def_nemo.xml


There are additional changes in the ``field_def*.xml`` files and the
``domain_def_nemo.xml`` and ``axis_def_nemo.xml`` files which are to do with the next
stage of exercising control over dataset chunking and compression.

Chunking and compression
------------------------

One goal of making one file output from XIOS more reliable is to eliminate the need for
any further post-processing of the output. With this in mind, it may be necessary  to
exercise control over the chunk sizes used for the output files since the optimum choice
will depend on future access requirements.

XIOS3 has a selection of XML attributes that control the chunk sizes but achieving
particular target chunk dimensions isn't straight-forward. These attributes are a range of
domain, axis and field settings listed here:

  =========================   ==============  ================
  attribute name              attribute type   default setting  
  =========================   ==============  ================
  chunking_weight_i           domain           1.0              
  chunking_weight_j           domain           1.0              
  chunking_weight             axis             1.0              
  chunking_blocksize_target   field            20.0      (MB)   
  prec                        field            4 or 8           
  compression_level           file             0                
  =========================   ==============  ================

The last does not actually affect the chunk size but is included as a reminder that one
major reason to activate chunking is to allow efficient dataset compression (which is off
by default).

`Ticket #191 <https://forge.ipsl.jussieu.fr/ioserver/ticket/191#comment:1>`_ on the XIOS
forge contains an explanation of the algorithm that is used. Based on this, a chunk size
calculator has been added in ``tools/MISCELLANEOUS/calc_xios_chunks.py``:

.. code-block:: sh

       python3 calc_xios_chunks.py --help
       usage: calc_xios_chunks.py [-h] [-i ISIZE] [-j JSIZE] [-k KSIZE] [-t TARGET]
                                  [-p PREC] [-wi WI] [-wj WJ] [-wk WK]
       
       Calculate netCDF4 chunks sizes that XIOS will use based on domain size
       and chunk_weight and chunk_blocksize_targets set as XML attributes, e.g.:
       
         python3 ./calc_xios_chunks.py -i isize -j jsize -k ksize
                                       -t target -p fp_precision
                                       -wi wgt_i -wj wgt_j -wk wgt_k
       
       All arguments are optional with default settings equivalent to
       XIOS defaults with a eORCA025-size domain
       
       optional arguments:
         -h, --help  show this help message and exit
         -i ISIZE    First dimension size of the domain (usually longitudinal) [1440]
         -j JSIZE    Second dimension size of the domain (usually latitudinal) [1206]
         -k KSIZE    Third dimension size of the domain (usually depth) [75]
         -t TARGET   Target chunk blocksize in MB [20.0]
         -p PREC     Floating-point byte-size of op variables, (usually 4 or 8) [4]
         -wi WI      Weight applied to the first dimension [1.0]
         -wj WJ      Weight applied to the second dimension [1.0]
         -wk WK      Weight applied to the third dimension [1.0]

So for ORCA2 with default settings we have:

.. code-block:: sh

      python3 calc_xios_chunks.py -i 180 -j 148 -k 31
      -----------------------------------------------------
       XYZ domain size     :  180 x 148 x 31
       Target chunksize    :  20 MB,  FP precision:  4
       i- j- and k- weights:  1.0 1.0 1.0
       4D TZYX chunk sizes :  1 31 148 180
       3D TYX chunk sizes  :  1 148 180
      -----------------------------------------------------

Thus, without any intervention, the default behaviour for ORCA2 is to have the entire
model volume as a single chunk. With compression, this can be wasteful since any future
access, even for a single datum, has to retrieve and uncompress the entire chunk.

Adjusting the various weights and block size target will change this, for example:

.. code-block:: sh

      python3 calc_xios_chunks.py -i 180 -j 148 -k 31 -wk 12. -t 3
      -----------------------------------------------------
       XYZ domain size     :  180 x 148 x 31
       Target chunksize    :  3 MB,  FP precision:  4
       i- j- and k- weights:  1.0 1.0 12.0
       4D TZYX chunk sizes :  1 6 148 180
       3D TYX chunk sizes  :  1 148 180
      -----------------------------------------------------

which is the choice provided with the demonstrator. These settings can be seen in situ
by examining the XML files provided with the demonstrator. I.e.:

.. code-block:: xml

       grep -e chunking_ -e compression *.xml
       axis_def_nemo.xml:  <axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" chunking_weight="12.0" />
       axis_def_nemo.xml:  <axis id="deptht300" axis_ref="deptht" chunking_weight="12.0" >
       axis_def_nemo.xml:  <axis id="depthu"  long_name="Vertical U levels"  unit="m" positive="down" chunking_weight="12.0" />
       axis_def_nemo.xml:  <axis id="depthv"  long_name="Vertical V levels"  unit="m" positive="down" chunking_weight="12.0" />
       axis_def_nemo.xml:  <axis id="depthw"  long_name="Vertical W levels"  unit="m" positive="down" chunking_weight="12.0" />
       axis_def_nemo.xml:  <axis id="depthf"  long_name="Vertical F levels"  unit="m" positive="down" chunking_weight="12.0" />
       axis_def_nemo.xml:  <axis id="nlayice" long_name="Ice layer"          unit="1" chunking_weight="1.0" />
       domain_def_nemo.xml:  <domain id="grid_T" long_name="grid T" chunking_weight_i="1.0" chunking_weight_j="1.0" />
       domain_def_nemo.xml:  <domain id="grid_T_inner" long_name="grid T inner"  chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_U" long_name="grid U" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_U_inner" long_name="grid U inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_V" long_name="grid V" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_V_inner" long_name="grid V inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_W" long_name="grid W" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_W_inner" long_name="grid W inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_F" long_name="grid F" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       domain_def_nemo.xml:  <domain id="grid_F_inner" long_name="grid F inner" chunking_weight_i="1.0" chunking_weight_j="1.0"/>
       field_def_nemo-ice.xml:  <field_group id="SBC" chunking_blocksize_target="3.0" > <!-- time step automatically defined based on nn_fsbc -->
       field_def_nemo-oce.xml: <field_group id="all_ocean" chunking_blocksize_target="3.0">
       field_def_nemo-pisces.xml: <field_group id="all_pisces" chunking_blocksize_target="3.0">
       file_def_nemo-ice.xml: <file_definition type="one_file" compression_level="1" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
       file_def_nemo-ice.xml:     <file id="file22" compression_level="0" name_suffix="_SBC_scalar" mode="write" gatherer="igatherer" writer="iwriter" using_server2="true" description="scalar variables" enabled=".true." >
       file_def_nemo-ice.xml:   <file_group id="1m"  compression_level="0" output_freq="1mo" output_level="10" enabled=".TRUE."> <!-- real monthly files -->
       file_def_nemo-oce.xml:    <file_definition type="one_file" compression_level="1" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
       file_def_nemo-oce.xml:        <file id="file15" compression_level="0" name_suffix="_scalar" mode="write" gatherer="tgatherer" writer="twriter" using_server2="true" description="scalar variables" >
       file_def_nemo-pisces.xml:    <file_definition type="one_file" compression_level="1" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1mo" min_digits="4">
       file_def_nemo-pisces.xml:        <file id="file31" compression_level="0" name_suffix="_bioscalar" mode="write" gatherer="pgatherer" writer="pwriter" using_server2="true" description="pisces sms variables" >
       

With this small model it is difficult to force division of the primary axes but it can be
done. Perhaps this is a reasonable choice if future access is likely to favour either
Northern or Southern hemispheres:

.. code-block:: sh

       python3 calc_xios_chunks.py -i 180 -j 148 -k 31 -wj 2 -wk 12. -t 1
       -----------------------------------------------------
        XYZ domain size     :  180 x 148 x 31
        Target chunksize    :  1 MB,  FP precision:  4
        i- j- and k- weights:  1.0 2.0 12.0
        4D TZYX chunk sizes :  1 8 74 180
        3D TYX chunk sizes  :  1 148 180
       -----------------------------------------------------

Summary of changes
------------------

The contents of ``cfgs/X3_ORCA2_ICE_PISCES/EXPREF`` parallel those of the parent
``ORCA2_ICE_PISCES`` with local copies of any changed files. This includes some files that
were originally symbolic links to files in the ``SHARED`` directory. Files which are
symbolic links to files in the ``SHARED`` directory have @ appended to their name in the
following table:

  ===========================  ========== ====  ==========================  =========== ==== ==========
   ORCA2_ICE_PISCES/EXPREF         sum          X3_ORCA2_ICE_PISCES/EXPREF       sum           changed?  
  ===========================  ========== ====  ==========================  =========== ==== ==========
   axis_def_nemo.xml@             53815     3   axis_def_nemo.xml               53184     3     yes   
   context_nemo.xml               08199     2   context_nemo.xml                08199     2     no    
   domain_def_nemo.xml@           17199    13   domain_def_nemo.xml             46480    14     yes   
   field_def_nemo-ice.xml@        32328    64   field_def_nemo-ice.xml          31824    64     yes   
   field_def_nemo-oce.xml@        13274   140   field_def_nemo-oce.xml          10094   140     yes   
   field_def_nemo-pisces.xml@     18919    33   field_def_nemo-pisces.xml       62713    33     yes   
   file_def_nemo-ice.xml          25184     9   file_def_nemo-ice.xml           28646     9     yes   
   file_def_nemo-oce.xml          31630    11   file_def_nemo-oce.xml           45129    11     yes   
   file_def_nemo-pisces.xml       53625     9   file_def_nemo-pisces.xml        16003    10     yes   
   grid_def_nemo.xml@             54429    11   grid_def_nemo.xml@              54429    11     no    
   iodef.xml                      25161     2   iodef.xml                       32297     3     yes   
   namelist_cfg                   06454    36   namelist_cfg                    06454    36     no    
   namelist_ice_cfg               00419     5   namelist_ice_cfg                00419     5     no    
   namelist_ice_ref@              49215    26   namelist_ice_ref@               49215    26     no    
   namelist_pisces_cfg            44377     6   namelist_pisces_cfg             44377     6     no    
   namelist_pisces_ref@           15677    30   namelist_pisces_ref@            15677    30     no    
   namelist_ref@                  14435   124   namelist_ref@                   14435   124     no    
   namelist_top_cfg               40559    12   namelist_top_cfg                40559    12     no    
   namelist_top_ref@              20216    13   namelist_top_ref@               20216    13     no    
  ===========================  ========== ====  ==========================  =========== ==== ==========