MetOffice · Yaswant Pradhan (yaswant) · Oct 31, 2025
@@ -0,0 +1,29 @@
+*~
+__pycache__/
+results/*.png
+results/*.txt
+processed_data/*.dat
+.*.sw?
+
+# ignore build output
+*build/
+*_build/
+user_guide/doc/_build
+user_guide/doc/build
+
+# ignore VS Code files
+/.idea
+
+# ignore envs
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# UV
+uv.lock
+.python-version
+pyproject.toml
@@ -0,0 +1,28 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+REPO := $(notdir $(shell git rev-parse --show-toplevel))
+BRANCH := $(shell git rev-parse --abbrev-ref HEAD)
+DEPLOYDIR  = $(HOME)/public_html
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+deploy:
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(DEPLOYDIR)/$(REPO)/$(BRANCH)" $(SPHINXOPTS) $(O)
+
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
@@ -0,0 +1,214 @@
+pre {
+  background-color: #f2f8ff;
+}
+
+tt {
+  background-color: #f1f5f7;
+  border: 1px solid #c6c9cb;
+  padding: 2px 4px;
+}
+
+dt tt:only-child {
+  display: inline-block;
+  margin-bottom: 2px;
+}
+
+h1 tt,
+h2 tt,
+h3 tt,
+h4 tt,
+h5 tt,
+h6 tt,
+a tt,
+dl.member dt tt {
+  border: 0;
+  padding: 0;
+  margin: 0;
+}
+
+a tt {
+  color: inherit;
+}
+
+p.rubric {
+  padding-top: 5px;
+  border-top: 1px solid #c6c9cb;
+  padding-left: 10px;
+}
+
+table.footnote {
+  margin: 0px 10px;
+}
+
+div.sphinxsidebar {
+  width: 20%;
+}
+
+div.bodywrapper {
+  margin: 0 0 0 20%;
+}
+
+div.sphinxsidebarwrapper {
+  padding-top: 10px;
+}
+
+div.sphinxsidebar p {
+  padding: 5px 10px;
+  margin-top: 0;
+}
+
+/* Namelist member formatting */
+dl {
+  margin: 0;
+}
+
+dl > dd {
+  margin-top: 5px;
+  margin-bottom: 15px;
+}
+
+dl > dd:empty {
+  margin-top: 0px;
+  margin-bottom: 0px;
+}
+
+dl.member > dt {
+  font-size: 1.1em;
+}
+
+dl.member > dd {
+  margin-bottom: 25px;
+}
+
+dl.member > dd:empty {
+  margin-bottom: 0px;
+}
+
+/* Admonition stuff */
+div.admonition {
+  padding: 7px 15px 15px;
+  border: 1px solid #c6c9cb;
+}
+
+div.admonition p.admonition-title {
+  position: relative;
+  top: -7px;
+  display: block;
+  background-color: #e1e5e7;
+  border-bottom: 1px solid #c6c9cb;
+  margin: -7px -15px 0px;
+  padding: 5px 15px;
+  font-size: 1.1em;
+}
+
+p.admonition-title:after {
+  content: "";
+}
+
+div.admonition p.admonition-title + p {
+  display: block;
+  margin-top: 5px;
+}
+
+div.admonition p.admonition-title + * {
+  margin-top: 5px;
+}
+
+div.admonition p.last,
+div.admonition div.last,
+div.admonition ul.last,
+div.admonition ol.last {
+  margin-bottom: 0px;
+}
+
+div.admonition dl.last > dd {
+  margin-bottom: 0;
+}
+
+div.admonition dl.last > dd > :last-child {
+  margin-bottom: 0;
+}
+
+tt.descclassname {
+  font-weight: normal;
+}
+
+dt {
+  font-weight: bold;
+}
+
+div.warning {
+  border: 1px solid #ff5050;
+}
+
+div.warning p.admonition-title {
+  border-bottom: 1px solid #ff5050;
+  background-color: #ff8080;
+}
+
+/* Tables */
+table.docutils th,
+table.docutils td {
+  border: 1px solid #c6c9cb !important;
+  padding: 7px 10px;
+}
+
+table.docutils th {
+  background-color: #e1e5e7;
+}
+
+table.docutils td[colspan] {
+  background-color: #ebeff1;
+  font-weight: bold;
+}
+
+table.docutils td .last {
+  margin-bottom: 0;
+}
+
+table.docutils tr.row-odd {
+  background-color: #f2f8ff;
+}
+
+table.field-list {
+  margin-top: 5px;
+}
+
+table.field-list tr.row-odd {
+  background-color: transparent;
+}
+
+table.field-list th,
+table.field-list td {
+  padding: 3px 8px 3px 5px;
+}
+
+table.field-list th {
+  text-align: right;
+}
+
+table.field-list td.field-body {
+  text-align: center;
+  min-width: 150px;
+  font-family: monospace;
+}
+
+/* Figures */
+div.figure {
+  text-align: center;
+}
+
+div.figure p.caption {
+  font-weight: bold;
+  font-size: 0.9em;
+}
+
+div.figure p.caption:before {
+  content: "Figure: ";
+}
+
+div.figure img {
+  border: 1px solid #c6c9cb;
+  box-shadow: 1px 1px 1px #d8d8d8;
+  padding: 10px;
+}
@@ -0,0 +1,2 @@
+<h3><a href="{{ pathto(master_doc) }}">{{ _('Table Of Contents') }}</a></h3>
+{{ toctree() }}
@@ -0,0 +1,35 @@
+Considerations
+==============
+
+Depending on your use case, there are two main things that you need to consider:
+
+Do I need NetCDF?
+-----------------
+
+`NetCDF <http://www.unidata.ucar.edu/software/netcdf/>`_ is a data format (and associated software libraries) specifically designed for large-scale scientific data. It has two major benefits over raw binary data:
+
+1. It is machine-independent, so `endianness <http://en.wikipedia.org/wiki/Endianness>`_ is not an issue when moving datasets between machines
+2. It is self-describing, so as well as containing raw data, NetCDF files also contain metadata describing the data (e.g. variable names, units, origin). Many tools are capable of exploiting this metadata to simplify processing.
+
+JULES can be built with or without NetCDF, however *building JULES without NetCDF limits the functionality of JULES*. Without NetCDF, JULES will use a dummy NetCDF library which allows the program to build but provides no functionality. Any attempt to use NetCDF files as input with this option will result in a runtime error. All input files must be columnar ASCII, meaning that the user is restricted to running at a single point only. Output files will automatically use a columnar ASCII format with headers. File formats are discussed in more detail in :doc:`/input/overview`.
+
+
+Do I need parallel processing?
+------------------------------
+
+.. note::
+    For running JULES at a single point, parallel processing provides no advantage. However, if JULES is already compiled with OpenMP or MPI enabled, it is still possible to run a single point by simply specifying the number of OpenMP threads and/or MPI tasks to be 1.
+
+JULES is capable of exploiting parallel processing techniques to reduce processing time for distributed/gridded simulations. There are two different methods JULES can use:
+
+OpenMP
+    `OpenMP <http://en.wikipedia.org/wiki/OpenMP>`_ is a form of compiler-assisted parallelisation that uses directives for shared-memory, loop-level parallelism across multiple cores on a machine (OpenMP is *not* capable of utilising a cluster of machines).
+
+    This form of parallelism is not as effective as MPI, but may provide some speedup and does not require a specially compiled NetCDF library.
+
+MPI
+    `MPI (Message Passing Interface) <http://en.wikipedia.org/wiki/Message_Passing_Interface>`_ is a standardised message passing interface. MPI coordinates the running of multiple 'tasks' in parallel, potentially on several machines (or nodes), and provides mechanisms for these tasks to communicate with each other.
+
+    JULES takes advantage of the parallel I/O features available in `HDF5 <http://www.hdfgroup.org/HDF5/>`_ and `NetCDF4 <http://www.unidata.ucar.edu/software/netcdf/>`_, which enable multiple MPI tasks to read from and write to the same NetCDF file(s) at the same time. These features must be explicitly enabled when NetCDF is compiled (see :doc:`required-software`).
+
+It is also possible to use MPI and OpenMP together, where each MPI task has a number of OpenMP threads, however this is very advanced and beyond the scope of this document.
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		@@ -0,0 +1,2 @@
		<h3><a href="{{ pathto(master_doc) }}">{{ _('Table Of Contents') }}</a></h3>
		{{ toctree() }}