Release/soca 1.0.0 (#330)

* specify docutils version (#311) * explanation for absolute difference (#285) Co-authored-by: mmiesch <[email protected]> * Update and augment MacOS instructions (#283) * Update and augment MacOS instructions * Add admin privileges warning * Remove reference to homebrew mpich. Other edits. * Add some additional module req's * No LAPACK module * Remove LAPACK troubleshooting section * Clarify lmod setup * Clarify lmod setup again Co-authored-by: mmiesch <[email protected]> * Documenting the DrawValueFromFile and DrawObsValueFromFile obsfunctions (#276) * ENH: Added basic documentation for DrawObsErrorFromFile and DrawValueFromFile * minor tweeks * MAINT: Self review changes Self review changes to DrawValueFromFile.rst Perhaps we should centrally document obsfuction capability to return different types. * MAINT: Further review changes * MAINT: Self review of DrawObsErrorFromFile.rst * Updated index * MAINT: Self review final * MAINT: Minor changes based on review * MAINT: Minor changes based on review * MAINT: Minor review changes * ENH: Total refactor * Typo * MAINT: Review changes for Mike * MAINT: Review changes for DrawObsErrorFromFile * MAINT: review changes of DrawbsErrorFromFile * MAINT: minor review changes * MAINT: minor review change Co-authored-by: mmiesch <[email protected]> * Basic doc skeleton * wip * wip * wip ... ws to github * wip * fixed build warnings * doc for marine ufo * WIP * inpu variables * added a few more var changes * start cleanup, left off at classes:Model * cleanup soca classes * extra space * Documentation to run the soca tutorial (#326) * added tutorial documentation * addressing Maryam's comments * move build section just before tutorial * addressed rev's comments ... I think. * capitalize un-italicify soca Co-authored-by: Travis Sluka <[email protected]> Co-authored-by: Clementine Gas <[email protected]> Co-authored-by: Steven Vahl <[email protected]> Co-authored-by: Carwyn Pelley <[email protected]> Co-authored-by: Guillaume Vernieres <[email protected]> Co-authored-by: Travis Sluka <[email protected]>
JCSDA · Oct 29, 2021 · b343b7e · b343b7e
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diff --git a/docs/inside/jedi-components/index.rst b/docs/inside/jedi-components/index.rst
@@ -11,4 +11,5 @@ JEDI Components
    ufo/index.rst
    fv3-jedi/index.rst
    mpas-jedi/index.rst
+   soca/index.rst
    configuration/index.rst
diff --git a/docs/inside/jedi-components/soca/build.rst b/docs/inside/jedi-components/soca/build.rst
@@ -0,0 +1,106 @@
+.. _top-soca-build:
+
+.. _Building SOCA in Singularity:
+
+Building SOCA in Singularity
+==============================
+
+This section describes how to configure and compile SOCA inside of a Singularity container.
+``ecbuild`` (a wrapper of ``cmake``) is used for the configuration of the build and ``ctest`` to
+confirm that the compiled code is working properly. Usage of ``cmake`` and ``ctest`` are described
+in the :doc:`JEDI CMake, CTest, and ecbuild </inside/developer_tools/cmake>` documentation.
+
+While SOCA can be complied on various architectures (HPC, workstations, ...),
+this section only describes how to compile SOCA inside of a Singularity container.
+Instruction on how to install and run Singularity is provided in the :doc:`JEDI development Singularity container
+</using/jedi_environment/singularity>`.
+
+Download and run a shell inside of a Singularity container:
+
+.. code-block:: bash
+
+    singularity pull library://jcsda/public/jedi-gnu-openmpi-dev  # download the development container
+    singularity shell -e jedi-gnu-openmpi-dev_latest.sif          # run a shell within a singularity container
+
+Clone the `1.0.0` tag of the SOCA repository
+
+.. code-block:: console
+
+    git clone --branch 1.0.0 https://github.com/jcsda/soca.git
+
+This will create a SOCA directory that contains the MOM6 interface to JEDI as well as the
+necessary dependencies provided as an ``ecbuild`` bundle in ``soca/bundle/CMakeLists.txt``
+
+Default configuration and build of SOCA
+-----------------------------------------
+
+.. code-block:: bash
+
+    mkdir build
+    cd build
+    ecbuild ../soca/bundle  # configure the build
+    make -j<nthreads>       # compile
+    ctest                   # test all JEDI components including `soca`
+
+Extra build configurations for SOCA
+-------------------------------------
+
+To enable the use of the `Community Radiative Transfer Model (CRTM) <https://github.com/jcsda/crtm>`_
+set the build option ``BUILD_CRTM`` for the ``ecbuild`` step above:
+
+.. code-block:: bash
+
+     ecbuild -DBUILD_CRTM=ON ../soca/bundle
+
+To enable the use of the biogeochemistry model
+`BLING <https://www.gfdl.noaa.gov/simplified-ocean-biogeochemistry-bling/>`_ set the build
+option ``ENABLE_OCEAN_BGC` for the ``ecbuild`` step above:
+
+.. code-block:: bash
+
+      ecbuild -DENABLE_OCEAN_BGC=ON ../soca/bundle
+
+Built executables
+-----------------
+
+After completing the SOCA build, users have access to executables under
+``build/bin``, many of which are generated when building the projects on which
+SOCA is dependent (
+:doc:`OOPS </inside/jedi-components/oops/index>`,
+:doc:`UFO </inside/jedi-components/ufo/index>`,
+:doc:`SABER </inside/jedi-components/saber/index>`).
+
+Most of these executables are model-specific implementations of generic applications that
+are derived from the :code:`oops::Application` class, i.e.,
+:code:`oops/src/oops/runs/Application.h`. Descriptions of the generic applications are located under
+the :doc:`OOPS Applications </inside/jedi-components/oops/applications/index>` documentation. Here
+we give short synopses of a few specific SOCA implementations.
+
+- Generic Applications
+
+   - :code:`soca_convertstate.x` (:code:`oops::ConvertState`)
+   - :code:`soca_dirac.x` (:code:`oops::Dirac`)
+   - :code:`soca_forecast.x` (:code:`oops::Forecast`): similar to the
+     :code:`mom6.x` executable, but through the JEDI generic framework via the SOCA interface.
+   - :code:`soca_enspert.x` (:code:`oops::GenEnsPertB`)
+   - :code:`soca_ensrecenter.x` (:code:`oops::EnsRecenter`)
+   - :code:`soca_ensvariance` (:code:`oops::EnsVariance`)
+   - :code:`soca_hofx.x` (:code:`oops::HofX4D`)
+   - :code:`soca_hofx3d.x` (:code:`oops::HofX3D`)
+   - :code:`soca_parameters.x` (:code:`saber::EstimateParams`): used to estimate static
+     background error covariance and localization matrices
+   - :code:`soca_staticbinit.x` (:code:`oops::StaticBInit`): used to initialize the covariance model
+   - :code:`soca_var.x` (:code:`oops::Variational`): carries out many different
+     flavors of variational data assimilation (3DVar, 3DEnVar, 3DFGAT, 4DEnVar) with a variety of
+     incremental minimization algorithms
+   - :code:`soca_letkf.x` (:code:`oops::LocalEnsembleDA`)
+   - :code:`soca_hybridgain.x` (:code:`oops::HybridGain`)
+   - :code:`soca_enshofx.x` (:code:`oops::EnsembleApplication<oops::HofX4D>`)
+
+- SOCA specific Applications
+
+   - :code:`soca_checkpoint_model.x` (:code:`soca::CheckpointModel`)
+   - :code:`soca_gridgen.x` (:code:`soca::GridGen`)
+
+Most of the SOCA executables are exercised in ctests.  As users learn how to use SOCA for
+larger-scale applications, it is useful to consider the ctests as examples and templates.